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P03354 (POL_RSVP) Reviewed, UniProtKB/Swiss-Prot

Last modified December 14, 2011. Version 94. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Gag-Pro-Pol polyprotein

Cleaved into the following 12 chains:

  1. Matrix protein p19
  2. p2A
  3. p2B
  4. p10
  5. Capsid protein p27
  6. p3
  7. Nucleocapsid protein p12
  8. Protease p15
    EC=3.4.23.-
  9. Reverse transcriptase beta-subunit
    Short name=RT-beta
    EC=2.7.7.49
    EC=2.7.7.7
    EC=3.1.26.4
  10. Reverse transcriptase alpha-subunit
    Short name=RT-alpha
    EC=2.7.7.49
    EC=2.7.7.7
    EC=3.1.26.4
  11. Integrase
    Short name=IN
    Alternative name(s):
    pp32
  12. p4
Gene names
Name:gag-pro-pol
OrganismRous sarcoma virus (strain Prague C) (RSV-PrC) [Complete proteome]
Taxonomic identifier11888 [NCBI]
Taxonomic lineageViruses › Retro-transcribing viruses › Retroviridae › Orthoretrovirinae › Alpharetrovirus
Virus hostGallus gallus (Chicken) [TaxID: 9031]

Protein attributes

Sequence length1603 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence 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.

Catalytic activity

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).

Endonucleolytic cleavage to 5'-phosphomonoester.

Cofactor

Binds 2 magnesium ions for reverse transcriptase polymerase activity By similarity.

Binds 2 magnesium ions for ribonuclease H (RNase H) activity. Substrate-binding is a precondition for magnesium binding By similarity.

Binds 8 magnesium ions per integrase homotetramer By similarity.

Subunit structure

The protease is active as a homodimer By similarity. The integrase forms a homotetramer. Reverse transcriptase is a heterodimer of alpha and beta subunits. Three forms of RT exist: alpha-alpha (alpha-Pol), beta-beta (beta-Pol), and alpha-beta, with the major form being the heterodimer. Both the polymerase and RNase H active sites are located in the alpha subunit of heterodimeric RT alpha-beta. Ref.6

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.

Integrase core domain contains the D-x(n)-D-x(35)-E motif, named for the phylogenetically conserved glutamic acid and aspartic acid residues and the invariant 35 amino acid spacing between the second and third acidic residues. Each acidic residue of the D,D(35)E motif is independently essential for the 3'-processing and strand transfer activities of purified integrase protein By similarity.

Post-translational modification

Specific enzymatic cleavages in vivo yield mature proteins.

Miscellaneous

The reverse transcriptase is an error-prone enzyme that lacks a proof-reading function. High mutations rate is a direct consequence of this characteristic. RT also displays frequent template switching leading to high recombination rate. Recombination mostly occurs between homologous regions of the two copackaged RNA genomes. If these two RNA molecules derive from different viral strains, reverse transcription will give rise to highly recombinated proviral DNAs.

Sequence similarities

Contains 2 CCHC-type zinc fingers.

Contains 1 integrase catalytic domain.

Contains 1 integrase-type DNA-binding domain.

Contains 1 integrase-type zinc finger.

Contains 1 peptidase A2 domain.

Contains 1 reverse transcriptase domain.

Contains 1 RNase H domain.

Sequence caution

The sequence AAB59933.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
   Biological processDNA integration
DNA recombination
Initiation of viral infection
Viral genome integration
   Cellular componentVirion
   Coding sequence diversityRibosomal frameshifting
   DomainRepeat
Zinc-finger
   LigandDNA-binding
Magnesium
Metal-binding
RNA-binding
Viral nucleoprotein
Zinc
   Molecular functionAspartyl protease
Capsid protein
DNA-directed DNA polymerase
Endonuclease
Hydrolase
Nuclease
Nucleotidyltransferase
Protease
RNA-directed DNA polymerase
Transferase
   Technical term3D-structure
Complete proteome
Multifunctional enzyme
Gene Ontology (GO)
   Biological processDNA integration

