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Entry version 148 (08 May 2019)
Sequence version 3 (23 Jan 2007)
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Protein

Gag-Pro-Pol polyprotein

Gene

gag-pro-pol

Organism
Human T-cell leukemia virus 1 (strain Japan ATK-1 subtype A) (HTLV-1)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Gag-Pro-Pol polyprotein: The matrix domain targets Gag, Gag-Pro and Gag-Pro-Pol polyproteins to the plasma membrane via a multipartite membrane binding signal, that includes its myristoylated N-terminus.By similarity
Matrix protein p19: Matrix protein.By similarity
Capsid protein p24: Forms the spherical core of the virus that encapsulates the genomic RNA-nucleocapsid complex.Curated
Nucleocapsid protein p15-pro: Binds strongly to viral nucleic acids and promote their aggregation. Also destabilizes the nucleic acids duplexes via highly structured zinc-binding motifs.By similarity
Protease: The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell. Cleaves the translation initiation factor eIF4G leading to the inhibition of host cap-dependent translation (PubMed:14610163).PROSITE-ProRule annotation3 Publications
Reverse transcriptase/ribonuclease H, p49 subunit: RT is a multifunctional enzyme that converts the viral RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell. This enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3' to 5'-endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires many steps. A tRNA-Pro binds to the primer-binding site (PBS) situated at the 5'-end of the viral RNA. RT uses the 3' end of the tRNA primer to perform a short round of RNA-dependent minus-strand DNA synthesis. The reading proceeds through the U5 region and ends after the repeated (R) region which is present at both ends of viral RNA. The portion of the RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA hybridizes with the identical R region situated at the 3' end of viral RNA. This template exchange, known as minus-strand DNA strong stop transfer, can be either intra- or intermolecular. RT uses the 3' end of this newly synthesized short ssDNA to perform the RNA-dependent minus-strand DNA synthesis of the whole template. RNase H digests the RNA template except for a polypurine tract (PPT) situated at the 5' end of the genome. It is not clear if both polymerase and RNase H activities are simultaneous. RNase H probably can proceed both in a polymerase-dependent (RNA cut into small fragments by the same RT performing DNA synthesis) and a polymerase-independent mode (cleavage of remaining RNA fragments by free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis using the PPT that has not been removed by RNase H as primer. PPT and tRNA primers are then removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. Strand displacement synthesis by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA copy of the viral genome that includes long terminal repeats (LTRs) at both ends (By similarity).By similarity
Reverse transcriptase/ribonuclease H, p62 subunit: RT is a multifunctional enzyme that converts the viral RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell. This enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3' to 5'-endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires many steps. A tRNA-Pro binds to the primer-binding site (PBS) situated at the 5'-end of the viral RNA. RT uses the 3' end of the tRNA primer to perform a short round of RNA-dependent minus-strand DNA synthesis. The reading proceeds through the U5 region and ends after the repeated (R) region which is present at both ends of viral RNA. The portion of the RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA hybridizes with the identical R region situated at the 3' end of viral RNA. This template exchange, known as minus-strand DNA strong stop transfer, can be either intra- or intermolecular. RT uses the 3' end of this newly synthesized short ssDNA to perform the RNA-dependent minus-strand DNA synthesis of the whole template. RNase H digests the RNA template except for a polypurine tract (PPT) situated at the 5' end of the genome. It is not clear if both polymerase and RNase H activities are simultaneous. RNase H probably can proceed both in a polymerase-dependent (RNA cut into small fragments by the same RT performing DNA synthesis) and a polymerase-independent mode (cleavage of remaining RNA fragments by free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis using the PPT that has not been removed by RNase H as primer. PPT and tRNA primers are then removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. Strand displacement synthesis by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA copy of the viral genome that includes long terminal repeats (LTRs) at both ends (By similarity).By similarity
Integrase: Catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions.Curated

Miscellaneous

Reverse transcriptase/ribonuclease H: The reverse transcriptase is an error-prone enzyme that lacks a proof-reading function. High mutations rate is a direct consequence of this characteristic. RT also displays frequent template swiching leading to high recombination rate. Recombination mostly occurs between homologous regions of the two copackaged RNA genomes. If these two RNA molecules derive from different viral strains, reverse transcription will give rise to highly recombinated proviral DNAs.PROSITE-ProRule annotation
HTLV-1 lineages are divided in four clades, A (Cosmopolitan), B (Central African group), C (Melanesian group) and D (New Central African group).Curated

