P03322 (GAG_RSVP) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Gag-Pro polyprotein

Cleaved into the following 8 chains:

1. p3
2. Matrix protein p19
3. p2A
4. p2B
5. p10
6. Capsid protein p27
7. Nucleocapsid protein p12
8. Protease p15
   EC=3.4.23.-

Gene names

Name:

gag-pro

Organism

Rous sarcoma virus (strain Prague C) (RSV-PrC) [Complete proteome]

Taxonomic identifier

11888 [NCBI]

Taxonomic lineage

Viruses › Retro-transcribing viruses › Retroviridae › Orthoretrovirinae › Alpharetrovirus

Virus host

Gallus gallus (Chicken) [TaxID: 9031]

Protein attributes

Sequence length	701 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	Capsid protein p27 forms the spherical core of the virus that encapsulates the genomic RNA-nucleocapsid complex By similarity. 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 By similarity.
Subunit structure	The protease is active as a homodimer.
Subcellular location	Matrix protein p19: Virion Potential. Capsid protein p27: Virion Potential. Nucleocapsid protein p12: 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. P2B contains one L domain: a PPXY motif which probably binds to the WW domains of HECT (homologous to E6-AP C-terminus) E3 ubiquitin ligases By similarity. Ref.4
Post-translational modification	Specific enzymatic cleavages in vivo yield mature proteins.
Sequence similarities	Contains 2 CCHC-type zinc fingers. Contains 1 peptidase A2 domain.

Ontologies

Keywords
Cellular component	Viral matrix protein Virion
Coding sequence diversity	Ribosomal frameshifting
Domain	Repeat Zinc-finger
Ligand	Metal-binding Zinc
Molecular function	Aspartyl protease Capsid protein Hydrolase Protease
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	proteolysis Inferred from electronic annotation. Source: UniProtKB-KW viral reproduction Inferred from electronic annotation. Source: InterPro
Cellular component	viral capsid Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	aspartic-type endopeptidase activity Inferred from electronic annotation. Source: UniProtKB-KW nucleic acid binding Inferred from electronic annotation. Source: InterPro structural molecule activity Inferred from electronic annotation. Source: InterPro zinc ion binding Inferred from electronic annotation. Source: InterPro
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-Pro. Ribosomal frameshifting at the gag-pro/pol genes boundary produces the Gag-Pro-Pol polyprotein.

Isoform Gag-Pro polyprotein (identifier: P03322-1)

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-Pro-Pol polyprotein (identifier: P03354-1)

The sequence of this isoform can be found in the external entry P03354.
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

Chain

1 – 155

155

Matrix protein p19

PRO_0000026113

Chain

156 – 166

11

p2A

PRO_0000026114

Chain

167 – 177

11

p2B

PRO_0000026115

Chain

178 – 239

62

p10

PRO_0000026116

Chain

240 – 479

240

Capsid protein p27

PRO_0000026117

Chain

480 – 488

9

p3

PRO_0000026118

Chain

489 – 577

89

Nucleocapsid protein p12

PRO_0000026119

Chain

578 – 701

124

Protease p15

PRO_0000026120

Regions

Domain

609 – 690

82

Peptidase A2

Zinc finger

507 – 524

18

CCHC-type 1

Zinc finger

533 – 550

18

CCHC-type 2

Motif

172 – 175

4

PPXY motif

Compositional bias

171 – 174

4

Poly-Pro

Sites

Active site

614

1

For protease activity; shared with dimeric partner By similarity

Site

155 – 156

2

Cleavage; by viral protease p15 By similarity

Site

166 – 167

2

Cleavage; by viral protease p15 By similarity

Site

177 – 178

2

Cleavage; by viral protease p15 By similarity

Site

239 – 240

2

Cleavage; by viral protease p15 By similarity

Site

479 – 480

2

Cleavage; by viral protease p15 By similarity

Site

488 – 489

2

Cleavage; by viral protease p15 By similarity

Site

577 – 578

2

Cleavage; by viral protease p15 By similarity

Experimental info

Sequence conflict

505

1

A → S AA sequence Ref.2

Sequence conflict

536

1

Q → E AA sequence Ref.2

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

701

Helix Strand Turn

Details...

