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Protein

Gag polyprotein

Gene

gag

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-Experimental evidence at protein leveli

Functioni

Matrix protein p19 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. Also mediates nuclear localization of the preintegration complex (By similarity).By similarity
Capsid protein p24 forms the conical core of the virus that encapsulates the genomic RNA-nucleocapsid complex.By similarity
Nucleocapsid protein p15 is involved in the packaging and encapsidation of two copies of the genome.By similarity

Regions

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

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Host-virus interaction

Keywords - Ligandi

Metal-binding, Viral nucleoprotein, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Gag polyprotein
Alternative name(s):
Pr53Gag
Cleaved into the following 3 chains:
Matrix protein p19
Short name:
MA
Capsid protein p24
Short name:
CA
Gene namesi
Name:gag
OrganismiHuman T-cell leukemia virus 1 (strain Japan ATK-1 subtype A) (HTLV-1)
Taxonomic identifieri11926 [NCBI]
Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeDeltaretrovirus
Virus hostiHomo sapiens (Human) [TaxID: 9606]
Proteomesi
  • UP000007683 Componenti: Genome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Virion

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi105S → A: 70% loss of viral particle release. 1 Publication1
Mutagenesisi118 – 120PPP → AAA: Complete loss of interaction with human NEDD4. 1 Publication3
Mutagenesisi124 – 127PTAP → ATAA: Complete loss of interaction with human TSG101. 1 Publication4

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved; by host
ChainiPRO_00002597712 – 429Gag polyproteinAdd BLAST428
ChainiPRO_00000388112 – 130Matrix protein p19Add BLAST129
ChainiPRO_0000038812131 – 344Capsid protein p24Add BLAST214
ChainiPRO_0000038813345 – 429Nucleocapsid protein p15-gagAdd BLAST85

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Lipidationi2N-myristoyl glycine; by host1 Publication1
Modified residuei105Phosphoserine; by host MAPK11 Publication1

Post-translational modificationi

Specific enzymatic cleavages by the viral protease yield mature proteins. The polyprotein is cleaved during and after budding, this process is termed maturation (By similarity).By similarity
Phosphorylation of the matrix protein p19 by MAPK1 seems to play a role in budding.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei130 – 131Cleavage; by viral protease2
Sitei344 – 345Cleavage; by viral protease2

Keywords - PTMi

Lipoprotein, Myristate, Phosphoprotein

PTM databases

iPTMnetiP03345.

Interactioni

Subunit structurei

Interacts with human TSG101 and NEDD4. These interactions are essential for budding and release of viral particles.1 Publication

Structurei

Secondary structure

1429
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi147 – 159Combined sources13
Helixi167 – 177Combined sources11
Helixi182 – 189Combined sources8
Turni190 – 192Combined sources3
Helixi195 – 214Combined sources20
Turni215 – 219Combined sources5
Turni222 – 224Combined sources3
Helixi228 – 231Combined sources4
Helixi238 – 251Combined sources14
Helixi263 – 265Combined sources3
Helixi274 – 286Combined sources13
Helixi296 – 303Combined sources8
Turni304 – 306Combined sources3
Helixi309 – 318Combined sources10
Beta strandi321 – 323Combined sources3
Helixi325 – 332Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1QRJNMR-A146-344[»]
ProteinModelPortaliP03345.
SMRiP03345.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP03345.

Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi118 – 121PPXY motif4
Motifi124 – 127PTAP/PSAP motif4

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi95 – 144Pro-richAdd BLAST50

Domaini

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 HECT (homologous to E6-AP C-terminus) E3 ubiquitin ligases, like NEDD4.1 Publication
The capsid protein N-terminus seems to be involved in Gag-Gag interactions.1 Publication

Sequence similaritiesi

Contains 2 CCHC-type zinc fingers.PROSITE-ProRule annotation

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

Gene3Di1.10.1200.30. 1 hit.
1.10.185.10. 1 hit.
1.10.375.10. 1 hit.
4.10.60.10. 1 hit.
InterProiIPR003139. D_retro_matrix.
IPR000721. Gag_p24.
IPR008916. Retrov_capsid_C.
IPR008919. Retrov_capsid_N.
IPR010999. Retrovr_matrix.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF02228. Gag_p19. 1 hit.
PF00607. Gag_p24. 1 hit.
PF00098. zf-CCHC. 1 hit.
[Graphical view]
SMARTiSM00343. ZnF_C2HC. 2 hits.
[Graphical view]
SUPFAMiSSF47353. SSF47353. 1 hit.
SSF47836. SSF47836. 1 hit.
SSF47943. SSF47943. 1 hit.
SSF57756. SSF57756. 1 hit.
PROSITEiPS50158. ZF_CCHC. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 3 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.
Isoform Gag polyprotein (identifier: P03345-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' 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
PEPEPEEDAL LLDLPADIPH PKNSIGGEV
Note: Produced by conventional translation.
Length:429
Mass (Da):47,496
Last modified:January 23, 2007 - v3
Checksum:i03FFD4E5A4500284
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.
Length:651
Mass (Da):71,558
GO
Isoform Gag-Pro-Pol polyprotein (identifier: P03362-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry P03362.
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 and gag-pol genes boundaries.
Length:1,462
Mass (Da):162,512
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti416A → T AA sequence (PubMed:6313426).Curated1
Sequence conflicti424S → F in AAA96672 (PubMed:6304725).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02029 Genomic DNA. Translation: AAA96672.1.
M13810 Genomic RNA. Translation: AAA46205.1.
PIRiB93954. FOLJGH.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02029 Genomic DNA. Translation: AAA96672.1.
M13810 Genomic RNA. Translation: AAA46205.1.
PIRiB93954. FOLJGH.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1QRJNMR-A146-344[»]
ProteinModelPortaliP03345.
SMRiP03345.
ModBaseiSearch...
MobiDBiSearch...

PTM databases

iPTMnetiP03345.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP03345.

Family and domain databases

Gene3Di1.10.1200.30. 1 hit.
1.10.185.10. 1 hit.
1.10.375.10. 1 hit.
4.10.60.10. 1 hit.
InterProiIPR003139. D_retro_matrix.
IPR000721. Gag_p24.
IPR008916. Retrov_capsid_C.
IPR008919. Retrov_capsid_N.
IPR010999. Retrovr_matrix.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF02228. Gag_p19. 1 hit.
PF00607. Gag_p24. 1 hit.
PF00098. zf-CCHC. 1 hit.
[Graphical view]
SMARTiSM00343. ZnF_C2HC. 2 hits.
[Graphical view]
SUPFAMiSSF47353. SSF47353. 1 hit.
SSF47836. SSF47836. 1 hit.
SSF47943. SSF47943. 1 hit.
SSF57756. SSF57756. 1 hit.
PROSITEiPS50158. ZF_CCHC. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiGAG_HTL1A
AccessioniPrimary (citable) accession number: P03345
Secondary accession number(s): Q85589
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 117 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

HTLV-1 lineages are divided in four clades, A (Cosmopolitan), B (Central African group), C (Melanesian group) and D (New Central African group).

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.