P03332 (GAG_MLVMS) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Gag polyprotein
Short name=Pr65gag

Alternative name(s):
Core polyprotein

Cleaved into the following 4 chains:

1. Matrix protein p15
   Short name=MA
2. RNA-binding phosphoprotein p12
   Alternative name(s):
   pp12
3. Capsid protein p30
   Short name=CA
4. Nucleocapsid protein p10
   Short name=NC-gag

Gene names

Name:

gag

Organism

Moloney murine leukemia virus (isolate Shinnick) (MoMLV) [Reference proteome]

Taxonomic identifier

928306 [NCBI]

Taxonomic lineage

Viruses › Retro-transcribing viruses › Retroviridae › Orthoretrovirinae › Gammaretrovirus › Mammalian virus group › Replication competent viruses › Murine leukemia virus › Moloney murine leukemia virus

Virus host

Mus musculus (Mouse) [TaxID: 10090]

Protein attributes

Sequence length	538 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	Gag polyprotein plays a role in budding and is processed by the viral protease during virion maturation outside the cell. During budding, it recruits, in a PPXY-dependent or independent manner, Nedd4-like ubiquitin ligases that conjugate ubiquitin molecules to Gag, or to Gag binding host factors. Interaction with HECT ubiquitin ligases probably link the viral protein to the host ESCRT pathway and facilitate release. Ref.9 Matrix protein p15 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 By similarity. Ref.9 Capsid protein p30 forms the spherical core of the virion that encapsulates the genomic RNA-nucleocapsid complex By similarity. Ref.9 Nucleocapsid protein p10 is involved in the packaging and encapsidation of two copies of the genome. Binds with high affinity to conserved UCUG elements within the packaging signal, located near the 5'-end of the genome. This binding is dependent on genome dimerization. Ref.9
Subunit structure	Capsid protein p30 is a homohexamer, that further associates as homomultimer. The virus core is composed of a lattice formed from hexagonal rings, each containing six capsid monomers By similarity. Capsid protein p30 interacts with mouse UBE2I and mouse PIAS4. Gag polyprotein interacts (via PPXY motif) with host NEDD4. Gag polyprotein interacts (via PSAP motif) with host TSG101. Gag polyprotein interacts (via LYPX(n)L motif) with host PDCD6IP. Ref.6 Ref.7
Subcellular location	Gag polyprotein: Virion By similarity. Host cell membrane; Lipid-anchor Potential. Host late endosome membrane; Lipid-anchor Potential. Host endosome › host multivesicular body By similarity. Note: These locations are probably linked to virus assembly sites By similarity. Matrix protein p15: Virion Potential. Capsid protein p30: Virion Potential. Nucleocapsid protein p10: Virion Potential.
Domain	Late-budding domains (L domains) are short sequence motifs essential for viral particle budding. They recruit proteins of the host ESCRT machinery (Endosomal Sorting Complex Required for Transport) or ESCRT-associated proteins. RNA-binding phosphoprotein p12 contains one L domain: a PPXY motif which interacts with the WW domain 3 of NEDD4 E3 ubiquitin ligase. PPXY motif is essential for virus egress. Matrix protein p15 contains one L domain: a PTAP/PSAP motif, which interacts with the UEV domain of TSG101. The junction between the matrix protein p15 and RNA-binding phosphoprotein p12 also contains one L domain: a LYPX(n)L motif which interacts with PDCD6IP. Both PSAP and LYPX(n)L domains might play little to no role in budding and possibly drive residual virus release.
Post-translational modification	Gag polyprotein is ubiquitinated by ITCH. Gag can recruit the ubiquitin ligase Itch in an L domain-independent manner to facilitate virus release via a mechanism that involves Gag ubiquitination. Specific enzymatic cleavages by the viral protease yield mature proteins. The protease is released by autocatalytic cleavage. The polyprotein is cleaved during and after budding, this process is termed maturation By similarity. Ref.8 Capsid protein p30 is sumoylated; which is required for virus replication. Ref.7 RNA-binding phosphoprotein p12 is phosphorylated on serine residues. Ref.5
Sequence similarities	Contains 1 CCHC-type zinc finger.

