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Protein

Gag-Pol polyprotein

Gene

gag-pol

Organism
Avian leukosis virus RSA (RSV-SRA) (Rous sarcoma virus (strain Schmidt-Ruppin A))
Status
Reviewed-Annotation score: -Protein inferred from homologyi

Functioni

Capsid protein p27: Self-associates to form the irregular polyhedron core composed of hexamers and pentamers, that encapsulates the genomic RNA-nucleocapsid complex. Assembles as a tube in vitro.By similarity
Spacer peptide: Plays a role in the oligomerization of the Gag polyprotein and in the stabilization of the immature particle. Essential layering element during tube assembly.By similarity
Nucleocapsid protein p12: Binds strongly to viral nucleic acids and promote their aggregation. Also destabilizes the nucleic acids duplexes via highly structured zinc-binding motifs.Curated
Protease p15: The aspartyl protease that 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.PROSITE-ProRule annotation
Integrase: Catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions (PubMed:2555556). This recombination event is an essential step in the viral replication cycle. Has a strong preference for using the 3'-OH at the viral DNA end as a nucleophile.By similarity1 Publication

Miscellaneous

Reverse transcriptase: 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.PROSITE-ProRule annotation

Catalytic activityi

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).PROSITE-ProRule annotation
Endonucleolytic cleavage to 5'-phosphomonoester.PROSITE-ProRule annotation

Cofactori

Protein has several cofactor binding sites:
  • Mg2+By similarityNote: The RT polymerase active site binds 2 magnesium ions.PROSITE-ProRule annotation
  • Mg2+By similarityNote: Binds 2 magnesium ions for ribonuclease H (RNase H) activity. Substrate-binding is a precondition for magnesium binding.By similarity
  • Mg2+By similarityNote: Binds 8 Mg2+ ions per integrase homotetramer.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei418Involved in capsid protein dimerization upon acidificationBy similarity1
Sitei430Involved in capsid protein dimerization upon acidificationBy similarity1
Active sitei614For protease activity; shared with dimeric partnerPROSITE-ProRule annotation1
Metal bindingi815Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi890Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi891Magnesium; catalytic; for reverse transcriptase activityPROSITE-ProRule annotation1
Metal bindingi1158Magnesium; catalytic; for RNase H activityCurated1
Metal bindingi1192Magnesium; catalytic; for RNase H activityCurated1
Metal bindingi1213Magnesium; catalytic; for RNase H activityCurated1
Metal bindingi1272Magnesium; catalytic; for RNase H activityCurated1
Metal bindingi1344Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation1
Metal bindingi1401Magnesium; catalytic; for integrase activityPROSITE-ProRule annotation1
Metal bindingi1437Magnesium; catalytic; for integrase activityBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri507 – 524CCHC-type 1PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri533 – 550CCHC-type 2PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri1280 – 1321Integrase-typePROSITE-ProRule annotationAdd BLAST42
DNA bindingi1502 – 1550Integrase-typePROSITE-ProRule annotationAdd BLAST49

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionAspartyl protease, DNA-binding, DNA-directed DNA polymerase, Endonuclease, Hydrolase, Multifunctional enzyme, Nuclease, Nucleotidyltransferase, Protease, RNA-binding, RNA-directed DNA polymerase, Transferase
Biological processDNA integration, DNA recombination, Viral genome integration, Virus entry into host cell
LigandMagnesium, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Gag-Pol polyprotein
Cleaved into the following 13 chains:
Protease p15 (EC:3.4.23.-PROSITE-ProRule annotation)
Reverse transcriptase alpha-subunit (EC:2.7.7.49PROSITE-ProRule annotation, EC:2.7.7.7PROSITE-ProRule annotation, EC:3.1.26.4PROSITE-ProRule annotation)
Short name:
RT-alpha
Integrase (EC:2.7.7.-1 Publication, EC:3.1.-.-1 Publication)
Short name:
IN
Alternative name(s):
pp32
Gene namesi
Name:gag-pol
OrganismiAvian leukosis virus RSA (RSV-SRA) (Rous sarcoma virus (strain Schmidt-Ruppin A))
Taxonomic identifieri269446 [NCBI]
Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeAlpharetrovirus
Virus hostiGallus gallus (Chicken) [TaxID: 9031]
Proteomesi
  • UP000002238 Componenti: Genome