Helix

222 – 226

5

Beta strand

241 – 243

3

Beta strand

245 – 250

6

Helix

255 – 268

14

Helix

273 – 282

10

Helix

289 – 299

11

Helix

302 – 325

24

Helix

342 – 345

4

Turn

350 – 354

5

Helix

356 – 362

7

Helix

365 – 385

21

Helix

403 – 415

13

Turn

416 – 418

3

Helix

421 – 435

15

Helix

438 – 446

9

Helix

454 – 464

11

Beta strand

579 – 581

3

Beta strand

584 – 586

3

Beta strand

589 – 596

8

Beta strand

605 – 613

9

Beta strand

621 – 623

3

Turn

624 – 626

3

Beta strand

633 – 635

3

Beta strand

650 – 655

6

Beta strand

657 – 662

6

Beta strand

672 – 674

3

Beta strand

677 – 680

4

Beta strand

682 – 686

5

Helix

688 – 693

6

Beta strand

697 – 699

3

Sequences

	Sequence		Length	Mass (Da)
	Isoform Gag-Pro polyprotein [UniParc]. Last modified July 21, 1986. Version 1. Checksum: 5FD365D9CFEF37F1	FASTA	701	74,527
	10 20 30 40 50 60 MEAVIKVISS ACKTYCGKTS PSKKEIGAML SLLQKEGLLM SPSDLYSPGS WDPITAALSQ 70 80 90 100 110 120 RAMILGKSGE LKTWGLVLGA LKAAREEQVT SEQAKFWLGL GGGRVSPPGP ECIEKPATER 130 140 150 160 170 180 RIDKGEEVGE TTVQRDAKMA PEETATPKTV GTSCYHCGTA IGCNCATASA PPPPYVGSGL 190 200 210 220 230 240 YPSLAGVGEQ QGQGGDTPPG AEQSRAEPGH AGQAPGPALT DWARVREELA STGPPVVAMP 250 260 270 280 290 300 VVIKTEGPAW TPLEPKLITR LADTVRTKGL RSPITMAEVE ALMSSPLLPH DVTNLMRVIL 310 320 330 340 350 360 GPAPYALWMD AWGVQLQTVI AAATRDPRHP ANGQGRGERT NLNRLKGLAD GMVGNPQGQA 370 380 390 400 410 420 ALLRPGELVA ITASALQAFR EVARLAEPAG PWADIMQGPS ESFVDFANRL IKAVEGSDLP 430 440 450 460 470 480 PSARAPVIID CFRQKSQPDI QQLIRTAPST LTTPGEIIKY VLDRQKTAPL TDQGIAAAMS 490 500 510 520 530 540 SAIQPLIMAV VNRERDGQTG SGGRARGLCY TCGSPGHYQA QCPKKRKSGN SRERCQLCNG 550 560 570 580 590 600 MGHNAKQCRK RDGNQGQRPG KGLSSGPWPG PEPPAVSLAM TMEHKDRPLV RVILTNTGSH 610 620 630 640 650 660 PVKQRSVYIT ALLDSGADIT IISEEDWPTD WPVMEAANPQ IHGIGGGIPM RKSRDMIELG 670 680 690 700 VINRDGSLER PLLLFPAVAM VRGSILGRDC LQGLGLRLTN L
	Isoform Gag-Pro-Pol polyprotein [UniParc]. See P03354.		–	–