Ontologies

Keywords
Biological process	Host-virus interaction Viral budding Viral budding via the host ESCRT complexes Virus exit from host cell
Cellular component	Host cell membrane Host endosome Host membrane Membrane Viral matrix protein Virion
Coding sequence diversity	Alternative initiation
Domain	Coiled coil Zinc-finger
Ligand	Metal-binding RNA-binding Viral nucleoprotein Zinc
Molecular function	Capsid protein
PTM	Lipoprotein Myristate Phosphoprotein Ubl conjugation
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	viral release from host cell Inferred from electronic annotation. Source: UniProtKB-KW virion assembly Inferred from electronic annotation. Source: InterPro virus-host interaction Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	host cell late endosome membrane Inferred from electronic annotation. Source: UniProtKB-SubCell host cell plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell host multivesicular body Inferred from electronic annotation. Source: UniProtKB-SubCell 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: InterPro zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
TRIM5	Q9C035-1	1	EBI-935477,EBI-924230	From a different organism.

Alternative products

This entry describes 2 isoforms produced by alternative initiation. [Align] [Select]

Isoform Pr65gag (identifier: P03332-1)

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.

Isoform Pr80gag (identifier: Q8UN02-1)

Also known as: GlycoGag;

The sequence of this isoform can be found in the external entry Q8UN02.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Note: Produced by an upstream CUG initiation codon.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed; by host Ref.3

Chain

2 – 538

537

Gag polyprotein

PRO_0000390815

Chain

2 – 131

130

Matrix protein p15 Potential

PRO_0000040912

Chain

132 – 215

84

RNA-binding phosphoprotein p12 Potential

PRO_0000040913

Chain

216 – 478

263

Capsid protein p30 Potential

PRO_0000040914

Chain

479 – 538

60

Nucleocapsid protein p10 Potential

PRO_0000040915

Regions

Zinc finger

502 – 519

18

CCHC-type

Region

345 – 393

49

Interaction with mouse PIAS4

Region

430 – 435

6

Interaction with mouse UBE2I

Coiled coil

438 – 478

41

Potential

Motif

111 – 114

4

PTAP/PSAP motif

Motif

130 – 134

5

LYPX(n)L motif

Motif

162 – 165

4

PPXY motif

Sites

Site

131 – 132

2

Cleavage; by viral protease p14

Site

215 – 216

2

Cleavage; by viral protease p14

Site

478 – 479

2

Cleavage; by viral protease p14

Amino acid modifications

Modified residue

192

1

Phosphoserine; by host Probable

Lipidation

2

1

N-myristoyl glycine; by host Ref.3

Experimental info

Mutagenesis

114

1

P → A: Slight reduction in the number of virus-like particles produced.

Mutagenesis

137

1

S → A: No effect on reverse transcription activity. Ref.5

Mutagenesis

148

1

S → A: No effect on reverse transcription activity; when associated with A-150. Ref.5

Mutagenesis

150

1

S → A: No effect on reverse transcription activity; when associated with A-148. Ref.5

Mutagenesis

165

1

Y → A: Drastic reduction in the number of virus-like particles produced. Ref.6

Mutagenesis

192

1

S → A: Complete loss of reverse transcription activity. Ref.5

Mutagenesis

192

1

S → D: Complete loss of reverse transcription activity. Ref.5

Mutagenesis

196

1

S → A: No effect on reverse transcription activity. Ref.5

Mutagenesis

209

1

S → A: Strongly reduced reverse transcription activity. Ref.5

Mutagenesis

209

1

S → D: Strongly reduced reverse transcription activity. Ref.5

Mutagenesis

212

1

S → A: No effect on reverse transcription activity. Ref.5

Secondary structure

1

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538

Helix Strand Turn

Details...