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the ‘Function’ section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Mg2+PROSITE-ProRule annotationNote: The RT polymerase active site binds 2 magnesium ions.PROSITE-ProRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei481For protease activity; shared with dimeric partnerPROSITE-ProRule annotation1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the ‘Description’ field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi680Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi755Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi756Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi1040Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1074Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1096Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1157Magnesium; catalytic; for RNase H activityPROSITE-ProRule annotation1
Metal bindingi1230Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation1
Metal bindingi1287Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section specifies the position(s) and type(s) of zinc fingers within the protein.<p><a href='/help/zn_fing' target='_top'>More...</a></p>Zinc fingeri355 – 372CCHC-type 1PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri378 – 395CCHC-type 2PROSITE-ProRule annotationAdd BLAST18
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section specifies the position and type of each DNA-binding domain present within the protein.<p><a href='/help/dna_bind' target='_top'>More...</a></p>DNA bindingi1393 – 1443Integrase-typePROSITE-ProRule annotationAdd BLAST51

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionAspartyl protease, DNA-binding, DNA-directed DNA polymerase, Endonuclease, Hydrolase, Multifunctional enzyme, Nuclease, Nucleotidyltransferase, Protease, RNA-binding, RNA-directed DNA polymerase, Transferase, Viral nucleoprotein
Biological processDNA integration, DNA recombination, Eukaryotic host gene expression shutoff by virus, Eukaryotic host translation shutoff by virus, Host gene expression shutoff by virus, Host-virus interaction, Viral genome integration, Virus entry into host cell
LigandMagnesium, Metal-binding, Zinc

Enzyme and pathway databases

BRENDA Comprehensive Enzyme Information System

More...
BRENDAi
3.4.23.B8 2706

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Gag-Pro-Pol polyprotein
Alternative name(s):
Pr160Gag-Pro-Pol
Cleaved into the following 8 chains:
Matrix protein p19
Short name:
MA
Capsid protein p24
Short name:
CA
Nucleocapsid protein p15-pro
Short name:
NC'
Short name:
NC-pro
Protease (EC:3.4.23.-PROSITE-ProRule annotation1 Publication)
Short name:
PR
Reverse transcriptase/ribonuclease H, p49 subunit (EC:2.7.7.49PROSITE-ProRule annotation, EC:2.7.7.7PROSITE-ProRule annotation, EC:3.1.26.4PROSITE-ProRule annotation)
Short name:
p49 RT
Reverse transcriptase/ribonuclease H, p62 subunit (EC:2.7.7.49PROSITE-ProRule annotation, EC:2.7.7.7PROSITE-ProRule annotation, EC:3.1.26.4PROSITE-ProRule annotation)
Short name:
p62 RT
Integrase (EC:2.7.7.-By similarity, EC:3.1.-.-By similarity)
Short name:
IN
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:gag-pro-pol
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiHuman T-cell leukemia virus 1 (strain Japan ATK-1 subtype A) (HTLV-1)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri11926 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiVirusesOrterviralesRetroviridaeOrthoretrovirinaeDeltaretrovirus
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section only exists in viral entries and indicates the host(s) either as a specific organism or taxonomic group of organisms that are susceptible to be infected by a virus.<p><a href='/help/virus_host' target='_top'>More...</a></p>Virus hostiHomo sapiens (Human) [TaxID: 9606]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000007683 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Genome

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Matrix protein p19 :
Capsid protein p24 :
Nucleocapsid protein p15-pro :

GO - Cellular componenti

Keywords - Cellular componenti

Capsid protein, Virion

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi2G → A: Complete loss of myristoylation the polyprotein. The concomitent loss of binding to the host cell membrane impairs the formation of viral particles. 1 Publication1
Mutagenesisi486M → A, D or N: Complete loss of protease activity. 1 Publication1
Mutagenesisi486M → I: Almost no effect on protease activity. 1 Publication1
Mutagenesisi486M → V: Decrease in protease activity. 1 Publication1
Mutagenesisi506L → G: Complete loss of protease activity. 1 Publication1
Mutagenesisi508A → I: Decrease in protease activity. 1 Publication1
Mutagenesisi516F → Q: Complete loss of protease activity. 1 Publication1
Mutagenesisi545N → T: Almost complete loss of protease activity. 1 Publication1
Mutagenesisi546N → P: Almost complete loss of protease activity. 1 Publication1
Mutagenesisi547W → V: Almost complete loss of protease activity. 1 Publication1

