Reviewed, UniProtKB/Swiss-Prot P04590 (GAG_HV2RO)

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 2 (isolate ROD subtype A) (HIV-2)

Taxonomic identifier

11720 [NCBI]

Taxonomic lineage

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

Virus host

Homo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length	522 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Matrix protein p17 targets Gag and Gag-pol polyproteins to the plasma membrane via a multipartite membrane binding signal. Also mediates nuclear localization of the preintegration complex By similarity. Capsid protein p24 forms the conical core of the virus that encapsulates the genomic RNA-nucleocapsid complex By similarity. Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers By similarity. 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	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.
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 Myristate
Gene Ontology (GO)
Biological process	interspecies interaction between organisms Inferred from electronic annotation. Source: UniProtKB-KW viral reproduction Inferred from electronic annotation. Source: InterPro
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-KW 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 protein binding Inferred from physical interaction. Source: IntAct structural molecule activity Inferred from electronic annotation. Source: UniProtKB-KW zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
PRPF4B	Q13523	3	EBI-780156,EBI-395940	From a different organism.

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: P04590-1)

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: P04584-1)

The sequence of this isoform can be found in the external entry P04584-1.
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 – 522	521	Gag polyprotein		PRO_0000261248
	Chain	2 – 135	134	Matrix protein p17 By similarity		PRO_0000038615
	Chain	136 – 365	230	Capsid protein p24 By similarity		PRO_0000038616
	Peptide	366 – 382	17	Spacer peptide p2 By similarity		PRO_0000042091
	Chain	383 – 431	49	Nucleocapsid protein p7 By similarity		PRO_0000042092
	Peptide	432 – 445	14	Spacer peptide p1 By similarity		PRO_0000042093
	Chain	446 – 522	77	p6-gag By similarity		PRO_0000042094
Regions
	Zinc finger	389 – 406	18	CCHC-type 1
	Zinc finger	410 – 427	18	CCHC-type 2
	Motif	16 – 22	7	Nuclear export signal By similarity
	Motif	26 – 32	7	Nuclear localization signal By similarity
	Motif	456 – 459	4	PTAP motif By similarity
	Motif	514 – 518	5	LXXLF motif By similarity
Sites
	Site	135 – 136	2	Cleavage; by viral protease By similarity
	Site	365 – 366	2	Cleavage; by viral protease By similarity
	Site	382 – 383	2	Cleavage; by viral protease By similarity
	Site	431 – 432	2	Cleavage; by viral protease By similarity
	Site	445 – 446	2	Cleavage; by viral protease By similarity
Amino acid modifications
	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: DC1FBA5280B577D9	FASTA	522	58,374
	10 20 30 40 50 60 MGARNSVLRG KKADELERIR LRPGGKKKYR LKHIVWAANK LDRFGLAESL LESKEGCQKI 70 80 90 100 110 120 LTVLDPMVPT GSENLKSLFN TVCVIWCIHA EEKVKDTEGA KQIVRRHLVA ETGTAEKMPS 130 140 150 160 170 180 TSRPTAPSSE KGGNYPVQHV GGNYTHIPLS PRTLNAWVKL VEEKKFGAEV VPGFQALSEG 190 200 210 220 230 240 CTPYDINQML NCVGDHQAAM QIIREIINEE AAEWDVQHPI PGPLPAGQLR EPRGSDIAGT 250 260 270 280 290 300 TSTVEEQIQW MFRPQNPVPV GNIYRRWIQI GLQKCVRMYN PTNILDIKQG PKEPFQSYVD 310 320 330 340 350 360 RFYKSLRAEQ TDPAVKNWMT QTLLVQNANP DCKLVLKGLG MNPTLEEMLT ACQGVGGPGQ 370 380 390 400 410 420 KARLMAEALK EVIGPAPIPF AAAQQRKAFK CWNCGKEGHS ARQCRAPRRQ GCWKCGKPGH 430 440 450 460 470 480 IMTNCPDRQA GFLGLGPWGK KPRNFPVAQV PQGLTPTAPP VDPAVDLLEK YMQQGKRQRE 490 500 510 520 QRERPYKEVT EDLLHLEQGE TPYREPPTED LLHLNSLFGK DQ
	Isoform Gag-Pol polyprotein. See P04584.	FASTA	–	–

References

[1]	"Genome organization and transactivation of the human immunodeficiency virus type 2." Guyader M., Emerman M., Sonigo P., Clavel F., Montagnier L., Alizon M. Nature 326:662-669(1987) [PubMed: 3031510] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	M15390 Genomic DNA. Translation: AAB00763.1. X05291 Genomic RNA. Translation: CAA28909.1.
PIR	FOLJG2. A26262.
3D structure databases
HSSP	HSSP built from PDB template 1NC8 based on UniProtKB P18041.
SMR	P04590. Positions 145-352, 146-353.
ModBase	Search...
Protein-protein interaction databases
IntAct	P04590. 4 interactions.
Family and domain databases
InterPro	IPR000721. Gag_p24. 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. 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_HV2RO

Accession

Primary (citable) accession number: P04590

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 13, 1987
Last sequence update:	January 23, 2007
Last modified:	June 16, 2009
This is version 86 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Virus (Virus annotation project)