Reviewed, UniProtKB/Swiss-Prot P04594 (GAG_HV1MA)

Names and origin

Protein names

Recommended name:
    Gag polyprotein
Alternative name(s):
    Pr55Gag
Cleaved into the following 6 chains:
    1- Recommended name:
            Matrix protein p17
                Short name=MA
    2- Recommended name:
            Capsid protein p24
                Short name=CA
    3- Recommended name:
            Spacer peptide p2
    4- Recommended name:
            Nucleocapsid protein p7
                Short name=NC
    5- Recommended name:
            Spacer peptide p1
    6- Recommended name:
            p6-gag

Gene names

Name:

gag

Organism

Human immunodeficiency virus type 1 (isolate MAL group M subtype A) (HIV-1)

Taxonomic identifier

11697 [NCBI]

Taxonomic lineage

Viruses › Retro-transcribing viruses › Retroviridae › Orthoretrovirinae › Lentivirus › Primate lentivirus group

Virus host

Homo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length	505 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Inferred from homology.

General annotation (Comments)

Function	Matrix protein p17 targets Gag and Gag-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. Implicated in the release from host cell mediated by Vpu. Capsid protein p24 forms the conical core of the virus that encapsulates the genomic RNA-nucleocapsid complex. Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers. p6-gag plays a role in budding of the assembled particle by interacting with the host class E VPS proteins TSG101 and PDCD6IP/AIP1 By similarity.
Subunit structure	Matrix protein p17 is a trimer. Interacts with gp120. p6-gag interacts with human TSG101 and PDCD6IP/AIP1 By similarity.
Subcellular location	Matrix protein p17: Virion Potential. Host nucleus By similarity. Host cytoplasm By similarity. Host cell membrane; Lipid-anchor Potential. Note: Following virus entry, the nuclear localization signal (NLS) of the matrix protein participates with Vpr to the nuclear localization of the viral genome. During virus production, the nuclear export activity of the matrix protein counteracts the NLS to maintain the Gag and Gag-Pol polyproteins in the cytoplasm, thereby directing unspliced RNA to the plasma membrane By similarity. Capsid protein p24: Virion Potential. Nucleocapsid protein p7: Virion Potential.
Domain	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. p6-gag contains two L domains: a PTAP/PSAP motif, which interacts with the UEV domain of TSG101 and a LXXLF motif which interacts with PDCD6IP/AIP1 By similarity.
Post-translational modification	Capsid protein p24 is phosphorylated. 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. Nucleocapsid protein p7 is methylated by host PRMT6, impairing its function by reducing RNA annealing and the initiation of reverse transcription By similarity.
Miscellaneous	HIV-1 lineages are divided in three main groups, M (for Major), O (for Outlier), and N (for New, or Non-M, Non-O). The vast majority of strains found worldwide belong to the group M. Group O seems to be endemic to and largely confined to Cameroon and neighboring countries in West Central Africa, where these viruses represent a small minority of HIV-1 strains. The group N is represented by a limited number of isolates from Cameroonian persons. The group M is further subdivided in 9 clades or subtypes (A to D, F to H, J and K).
Sequence similarities	Belongs to the primate lentivirus group gag polyprotein family. Contains 2 CCHC-type zinc fingers.

Ontologies

Keywords
Biological process	Host-virus interaction
Cellular component	Capsid protein Cell membrane Cytoplasm Membrane Nucleus Virion
Coding sequence diversity	Ribosomal frameshifting
Disease	AIDS
Domain	Repeat Zinc-finger
Ligand	Metal-binding RNA-binding Viral nucleoprotein Zinc
PTM	Lipoprotein Methylation Myristate Phosphoprotein
Gene Ontology (GO)
Biological process	initiation of viral infection Inferred from Experiment. Source: Reactome interspecies interaction between organisms Inferred from electronic annotation. Source: UniProtKB-KW provirus integration Inferred from Experiment. Source: Reactome
Cellular component	cytosol Inferred from Experiment. Source: Reactome host cell cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell host cell nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell host cell plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell nucleus Inferred from electronic annotation. Source: UniProtKB-KW plasma membrane Inferred from electronic annotation. Source: UniProtKB-KW viral capsid Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	RNA binding Inferred from electronic annotation. Source: UniProtKB-KW structural molecule activity Inferred from electronic annotation. Source: UniProtKB-KW zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by ribosomal frameshifting. [Align] [Select]

Note: Translation results in the formation of the Gag polyprotein most of the time. Ribosomal frameshifting at the gag-pol genes boundary occurs at low frequency and produces the Gag-Pol polyprotein. This strategy of translation probably allows the virus to modulate the quantity of each viral protein. Maintenance of a correct Gag to Gag-Pol ratio is essential for RNA dimerization and viral infectivity.

Isoform Gag polyprotein (identifier: P04594-1)

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.

Note: Produced by conventional translation.