Subcellular locationi

Matrix protein p19 :
  • Virion By similarity
Capsid protein p27, alternate cleaved 1 :
  • Virion By similarity
Capsid protein p27, alternate cleaved 2 :
  • Virion By similarity
Nucleocapsid protein p12 :
  • Virion By similarity

GO - Cellular componenti

Keywords - Cellular componenti

Virion

Pathology & Biotechi

Chemistry databases

DrugBankiDB04272 Citric Acid
DB02413 Hydroxyethylcysteine
DB02325 Isopropyl Alcohol

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004424781 – 1603Gag-Pol polyproteinAdd BLAST1603
ChainiPRO_00003970481 – 155Matrix protein p19Add BLAST155
ChainiPRO_0000397049156 – 166p2AAdd BLAST11
ChainiPRO_0000397050167 – 177p2BAdd BLAST11
ChainiPRO_0000397051178 – 239p10Add BLAST62
ChainiPRO_0000397052240 – 479Capsid protein p27, alternate cleaved 2Add BLAST240
ChainiPRO_0000442479240 – 476Capsid protein p27, alternate cleaved 1Add BLAST237
ChainiPRO_0000397053480 – 488p39
ChainiPRO_0000397054489 – 577Nucleocapsid protein p12Add BLAST89
ChainiPRO_0000397055578 – 708Protease p15Add BLAST131
ChainiPRO_0000397056709 – 1567Reverse transcriptase beta-subunitAdd BLAST859
ChainiPRO_0000040982709 – 1280Reverse transcriptase alpha-subunitAdd BLAST572
ChainiPRO_00000409831281 – 1567IntegraseAdd BLAST287
ChainiPRO_00003970571568 – 1603p4Add BLAST36

Post-translational modificationi

Gag-pol polyprotein: Specific enzymatic cleavages in vivo yield mature proteins.By similarity
Capsid protein p27: The cleavage at the C-terminus is slowly trimmed by the viral protease, sometimes being cut internally thereby generating the short version of the capsid protein and a capsid protein C-terminally extended by 3 amino acids in a ratio of 2:1.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei155 – 156Cleavage; by viral protease p15By similarity2
Sitei166 – 167Cleavage; by viral protease p15By similarity2
Sitei177 – 178Cleavage; by viral protease p15By similarity2
Sitei239 – 240Cleavage; by viral protease p15By similarity2
Sitei476 – 477Cleavage; by viral protease p15By similarity2
Sitei479 – 480Cleavage; by viral protease p15By similarity2
Sitei488 – 489Cleavage; by viral protease p15By similarity2
Sitei577 – 578Cleavage; by viral protease p15By similarity2
Sitei708 – 709Cleavage; by viral protease p15By similarity2
Sitei1280 – 1281Cleavage; by viral protease p15By similarity2
Sitei1567 – 1568Cleavage; by viral protease p15By similarity2

Proteomic databases

PRIDEiQ04095

Interactioni

Subunit structurei

Protease p15: Active as a homodimer. Integrase: Homodimer; further associates as a homooctamer (PubMed:28458055). Reverse transcriptase: Heterodimer of alpha and beta subunits. Reverse transcriptase: 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.1 PublicationBy similarity

Structurei

3D structure databases

SMRiQ04095
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini609 – 690Peptidase A2PROSITE-ProRule annotationAdd BLAST82
Domaini750 – 938Reverse transcriptasePROSITE-ProRule annotationAdd BLAST189
Domaini1163 – 1280RNase HPROSITE-ProRule annotationAdd BLAST118
Domaini1333 – 1496Integrase catalyticPROSITE-ProRule annotationAdd BLAST164

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1548 – 1567Involved in homooctamerizationBy similarityAdd BLAST20

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi172 – 175PPXY motif4
Motifi180 – 184LYPX(n)L motifBy similarity5
Motifi219 – 229Nuclear export signalBy similarityAdd BLAST11

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi171 – 174Poly-Pro4

Domaini

Gag-Pol polyprotein: 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 two L domain: a PPXY motif which probably binds to the WW domains of HECT (homologous to E6-AP C-terminus) E3 ubiquitin ligases and a LYPX(n)L domain which is known to bind the Alix adaptator protein.By similarity
Integrase: The 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).By similarity
Gag-Pol polyprotein: contains a nuclear export signal in p10 and a nucleolar localization signal in nucleocapsid protein p12.By similarity
Capsid protein p27: Proton-driven dimerization of the C-terminus facilitates capsid assembly.By similarity