Inferred from electronic annotation. Source: UniProtKB-KW

DNA recombination

Inferred from electronic annotation. Source: UniProtKB-KW

RNA-dependent DNA replication

Inferred from electronic annotation. Source: InterPro

proteolysis

Inferred from electronic annotation. Source: UniProtKB-KW

viral reproduction

Inferred from electronic annotation. Source: InterPro

   Cellular componentviral capsid

Inferred from electronic annotation. Source: UniProtKB-KW

   Molecular functionDNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

DNA-directed DNA polymerase activity

Inferred from electronic annotation. Source: UniProtKB-KW

RNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

RNA-directed DNA polymerase activity

Inferred from electronic annotation. Source: UniProtKB-KW

aspartic-type endopeptidase activity

Inferred from electronic annotation. Source: UniProtKB-KW

ribonuclease H activity

Inferred from electronic annotation. Source: EC

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-Pol polyprotein (identifier: P03354-1)

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 -1 ribosomal frameshifting.
Isoform Gag-Pro polyprotein (identifier: P03322-1)

The sequence of this isoform can be found in the external entry P03322.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by conventional translation.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 155155Matrix protein p19
PRO_5000053588
Chain156 – 16611p2A
PRO_0000397068
Chain167 – 17711p2B
PRO_0000397069
Chain178 – 23962p10
PRO_5000053589
Chain240 – 479240Capsid protein p27
PRO_5000053590
Chain480 – 4889p3
PRO_0000397070
Chain489 – 57789Nucleocapsid protein p12
PRO_5000053591
Chain578 – 708131Protease p15
PRO_5000053592
Chain709 – 1567859Reverse transcriptase beta-subunit
PRO_0000397071
Chain709 – 1280572Reverse transcriptase alpha-subunit
PRO_0000040986
Chain1281 – 1567287Integrase
PRO_0000040987
Chain1568 – 160336p4
PRO_0000397072

Regions

Domain609 – 69082Peptidase A2
Domain750 – 938189Reverse transcriptase
Domain1149 – 1280132RNase H
Domain1333 – 1496164Integrase catalytic
Zinc finger507 – 52418CCHC-type 1
Zinc finger533 – 55018CCHC-type 2
Zinc finger1280 – 132142Integrase-type
DNA binding1502 – 155049Integrase-type
Motif172 – 1754PPXY motif By similarity
Compositional bias171 – 1744Poly-Pro

Sites

Active site6141For protease activity; shared with dimeric partner By similarity
Metal binding8151Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal binding8901Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal binding8911Magnesium; catalytic; for reverse transcriptase activity By similarity
Metal binding11581Magnesium; catalytic; for RNase H activity By similarity
Metal binding11921Magnesium; catalytic; for RNase H activity By similarity
Metal binding12131Magnesium; catalytic; for RNase H activity By similarity
Metal binding12721Magnesium; catalytic; for RNase H activity By similarity
Metal binding13441Magnesium; catalytic; for integrase activity By similarity
Metal binding14011Magnesium; catalytic; for integrase activity By similarity
Metal binding14371Magnesium; catalytic; for integrase activity By similarity
Site155 – 1562Cleavage; by viral protease p15
Site166 – 1672Cleavage; by viral protease p15
Site177 – 1782Cleavage; by viral protease p15
Site239 – 2402Cleavage; by viral protease p15
Site479 – 4802Cleavage; by viral protease p15
Site488 – 4892Cleavage; by viral protease p15
Site577 – 5782Cleavage; by viral protease p15
Site708 – 7092Cleavage; by viral protease p15
Site1280 – 12812Cleavage; by viral protease p15
Site1567 – 15682Cleavage; by viral protease p15

Natural variations

Natural variant7221P → S.
Natural variant7241H → R.
Natural variant8841C → R.
Natural variant9071E → K.
Natural variant9551A → T.
Natural variant10121R → Q.
Natural variant11821A → V.
Natural variant12431S → G.
Natural variant15751E → G.
Natural variant15771E → K.