Helix

8 – 14

7

Helix

16 – 25

10

Helix

32 – 40

9

Helix

43 – 46

4

Helix

58 – 68

11

Helix

77 – 79

3

Helix

80 – 91

12

Turn

356 – 360

5

Helix

361 – 363

3

Helix

364 – 378

15

Beta strand

494 – 496

3

Beta strand

501 – 503

3

Beta strand

505 – 507

3

Beta strand

510 – 512

3

Helix

514 – 516

3

Beta strand

518 – 520

3

Beta strand

522 – 524

3

Sequences

	Sequence		Length	Mass (Da)
	Isoform Pr65gag [UniParc]. Last modified January 23, 2007. Version 4. Checksum: 8A7652439B464495	FASTA	538	60,858
	10 20 30 40 50 60 MGQTVTTPLS LTLGHWKDVE RIAHNQSVDV KKRRWVTFCS AEWPTFNVGW PRDGTFNRDL 70 80 90 100 110 120 ITQVKIKVFS PGPHGHPDQV PYIVTWEALA FDPPPWVKPF VHPKPPPPLP PSAPSLPLEP 130 140 150 160 170 180 PRSTPPRSSL YPALTPSLGA KPKPQVLSDS GGPLIDLLTE DPPPYRDPRP PPSDRDGNGG 190 200 210 220 230 240 EATPAGEAPD PSPMASRLRG RREPPVADST TSQAFPLRAG GNGQLQYWPF SSSDLYNWKN 250 260 270 280 290 300 NNPSFSEDPG KLTALIESVL ITHQPTWDDC QQLLGTLLTG EEKQRVLLEA RKAVRGDDGR 310 320 330 340 350 360 PTQLPNEVDA AFPLERPDWD YTTQAGRNHL VHYRQLLLAG LQNAGRSPTN LAKVKGITQG 370 380 390 400 410 420 PNESPSAFLE RLKEAYRRYT PYDPEDPGQE TNVSMSFIWQ SAPDIGRKLE RLEDLKNKTL 430 440 450 460 470 480 GDLVREAEKI FNKRETPEER EERIRRETEE KEERRRTEDE QKEKERDRRR HREMSKLLAT 490 500 510 520 530 VVSGQKQDRQ GGERRRSQLD RDQCAYCKEK GHWAKDCPKK PRGPRGPRPQ TSLLTLDD
	Isoform Pr80gag (GlycoGag) [UniParc]. See Q8UN02.		–	–