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section indicates that the initiator methionine is cleaved from the mature protein.<p><a href='/help/init_met' target='_top'>More...</a></p>Initiator methionineiRemoved; by hostSequence analysis
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00002598282 – 1462Gag-Pro-Pol polyproteinAdd BLAST1461
ChainiPRO_00002598292 – 130Matrix protein p19Add BLAST129
ChainiPRO_0000259830131 – 344Capsid protein p24Add BLAST214
ChainiPRO_0000259831345 – 449Nucleocapsid protein p15-proAdd BLAST105
ChainiPRO_0000259832450 – 574ProteaseAdd BLAST125
<p>This subsection of the ‘PTM / Processing’ section describes the position and length of an active peptide in the mature protein.<p><a href='/help/peptide' target='_top'>More...</a></p>PeptideiPRO_0000259833575 – 582p18
ChainiPRO_0000038873583 – 1167Reverse transcriptase/ribonuclease H, p62 subunitAdd BLAST585
ChainiPRO_0000442547583 – 1021Reverse transcriptase/ribonuclease H, p49 subunitAdd BLAST439
ChainiPRO_00000388741168 – 1462IntegraseAdd BLAST295

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section specifies the position(s) and the type of covalently attached lipid group(s).<p><a href='/help/lipid' target='_top'>More...</a></p>Lipidationi2N-myristoyl glycine; by hostSequence analysis1 Publication1
<p>This subsection of the ‘PTM / Processing’ section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei105Phosphoserine; by host MAPK1By similarity1

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>Post-translational modificationi

Matrix protein p19: Phosphorylation of the matrix protein p19 by MAPK1 seems to play a role in budding.By similarity
Gag-Pro-Pol polyprotein: Myristoylated. Myristoylation of the matrix (MA) domain mediates the transport and binding of Gag polyproteins to the host plasma membrane and is required for the assembly of viral particles.By similarity
Gag-Pro-Pol polyprotein: Specific enzymatic cleavages by the viral protease yield mature proteins. The polyprotein is cleaved during and after budding, this process is termed maturation. The protease is autoproteolytically processed at its N- and C-termini.6 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections (‘Function’, ‘PTM / Processing’, ‘Pathology and Biotech’) according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei130 – 131Cleavage; by viral protease1 Publication2
Sitei344 – 345Cleavage; by viral protease1 Publication2
Sitei449 – 450Cleavage; by viral protease1 Publication2
Sitei574 – 575Cleavage; by viral protease2 Publications2
Sitei582 – 583Cleavage; by viral protease1 Publication2
Sitei1021 – 1022Cleavage; by viral protease1 Publication2
Sitei1167 – 1168Cleavage; by viral protease1 Publication2

Keywords - PTMi

Lipoprotein, Myristate, Phosphoprotein

Proteomic databases

PRoteomics IDEntifications database

More...
PRIDEi
P03362

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Gag-Pro-Pol polyprotein: Homodimer; the homodimers are part of the immature particles. Gag-Pro-Pol polyprotein:

Interacts with human TSG101 and NEDD4; these interactions are essential for budding and release of viral particles. Matrix protein p19: Homodimer; further assembles as homohexamers.

By similarity

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

11462
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
P03362

Database of comparative protein structure models

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ModBasei
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
P03362

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini476 – 554Peptidase A2PROSITE-ProRule annotationAdd BLAST79
Domaini614 – 804Reverse transcriptasePROSITE-ProRule annotationAdd BLAST191
Domaini1031 – 1165RNase HPROSITE-ProRule annotationAdd BLAST135
Domaini1219 – 1388Integrase catalyticPROSITE-ProRule annotationAdd BLAST170

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a short (usually not more than 20 amino acids) conserved sequence motif of biological significance.<p><a href='/help/motif' target='_top'>More...</a></p>Motifi118 – 121PPXY motifBy similarity4
Motifi124 – 127PTAP/PSAP motifBy similarity4

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes the position of regions of compositional bias within the protein and the particular amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi95 – 144Pro-richPROSITE-ProRule annotationAdd BLAST50

<p>This subsection of the ‘Family and domains’ section provides general information on the biological role of a domain. The term ‘domain’ is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