Experimental info

Sequence conflict7561E → V in CAA48535. Ref.3
Sequence conflict12061T → A in CAA48535. Ref.3
Sequence conflict12741Q → K in CAA48535. Ref.3
Sequence conflict13811V → A in CAA48535. Ref.3

Secondary structure

1 ......................................... 1603
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform Gag-Pro-Pol polyprotein [UniParc].

Last modified August 10, 2010. Version 2.
Checksum: 01AF800FDF929CB6

FASTA1,603173,881
        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        710        720 
VINRDGSLER PLLLFPAVAM VRGSILGRDC LQGLGLRLTN LIGRATVLTV ALHLAIPLKW 

       730        740        750        760        770        780 
KPDHTPVWID QWPLPEGKLV ALTQLVEKEL QLGHIEPSLS CWNTPVFVIR KASGSYRLLH 

       790        800        810        820        830        840 
DLRAVNAKLV PFGAVQQGAP VLSALPRGWP LMVLDLKDCF FSIPLAEQDR EAFAFTLPSV 

       850        860        870        880        890        900 
NNQAPARRFQ WKVLPQGMTC SPTICQLVVG QVLEPLRLKH PSLCMLHYMD DLLLAASSHD 

       910        920        930        940        950        960 
GLEAAGEEVI STLERAGFTI SPDKVQREPG VQYLGYKLGS TYVAPVGLVA EPRIATLWDV 

       970        980        990       1000       1010       1020 
QKLVGSLQWL RPALGIPPRL MGPFYEQLRG SDPNEAREWN LDMKMAWREI VRLSTTAALE 

      1030       1040       1050       1060       1070       1080 
RWDPALPLEG AVARCEQGAI GVLGQGLSTH PRPCLWLFST QPTKAFTAWL EVLTLLITKL 

      1090       1100       1110       1120       1130       1140 
RASAVRTFGK EVDILLLPAC FREDLPLPEG ILLALKGFAG KIRSSDTPSI FDIARPLHVS 

      1150       1160       1170       1180       1190       1200 
LKVRVTDHPV PGPTVFTDAS SSTHKGVVVW REGPRWEIKE IADLGASVQQ LEARAVAMAL 

      1210       1220       1230       1240       1250       1260 
LLWPTTPTNV VTDSAFVAKM LLKMGQEGVP STAAAFILED ALSQRSAMAA VLHVRSHSEV 

      1270       1280       1290       1300       1310       1320 
PGFFTEGNDV ADSQATFQAY PLREAKDLHT ALHIGPRALS KACNISMQQA REVVQTCPHC 

      1330       1340       1350       1360       1370       1380 
NSAPALEAGV NPRGLGPLQI WQTDFTLEPR MAPRSWLAVT VDTASSAIVV TQHGRVTSVA 

      1390       1400       1410       1420       1430       1440 
VQHHWATAIA VLGRPKAIKT DNGSCFTSKS TREWLARWGI AHTTGIPGNS QGQAMVERAN 

      1450       1460       1470       1480       1490       1500 
RLLKDRIRVL AEGDGFMKRI PTSKQGELLA KAMYALNHFE RGENTKTPIQ KHWRPTVLTE 

      1510       1520       1530       1540       1550       1560 
GPPVKIRIET GEWEKGWNVL VWGRGYAAVK NRDTDKVIWV PSRKVKPDIT QKDEVTKKDE 

      1570       1580       1590       1600 
ASPLFAGISD WIPWEDEQEG LQGETASNKQ ERPGEDTLAA NES

« Hide

Isoform Gag-Pro polyprotein [UniParc].

See P03322.