References

[1]	"Nucleotide sequence of Rous sarcoma virus." Schwartz D., Tizard R., Gilbert W. Cell 32:853-869(1983) [PubMed: 6299578] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]	"Primary structure of Rous sarcoma virus RNA-associated polypeptide." Misono K.S., Sharief F.S., Leis J. Fed. Proc. 39:1611-1611(1980) Cited for: PROTEIN SEQUENCE OF 489-577.
[3]	"Comparative studies on the substrate specificity of avian myeloblastosis virus proteinase and lentiviral proteinases." Tozser J., Bagossi P., Weber I.T., Copeland T.D., Oroszlan S. J. Biol. Chem. 271:6781-6788(1996) [PubMed: 8636100] [Abstract] Cited for: PROTEOLYTIC PROCESSING OF POLYPROTEIN.
[4]	"Crystal structure of a retroviral protease proves relationship to aspartic protease family." Miller M., Jaskolski M., Rao J.K.M., Leis J., Wlodawer A. Nature 337:576-579(1989) [PubMed: 2536902] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF PROTEASE DOMAIN.
[5]	"Solution structure and dynamics of the bioactive retroviral M domain from Rous sarcoma virus." McDonnell J.M., Fushman D., Cahill S.M., Zhou W., Wolven A., Wilson C.B., Nelle T.D., Resh M.D., Wills J., Cowburn D. J. Mol. Biol. 279:921-928(1998) [PubMed: 9642071] [Abstract] Cited for: STRUCTURE BY NMR OF 1-87.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J02342 Genomic RNA. Translation: AAB59932.1.
V01197 Genomic DNA. Translation: CAA24512.1.

PIR

FOFV1R. A90834.

RefSeq

NP_056887.1. NC_001407.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1A6S	NMR	-	A	2-87	[»]
1BAI	X-ray	2.40	A/B	578-701	[»]
1EM9	X-ray	2.05	A/B	240-393	[»]
1EOQ	NMR	-	A	394-488	[»]
1P7N	X-ray	2.60	A	215-386	[»]
2IHX	NMR	-	A	503-563	[»]
2RSP	X-ray	2.00	A/B	578-701	[»]
2X8Q	electron microscopy	18.30	A	240-465	[»]
3G0V	X-ray	2.00	A	389-465	[»]
3G1G	X-ray	2.01	A/B	390-476	[»]
3G1I	X-ray	2.10	A/B	389-465	[»]
3G21	X-ray	0.90	A	389-465	[»]
3G26	X-ray	1.55	A	389-465	[»]
3G28	X-ray	1.64	A	389-465	[»]
3G29	X-ray	2.50	A/B	389-465	[»]

ProteinModelPortal

P03322.

SMR

P03322. Positions 2-87, 214-469, 503-552, 578-701.

ModBase

Search...

Protein-protein interaction databases

MINT

MINT-6616346.

Protein family/group databases

MEROPS

A02.015.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

1491923.

Family and domain databases

InterPro

IPR004028. Gag_M.
IPR000721. Gag_p24.
IPR012344. Matrix_N_HIV/RSV.
IPR018061. Pept_A2A_retrovirus_sg.
IPR001995. Peptidase_A2_cat.
IPR021109. Peptidase_aspartic.
IPR001969. Peptidase_aspartic_AS.
IPR009007. Peptidase_aspartic_catalytic.
IPR008916. Retrov_capsid_C.
IPR008919. Retrov_capsid_N.
IPR010999. Retrovr_matrix_N.
IPR013084. Znf_CCH_retrovir.
IPR001878. Znf_CCHC.
[Graphical view]

Gene3D

G3DSA:1.10.150.90. Matrix_HIV/RSV_N. 1 hit.
G3DSA:2.40.70.10. Pept_Aspartc_cat. 1 hit.
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

PF00607. Gag_p24. 1 hit.
PF02813. Retro_M. 1 hit.
PF00077. RVP. 1 hit.
PF00098. zf-CCHC. 2 hits.
[Graphical view]

ProDom

PD002871. Gag_M. 1 hit.
[Graphical view] [Entries sharing at least one domain]

SMART

SM00343. ZnF_C2HC. 2 hits.
[Graphical view]

SUPFAM

SSF50630. Pept_Aspartic. 1 hit.
SSF47353. Retrov_capsid_C. 1 hit.
SSF47943. Retrov_capsid_N. 1 hit.
SSF47836. Retrovir_matrix. 1 hit.

PROSITE

PS50175. ASP_PROT_RETROV. 1 hit.
PS00141. ASP_PROTEASE. 1 hit.
PS50158. ZF_CCHC. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

GAG_RSVP

Accession

Primary (citable) accession number: P03322

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	July 21, 1986
Last modified:	November 16, 2011
This is version 104 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program