Gag polyprotein: Late-budding domains (L domains) are short sequence motifs essential for viral particle release. They can occur individually or in close proximity within structural proteins. They interacts with sorting cellular proteins of the multivesicular body (MVB) pathway. Most of these proteins are class E vacuolar protein sorting factors belonging to ESCRT-I, ESCRT-II or ESCRT-III complexes. Matrix protein p19 contains two L domains: a PTAP/PSAP motif which interacts with the UEV domain of TSG101, and a PPXY motif which binds to the WW domains of the ubiquitin ligase NEDD4.By similarity
Capsid protein p24: The capsid protein N-terminus seems to be involved in Gag-Gag interactions.1 Publication

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri355 – 372CCHC-type 1PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri378 – 395CCHC-type 2PROSITE-ProRule annotationAdd BLAST18

Keywords - Domaini

Repeat, Zinc-finger

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
1.10.1200.30, 1 hit
1.10.185.10, 1 hit
1.10.375.10, 1 hit
2.40.70.10, 1 hit
3.30.420.10, 2 hits

Integrated resource of protein families, domains and functional sites

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InterProi
View protein in InterPro
IPR001969 Aspartic_peptidase_AS
IPR003139 D_retro_matrix
IPR036989 D_retro_matrix_sf
IPR000721 Gag_p24
IPR036862 Integrase_C_dom_sf_retrovir
IPR001037 Integrase_C_retrovir
IPR001584 Integrase_cat-core
IPR003308 Integrase_Zn-bd_dom_N
IPR001995 Peptidase_A2_cat
IPR021109 Peptidase_aspartic_dom_sf
IPR018061 Retropepsins
IPR008916 Retrov_capsid_C
IPR008919 Retrov_capsid_N
IPR010999 Retrovr_matrix
IPR012337 RNaseH-like_sf
IPR002156 RNaseH_domain
IPR036397 RNaseH_sf
IPR000477 RT_dom
IPR001878 Znf_CCHC
IPR036875 Znf_CCHC_sf

Pfam protein domain database

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Pfami
View protein in Pfam
PF02228 Gag_p19, 1 hit
PF00607 Gag_p24, 1 hit
PF00552 IN_DBD_C, 1 hit
PF02022 Integrase_Zn, 1 hit
PF00075 RNase_H, 1 hit
PF00665 rve, 1 hit
PF00077 RVP, 1 hit
PF00078 RVT_1, 1 hit
PF00098 zf-CCHC, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

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SMARTi
View protein in SMART
SM00343 ZnF_C2HC, 2 hits

Superfamily database of structural and functional annotation

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SUPFAMi
SSF47836 SSF47836, 1 hit
SSF47943 SSF47943, 1 hit
SSF50122 SSF50122, 1 hit
SSF50630 SSF50630, 1 hit
SSF53098 SSF53098, 1 hit
SSF57756 SSF57756, 1 hit

PROSITE; a protein domain and family database

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PROSITEi
View protein in PROSITE
PS50175 ASP_PROT_RETROV, 1 hit
PS00141 ASP_PROTEASE, 1 hit
PS50994 INTEGRASE, 1 hit
PS51027 INTEGRASE_DBD, 1 hit
PS50879 RNASE_H, 1 hit
PS50878 RT_POL, 1 hit
PS50158 ZF_CCHC, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequences (3)i