References

[1]	"Nucleotide sequence of Moloney murine leukaemia virus." Shinnick T.M., Lerner R.A., Sutcliffe J.G. Nature 293:543-548(1981) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] (CLONE PMLV-1).
[2]	Chappey C. Submitted (NOV-1997) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[3]	"Myristyl amino-terminal acylation of murine retrovirus proteins: an unusual post-translational proteins modification." Henderson L.E., Krutzsch H.C., Oroszlan S. Proc. Natl. Acad. Sci. U.S.A. 80:339-343(1983) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-31, MYRISTOYLATION AT GLY-2.
[4]	"Primary structure of the low molecular weight nucleic acid-binding proteins of murine leukemia viruses." Henderson L.E., Copeland T.D., Sowder R.C., Smythers G.W., Oroszlan S. J. Biol. Chem. 256:8400-8406(1981) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 479-529.
[5]	"Phosphorylated serine residues and an arginine-rich domain of the moloney murine leukemia virus p12 protein are required for early events of viral infection." Yueh A., Goff S.P. J. Virol. 77:1820-1829(2003) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION AT SER-192, MUTAGENESIS OF SER-137; SER-148; SER-150; SER-192; SER-196; SER-209 AND SER-212.
[6]	"Tsg101 and Alix interact with murine leukemia virus Gag and cooperate with Nedd4 ubiquitin ligases during budding." Segura-Morales C., Pescia C., Chatellard-Causse C., Sadoul R., Bertrand E., Basyuk E. J. Biol. Chem. 280:27004-27012(2005) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH MOUSE NEDD4; TSG101 AND PDCD6IP/ALIX, MUTAGENESIS OF TYR-165.
[7]	"Interaction of moloney murine leukemia virus capsid with Ubc9 and PIASy mediates SUMO-1 addition required early in infection." Yueh A., Leung J., Bhattacharyya S., Perrone L.A., de los Santos K., Pu S.-Y., Goff S.P. J. Virol. 80:342-352(2006) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH UBE2I AND PIAS4, SUMOYLATION.
[8]	"Characterization of the murine leukemia virus protease and its comparison with the human immunodeficiency virus type 1 protease." Feher A., Boross P., Sperka T., Miklossy G., Kadas J., Bagossi P., Oroszlan S., Weber I.T., Tozser J. J. Gen. Virol. 87:1321-1330(2006) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEOLYTIC PROCESSING OF POLYPROTEIN.
[9]	"Late domain-independent rescue of a release-deficient Moloney murine leukemia virus by the ubiquitin ligase Itch." Jadwin J.A., Rudd V., Sette P., Challa S., Bouamr F. J. Virol. 84:704-715(2010) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[10]	"Three-dimensional 1H NMR structure of the nucleocapsid protein NCp10 of Moloney murine leukemia virus." Demene H., Jullian N., Morellet N., de Rocquigny H., Cornille F., Maigret B., Roques B.P. J. Biomol. NMR 4:153-170(1994) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR OF 492-531.
[11]	"Solution structures of human immunodeficiency virus type 1 (HIV-1) and moloney murine leukemia virus (MoMLV) capsid protein major-homology-region peptide analogs by NMR spectroscopy." Clish C.B., Peyton D.H., Barklis E. Eur. J. Biochem. 257:69-77(1998) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR OF 352-382.
[12]	"Atomic resolution structure of Moloney murine leukemia virus matrix protein and its relationship to other retroviral matrix proteins." Riffel N., Harlos K., Iourin O., Rao Z., Kingsman A., Stuart D., Fry E. Structure 10:1627-1636(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.0 ANGSTROMS) OF 1-99.
[13]	"Structural basis for packaging the dimeric genome of Moloney murine leukaemia virus." D'Souza V., Summers M.F. Nature 431:586-590(2004) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR OF 479-534.
[14]	"Composition and sequence-dependent binding of RNA to the nucleocapsid protein of Moloney murine leukemia virus." Dey A., York D., Smalls-Mantey A., Summers M.F. Biochemistry 44:3735-3744(2005) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR OF 479-534.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J02255 Genomic RNA. Translation: AAB59942.1.
AF033811 Genomic RNA. Translation: AAC82566.1.

PIR

FOMV1M. A03930.

RefSeq

NP_057934.1. NC_001501.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1A6B	NMR	-	B	492-531	[»]
1BM4	NMR	-	A	352-382	[»]
1MN8	X-ray	1.00	A/B/C/D	1-99	[»]
1U6P	NMR	-	A	479-534	[»]
1WWD	NMR	-	A	479-534	[»]
1WWE	NMR	-	A	479-534	[»]
1WWF	NMR	-	A	479-534	[»]
1WWG	NMR	-	A	479-534	[»]

ProteinModelPortal

P03332.

SMR

P03332. Positions 2-98, 216-347, 352-382, 479-534.

ModBase

Search...

Protein-protein interaction databases

IntAct

P03332. 1 interaction.

MINT

MINT-2490859.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

Gene3D

1.10.150.180. 1 hit.
1.10.375.10. 1 hit.
4.10.60.10. 1 hit.

InterPro

IPR000840. G_retro_matrix_N.
IPR002079. Gag_p12.
IPR003036. Gag_p30.
IPR008919. Retrov_capsid_N.
IPR010999. Retrovr_matrix_N.
IPR001878. Znf_CCHC.
[Graphical view]

Pfam

PF01140. Gag_MA. 1 hit.
PF01141. Gag_p12. 1 hit.
PF02093. Gag_p30. 1 hit.
PF00098. zf-CCHC. 1 hit.
[Graphical view]

SMART

SM00343. ZnF_C2HC. 1 hit.
[Graphical view]

SUPFAM

SSF47943. Retrov_capsid_N. 1 hit.
SSF47836. Retrovir_matrix. 1 hit.
SSF57756. SSF57756. 1 hit.

PROSITE

PS50158. ZF_CCHC. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P03332.

Entry information

Entry name

GAG_MLVMS

Accession

Primary (citable) accession number: P03332
Secondary accession number(s): Q9WJP4

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	January 23, 2007
Last modified:	April 3, 2013
This is version 119 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program