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri507 – 524CCHC-type 1PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri533 – 550CCHC-type 2PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri1280 – 1321Integrase-typePROSITE-ProRule annotationAdd BLAST42

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

OrthoDBiVOG09000135

Family and domain databases

CDDicd05482 HIV_retropepsin_like, 1 hit
Gene3Di1.10.10.200, 1 hit
1.10.1200.30, 1 hit
1.10.150.90, 1 hit
1.10.375.10, 1 hit
2.30.30.10, 1 hit
2.40.70.10, 1 hit
3.30.420.10, 2 hits
InterProiView protein in InterPro
IPR001969 Aspartic_peptidase_AS
IPR004028 Gag_M
IPR000721 Gag_p24
IPR017856 Integrase-like_N
IPR036862 Integrase_C_dom_sf_retrovir
IPR001037 Integrase_C_retrovir
IPR001584 Integrase_cat-core
IPR003308 Integrase_Zn-bd_dom_N
IPR012344 Matrix_HIV/RSV_N
IPR001995 Peptidase_A2_cat
IPR021109 Peptidase_aspartic_dom_sf
IPR034170 Retropepsin-like_cat_dom
IPR018061 Retropepsins
IPR008916 Retrov_capsid_C
IPR008919 Retrov_capsid_N
IPR010999 Retrovr_matrix
IPR012337 RNaseH-like_sf
IPR002156 RNaseH_domain
IPR036397 RNaseH_sf
IPR000477 RT_dom
IPR010661 RVT_thumb
IPR001878 Znf_CCHC
IPR036875 Znf_CCHC_sf
PfamiView protein in Pfam
PF00607 Gag_p24, 1 hit
PF00552 IN_DBD_C, 1 hit
PF02022 Integrase_Zn, 1 hit
PF02813 Retro_M, 1 hit
PF00665 rve, 1 hit
PF00077 RVP, 1 hit
PF00078 RVT_1, 1 hit
PF06817 RVT_thumb, 1 hit
PF00098 zf-CCHC, 1 hit
ProDomiView protein in ProDom or Entries sharing at least one domain
PD002871 Gag_M, 1 hit
SMARTiView protein in SMART
SM00343 ZnF_C2HC, 2 hits
SUPFAMiSSF46919 SSF46919, 1 hit
SSF47836 SSF47836, 1 hit
SSF47943 SSF47943, 1 hit
SSF50122 SSF50122, 1 hit
SSF50630 SSF50630, 1 hit
SSF53098 SSF53098, 2 hits
SSF57756 SSF57756, 1 hit
PROSITEiView protein in PROSITE
PS50175 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

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by ribosomal frameshifting. AlignAdd to basket