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 3 <p>This subsection of the ‘Sequence’ section lists the alternative protein sequences (isoforms) that can be generated from the same gene by a single or by the combination of up to four biological events (alternative promoter usage, alternative splicing, alternative initiation and ribosomal frameshifting). Additionally, this section gives relevant information on each alternative protein isoform.<p><a href='/help/alternative_products' target='_top'>More...</a></p> isoformsi produced by ribosomal frameshifting. AlignAdd to basket
Note: This strategy of translation probably allows the virus to modulate the quantity of each viral protein.Curated
Isoform Gag-Pro-Pol polyprotein (identifier: P03362-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the <div> <p><b>What is the canonical sequence?</b><p><a href='/help/canonical_and_isoforms' target='_top'>More...</a></p>canonicali sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MGQIFSRSAS PIPRPPRGLA AHHWLNFLQA AYRLEPGPSS YDFHQLKKFL
60 70 80 90 100
KIALETPARI CPINYSLLAS LLPKGYPGRV NEILHILIQT QAQIPSRPAP
110 120 130 140 150
PPPSSPTHDP PDSDPQIPPP YVEPTAPQVL PVMHPHGAPP NHRPWQMKDL
160 170 180 190 200
QAIKQEVSQA APGSPQFMQT IRLAVQQFDP TAKDLQDLLQ YLCSSLVASL
210 220 230 240 250
HHQQLDSLIS EAETRGITGY NPLAGPLRVQ ANNPQQQGLR REYQQLWLAA
260 270 280 290 300
FAALPGSAKD PSWASILQGL EEPYHAFVER LNIALDNGLP EGTPKDPILR
310 320 330 340 350
SLAYSNANKE CQKLLQARGH TNSPLGDMLR ACQTWTPKDK TKVLVVQPKK
360 370 380 390 400
PPPNQPCFRC GKAGHWSRDC TQPRPPPGPC PLCQDPTHWK RDCPRLKPTI
410 420 430 440 450
PEPEPEEDAL LLDLPADIPH PKNLHRGGGL TSPPTLQQVL PNQDPASILP
460 470 480 490 500
VIPLDPARRP VIKAQVDTQT SHPKTIEALL DTGADMTVLP IALFSSNTPL
510 520 530 540 550
KNTSVLGAGG QTQDHFKLTS LPVLIRLPFR TTPIVLTSCL VDTKNNWAII
560 570 580 590 600
GRDALQQCQG VLYLPEAKRP PVILPIQAPA VLGLEHLPRP PQISQFPLNP
610 620 630 640 650
ERLQALQHLV RKALEAGHIE PYTGPGNNPV FPVKKANGTW RFIHDLRATN
660 670 680 690 700
SLTIDLSSSS PGPPDLSSLP TTLAHLQTID LRDAFFQIPL PKQFQPYFAF
710 720 730 740 750
TVPQQCNYGP GTRYAWKVLP QGFKNSPTLF EMQLAHILQP IRQAFPQCTI
760 770 780 790 800
LQYMDDILLA SPSHEDLLLL SEATMASLIS HGLPVSENKT QQTPGTIKFL
810 820 830 840 850
GQIISPNHLT YDAVPTVPIR SRWALPELQA LLGEIQWVSK GTPTLRQPLH
860 870 880 890 900
SLYCALQRHT DPRDQIYLNP SQVQSLVQLR QALSQNCRSR LVQTLPLLGA
910 920 930 940 950
IMLTLTGTTT VVFQSKEQWP LVWLHAPLPH TSQCPWGQLL ASAVLLLDKY
960 970 980 990 1000
TLQSYGLLCQ TIHHNISTQT FNQFIQTSDH PSVPILLHHS HRFKNLGAQT
1010 1020 1030 1040 1050
GELWNTFLKT AAPLAPVKAL MPVFTLSPVI INTAPCLFSD GSTSRAAYIL
1060 1070 1080 1090 1100
WDKQILSQRS FPLPPPHKSA QRAELLGLLH GLSSARSWRC LNIFLDSKYL
1110 1120 1130 1140 1150
YHYLRTLALG TFQGRSSQAP FQALLPRLLS RKVVYLHHVR SHTNLPDPIS
1160 1170 1180 1190 1200
RLNALTDALL ITPVLQLSPA ELHSFTHCGQ TALTLQGATT TEASNILRSC
1210 1220 1230 1240 1250
HACRGGNPQH QMPRGHIRRG LLPNHIWQGD ITHFKYKNTL YRLHVWVDTF
1260 1270 1280 1290 1300
SGAISATQKR KETSSEAISS LLQAIAHLGK PSYINTDNGP AYISQDFLNM
1310 1320 1330 1340 1350
CTSLAIRHTT HVPYNPTSSG LVERSNGILK TLLYKYFTDK PDLPMDNALS
1360 1370 1380 1390 1400
IALWTINHLN VLTNCHKTRW QLHHSPRLQP IPETRSLSNK QTHWYYFKLP
1410 1420 1430 1440 1450
GLNSRQWKGP QEALQEAAGA ALIPVSASSA QWIPWRLLKR AACPRPVGGP
1460
ADPKEKDLQH HG
Note: Produced by -1 ribosomal frameshiftings at the gag-pro and gag-pol genes boundaries.1 Publication
Length:1,462
Mass (Da):162,512
Last modified:January 23, 2007 - v3
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iDCC70251EC729E87
GO
Isoform Gag-Pro polyprotein (identifier: P10274-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry P10274.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by -1 ribosomal frameshifting at the gag-pro genes boundary.1 Publication
Length:651
Mass (Da):71,558
GO
Isoform Gag polyprotein (identifier: P03345-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry P03345.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by conventional translation.1 Publication
Length:429
Mass (Da):47,496
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti545 – 547NNW → GSM AA sequence (PubMed:11469799).Curated3
Sequence conflicti569R → G AA sequence (PubMed:11469799).Curated1
Sequence conflicti592Q → E AA sequence (PubMed:11469799).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section describes natural variant(s) of the protein sequence.<p><a href='/help/variant' target='_top'>More...</a></p>Natural varianti440 – 441LP → FL. 2
Natural varianti569R → G. 1
Natural varianti621P → S. 1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
J02029 Genomic DNA Translation: AAA96673.1 Sequence problems.
M13810 Genomic RNA Translation: AAA46207.1 Sequence problems.
X14144 Genomic DNA Translation: CAA32360.1