––

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 DNA].
[2]"Rous sarcoma virus encodes a transcriptional activator."
Broome S., Gilbert W.
Cell 40:537-546(1985) [PubMed: 2982497] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA], POST-TRANSLATIONAL MODIFICATIONS.
[3]"Complete nucleotide sequence of Rous sarcoma virus variants adapted to duck cells."
Kashuba V.I., Kavsan V.M., Ryndich A.V., Lazurkevich Z.V., Zubak S.V., Popov S.V., Dostalova V., Glozhanek I.
Mol. Biol. (Mosk.) 27:436-450(1993) [PubMed: 8387633] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]Chappey C.
Submitted (NOV-1997) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[5]"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.
[6]"Asymmetric subunit organization of heterodimeric Rous sarcoma virus reverse transcriptase alphabeta: localization of the polymerase and RNase H active sites in the alpha subunit."
Werner S., Woehrl B.M.
J. Virol. 74:3245-3252(2000) [PubMed: 10708441] [Abstract]
Cited for: SUBUNIT.
[7]"Structural basis for specificity of retroviral proteases."
Wu J., Adomat J.M., Ridky T.W., Louis J.M., Leis J., Harrison R.W., Weber I.T.
Biochemistry 37:4518-4526(1998) [PubMed: 9521772] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 578-701 OF MUTANT SER-615; ILE-619; ILE-621; MET-650; ALA-677; VAL-681; ARG-682; GLY-683; SER-684 WITH INHIBITOR.
[8]"Crystal structure of an active two-domain derivative of Rous sarcoma virus integrase."
Yang Z.-N., Mueser T.C., Bushman F.D., Hyde C.C.
J. Mol. Biol. 296:535-548(2000) [PubMed: 10669607] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.53 ANGSTROMS) OF 1329-1566.
Strain: Clone pATV8.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		V01197 Genomic DNA. No translation available.
J02342 Genomic RNA. Translation: AAB59933.1. Different initiation.
X68524 Genomic DNA. Translation: CAA48535.1.
AF033808 Genomic RNA. Translation: AAC82561.1.
PIRGNFV1R. A03955.
RefSeqNP_056886.1. NC_001407.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1BAIX-ray2.4A/B578-701[»]
1C0MX-ray2.53A/B/C/D1329-1566[»]
1C1AX-ray3.10A/B1329-1566[»]
ProteinModelPortalP03354.
SMRP03354. Positions 2-87, 214-469, 503-552, 578-701, 1329-1550.
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

InterProIPR004028. Gag_M.
IPR000721. Gag_p24.
IPR001037. Integrase_C_retrovir.
IPR001584. Integrase_cat-core.
IPR017856. Integrase_Zn-bd_dom-like_N.
IPR003308. Integrase_Zn-bd_dom_N.
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.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR000477. RVT.
IPR013084. Znf_CCH_retrovir.
IPR001878. Znf_CCHC.
[Graphical view]
Gene3DG3DSA:2.30.30.10. Integrase_C. 1 hit.
G3DSA:1.10.10.200. Intgrase_N_Zn_bd. 1 hit.
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.
PfamPF00607. Gag_p24. 1 hit.
PF00552. IN_DBD_C. 1 hit.
PF02022. Integrase_Zn. 1 hit.
PF02813. Retro_M. 1 hit.
PF00075. RNase_H. 1 hit.
PF00665. rve. 1 hit.
PF00077. RVP. 1 hit.
PF00078. RVT_1. 1 hit.
PF00098. zf-CCHC. 2 hits.
[Graphical view]
ProDomPD002871. Gag_M. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SMARTSM00343. ZnF_C2HC. 2 hits.
[Graphical view]
SUPFAMSSF50122. Integrase_C. 1 hit.
SSF46919. Integrase_Zn_N. 1 hit.
SSF50630. Pept_Aspartic. 1 hit.
SSF47353. Retrov_capsid_C. 1 hit.
SSF47943. Retrov_capsid_N. 1 hit.
SSF47836. Retrovir_matrix. 1 hit.
SSF53098. RNaseH_fold. 2 hits.
PROSITEPS50175. ASP_PROT_RETROV. 1 hit.
PS00141. ASP_PROTEASE. 1 hit.
PS50994. INTEGRASE. 1 hit.
PS51027. INTEGRASE_DBD. 1 hit.
PS50879. RNASE_H. 1 hit.
PS50878. RT_POL. 1 hit.
PS50158. ZF_CCHC. 1 hit.
PS50876. ZF_INTEGRASE. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry namePOL_RSVP
AccessionPrimary (citable) accession number: P03354
Secondary accession number(s): O92805, Q07462, Q64983
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: August 10, 2010
Last modified: December 14, 2011
This is version 94 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

Peptidase families

Classification of peptidase families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

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