Note: Translation results in the formation of the Gag polyprotein. Ribosomal frameshifting at the gag/pol genes boundary produces the Gag-Pol polyprotein.1 Publication
Isoform Gag-Pol polyprotein (identifier: Q04095-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MEAVIKVISS ACKTYCGKIS PSKKEIGAML SLLQKEGLLM SPSDLYSPGS
60 70 80 90 100
WDPITAALSQ RAMVLGKSGE LKTWGLVLGA LKAAREEQVT SEQAKFWLGL
110 120 130 140 150
GGGRVSPPGP ECIEKPATER RIDKGEEVGE TTAQRDAKMA PEKMATPKTV
160 170 180 190 200
GTSCYQCGTA TGCNCATASA PPPPYVGSGL YPSLAGVGEQ QGQGGDTPWG
210 220 230 240 250
AEQPRAEPGH AGLAPGPALT DWARIREELA STGPPVVAMP VVIKTEGPAW
260 270 280 290 300
TPLEPKLITR LADTVRTKGL RSPITMAEVE ALMSSPLLPH DVTNLMRVIL
310 320 330 340 350
GPAPYALWMD AWGVQLQTVI AAATRDPRHP ANGQGRGERT NLDRLKGLAD
360 370 380 390 400
GMVGNPQGQA ALLRPGELVA ITASALQAFR EVARLAEPAG PWADITQGPS
410 420 430 440 450
ESFVDFANRL IKAVEGSDLP PSARAPVIID CFRQKSQPDI QQLIRAAPST
460 470 480 490 500
LTTPGEIIKY VLDRQKIAPL TDQGIAAAMS SAIQPLVMAV VNRERDGQTG
510 520 530 540 550
SGGRARGLCY TCGSPGHYQA QCPKKRKSGN SRERCQLCDG MGHNAKQCRR
560 570 580 590 600
RDGNQGQRPG KGLSSGSWPV SEQPAVSLAM TMEHKDRPLV RVILTNTGSH
610 620 630 640 650
PVKQRSVYIT ALLDSGADIT IISEEDWPTD WPVMEAANPQ IHGIGGGIPM
660 670 680 690 700
RKSRDMIEVG VINRDGSLER PLLLFPAVAM VRGSILGRDC LQGLGLRLTN
710 720 730 740 750
LIGRATVLTV ALHLAIPLKW KPDHTPVWID QWPLPEGKLV ALTQLVEKEL
760 770 780 790 800
QLGHIEPSLS CWNTPVFVIR KASGSYRLLH DLRAVNAKLV PFGAVQQGAP
810 820 830 840 850
VLSALPRGWP LMVLDLKDCF FSIPLAEQDR EAFAFTLPSV NNQAPARRFQ
860 870 880 890 900
WKVLPQGMTC SPTICQLVVG QVLEPLRLKH PSLRMLHYMD DLLLAASSHD
910 920 930 940 950
GLEAAGEEVI STLERAGFTI SPDKIQREPG VQYLGYKLGS TYVAPVGLVA
960 970 980 990 1000
EPRIATLWDV QKLVGSLQWL RPALGIPPRL MGPFYEQLRG SDPNEAREWN
1010 1020 1030 1040 1050
LDMKMAWREI VQLSTTAALE RWDPALPLEG AVARCEQGAI GVLGQGLSTH
1060 1070 1080 1090 1100
PRPCLWLFST QPTKAFTAWL EVLTLLITKL RASAVRTFGK EVDILLLPAC
1110 1120 1130 1140 1150
FREDLPLPEG ILLALRGFAG KIRSSDTPSI FDIARPLHVS LKVRVTDHPV
1160 1170 1180 1190 1200
PGPTAFTDAS SSTHKGVVVW REGPRWEIKE IADLGASVQQ LEARAVAMAL
1210 1220 1230 1240 1250
LLWPTTPTNV VTDSAFVAKM LLKMGQEGVP STAAAFILED ALSQRSAMAA
1260 1270 1280 1290 1300
VLHVRSHSEV PGFFTEGNDV ADSQATFQAY PLREAKDLHT ALHIGPRALS
1310 1320 1330 1340 1350
KACNISMQQA REVVQTCPHC NSAPALEAGV NPRGLGPLQI WQTDFTLEPR
1360 1370 1380 1390 1400
MAPRSWLAVT VDTASSAIVV TQHGRVTSVA AQHHWATAIA VLGRPKAIKT
1410 1420 1430 1440 1450
DNGSCFTSKS TREWLARWGI AHTTGIPGNS QGQAMVERAN RLLKDKIRVL
1460 1470 1480 1490 1500
AEGDGFMKRI PTSKQGELLA KAMYALNHFE RGENTKTPIQ KHWRPTVLTE
1510 1520 1530 1540 1550
GPPVKIRIET GEWEKGWNVL VWGRGYAAVK NRDTDKVIWV PSRKVKPDVT
1560 1570 1580 1590 1600
QKDEVTKKDE ASPLFAGISD WIPWEDEQEG LQGETASNKQ ERPGEDTLAA

NES
Note: Produced by -1 ribosomal frameshifting.1 Publication
Length:1,603
Mass (Da):173,933
Last modified:August 10, 2010 - v2
Checksum:i1F7CE50FE96A5283
GO
Isoform Gag polyprotein (identifier: P0C776-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry P0C776.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by conventional translation.1 Publication
Length:701
Mass (Da):74,610
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M37980 Genomic RNA Translation: AAA91269.1
PIRiS35429
RefSeqiNP_040550.1, NC_001408.1

Genome annotation databases

GeneIDi1491910
KEGGivg:1491910

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Similar proteinsi

Entry informationi

Entry nameiPOL_RSVSA
AccessioniPrimary (citable) accession number: Q04095
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 27, 2004
Last sequence update: August 10, 2010
Last modified: May 23, 2018
This is version 110 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

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