Protein sequence database of the Protein Information Resource

More...
PIRi
A03961 GNLJGH

Keywords - Coding sequence diversityi

Ribosomal frameshifting

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02029 Genomic DNA Translation: AAA96673.1 Sequence problems.
M13810 Genomic RNA Translation: AAA46207.1 Sequence problems.
X14144 Genomic DNA Translation: CAA32360.1
PIRiA03961 GNLJGH

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1O0Jmodel-A/B450-564[»]
1TP1model-A/B450-564[»]
2B7FX-ray2.60A/B/C/D/E/F450-565[»]
4YDGX-ray3.25A/B450-565[»]
SMRiP03362
ModBaseiSearch...

Proteomic databases

PRIDEiP03362

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

BRENDAi3.4.23.B8 2706

Miscellaneous databases

EvolutionaryTraceiP03362

Family and domain databases

Gene3Di1.10.1200.30, 1 hit
1.10.185.10, 1 hit
1.10.375.10, 1 hit
2.40.70.10, 1 hit
3.30.420.10, 2 hits
InterProiView protein in InterPro
IPR001969 Aspartic_peptidase_AS
IPR003139 D_retro_matrix
IPR036989 D_retro_matrix_sf
IPR000721 Gag_p24
IPR036862 Integrase_C_dom_sf_retrovir
IPR001037 Integrase_C_retrovir
IPR001584 Integrase_cat-core
IPR003308 Integrase_Zn-bd_dom_N
IPR001995 Peptidase_A2_cat
IPR021109 Peptidase_aspartic_dom_sf
IPR018061 Retropepsins
IPR008916 Retrov_capsid_C
IPR008919 Retrov_capsid_N
IPR010999 Retrovr_matrix
IPR012337 RNaseH-like_sf
IPR002156 RNaseH_domain
IPR036397 RNaseH_sf
IPR000477 RT_dom
IPR001878 Znf_CCHC
IPR036875 Znf_CCHC_sf
PfamiView protein in Pfam
PF02228 Gag_p19, 1 hit
PF00607 Gag_p24, 1 hit
PF00552 IN_DBD_C, 1 hit
PF02022 Integrase_Zn, 1 hit
PF00075 RNase_H, 1 hit
PF00665 rve, 1 hit
PF00077 RVP, 1 hit
PF00078 RVT_1, 1 hit
PF00098 zf-CCHC, 1 hit
SMARTiView protein in SMART
SM00343 ZnF_C2HC, 2 hits
SUPFAMiSSF47836 SSF47836, 1 hit
SSF47943 SSF47943, 1 hit
SSF50122 SSF50122, 1 hit
SSF50630 SSF50630, 1 hit
SSF53098 SSF53098, 1 hit
SSF57756 SSF57756, 1 hit
PROSITEiView protein in PROSITE
PS50175 ASP_PROT_RETROV, 1 hit
PS00141 ASP_PROTEASE, 1 hit
PS50994 INTEGRASE, 1 hit
PS51027 INTEGRASE_DBD, 1 hit
PS50879 RNASE_H, 1 hit
PS50878 RT_POL, 1 hit
PS50158 ZF_CCHC, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiPOL_HTL1A
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P03362
Secondary accession number(s): Q85590
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: May 8, 2019
This is version 148 of the entry and version 3 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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