Isoform Gag-Pol polyprotein (identifier: P04588-1)

The sequence of this isoform can be found in the external entry P04588-1.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Note: Produced by -1 ribosomal frameshifting.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Initiator methionine	1	1	Removed; by host By similarity
	Chain	2 – 505	504	Gag polyprotein		PRO_0000261220
	Chain	2 – 138	137	Matrix protein p17 By similarity		PRO_0000038553
	Chain	139 – 369	231	Capsid protein p24 By similarity		PRO_0000038554
	Peptide	370 – 384	15	Spacer peptide p2 By similarity		PRO_0000038555
	Chain	385 – 438	54	Nucleocapsid protein p7 By similarity		PRO_0000038556
	Peptide	439 – 454	16	Spacer peptide p1 By similarity		PRO_0000038557
	Chain	455 – 505	51	p6-gag By similarity		PRO_0000038558
Regions
	Zinc finger	396 – 413	18	CCHC-type 1
	Zinc finger	417 – 434	18	CCHC-type 2
	Motif	16 – 22	7	Nuclear export signal By similarity
	Motif	26 – 32	7	Nuclear localization signal By similarity
	Motif	461 – 464	4	PTAP motif By similarity
	Motif	494 – 498	5	LXXLF motif By similarity
Sites
	Site	138 – 139	2	Cleavage; by viral protease By similarity
	Site	369 – 370	2	Cleavage; by viral protease By similarity
	Site	384 – 385	2	Cleavage; by viral protease By similarity
	Site	438 – 439	2	Cleavage; by viral protease By similarity
	Site	454 – 455	2	Cleavage; by viral protease By similarity
Amino acid modifications
	Modified residue	415	1	Asymmetric dimethylarginine; in Nucleocapsid protein p7; by host PRMT6 By similarity
	Lipidation	2	1	N-myristoyl glycine; by host By similarity

Sequences

	Sequence		Length	Mass (Da)
	Isoform Gag polyprotein [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 6303D55683D3B8B3	FASTA	505	56,132
	10 20 30 40 50 60 MGARASVLSG GKLDAWEKIR LRPGGKKKYR LKHLVWASRE LERFALNPGL LETGEGCQQI 70 80 90 100 110 120 MEQLQSTLKT GSEEIKSLYN TVATLYCVHQ RIDVKDTKEA LDKIEEIQNK SRQKTQQAAA 130 140 150 160 170 180 AQQAAAATKN SSSVSQNYPI VQNAQGQMIH QAISPRTLNA WVKVIEEKAF SPEVIPMFSA 190 200 210 220 230 240 LSEGATPQDL NMMLNIVGGH QAAMQMLKDT INEEAADWDR VHPVHAGPIP PGQMREPRGS 250 260 270 280 290 300 DIAGTTSTLQ EQIGWMTSNP PIPVGDIYKR WIILGLNKIV RMYSPVSILD IRQGPKEPFR 310 320 330 340 350 360 DYVDRFFKTL RAEQATQEVK NWMTETLLVQ NANPDCKTIL KALGPGATLE EMMTACQGVG 370 380 390 400 410 420 GPSHKARVLA EAMSQATNST AAIMMQRGNF KGQKRIKCFN CGKEGHLARN CRAPRKKGCW 430 440 450 460 470 480 KCGKEGHQMK DCTERQANFL GKIWPSHKGR PGNFLQSRPE PTAPPAESFG FGEEIKPSQK 490 500 QEQKDKELYP LASLKSLFGN DQLSQ
	Isoform Gag-Pol polyprotein. See P04588.	FASTA	–	–

References

[1]	"Genetic variability of the AIDS virus: nucleotide sequence analysis of two isolates from African patients." Alizon M., Wain-Hobson S., Montagnier L., Sonigo P. Cell 46:63-74(1986) [PubMed: 2424612] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]	"Role of HIV-1 Gag domains in viral assembly." Scarlata S., Carter C. Biochim. Biophys. Acta 1614:62-72(2003) [PubMed: 12873766] [Abstract] Cited for: REVIEW.

Cross-references

Sequence databases
EMBLGenBankDDBJ	X04415 Genomic RNA. Translation: CAA28011.1.
PIR	T01667.
3D structure databases
HSSP	HSSP built from PDB template 1NCP based on UniProtKB P24736.
SMR	P04594. Positions 2-289, 149-357, 385-438, 455-505.
ModBase	Search...
Enzyme and pathway databases
Reactome	REACT_6185. HIV Infection.
Family and domain databases
InterPro	IPR000721. Gag_p24. IPR014817. Gag_p6. IPR000071. Lentvrl_matrix_N. IPR008916. Retrov_capsid_C. IPR008919. Retrov_capsid_N. IPR013084. Znf_CCH_retrovir. IPR001878. Znf_CCHC. [Graphical view]
Gene3D	G3DSA:1.10.1200.30. Retrov_capsid_C. 1 hit. G3DSA:1.10.375.10. Retrov_capsid_N. 1 hit. G3DSA:4.10.60.10. Znf_CCH_retrovir. 1 hit.
Pfam	PF00540. Gag_p17. 1 hit. PF00607. Gag_p24. 1 hit. PF08705. Gag_p6. 1 hit. PF00098. zf-CCHC. 2 hits. [Graphical view]
PRINTS	PR00234. HIV1MATRIX.
SMART	SM00343. ZnF_C2HC. 2 hits. [Graphical view]
PROSITE	PS50158. ZF_CCHC. 2 hits. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

GAG_HV1MA

Accession

Primary (citable) accession number: P04594

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 13, 1987
Last sequence update:	January 23, 2007
Last modified:	June 16, 2009
This is version 96 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Virus (Virus annotation project)