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Protein

Gag-Pro-Pol polyprotein

Gene

gag-pro-pol

Organism
Avian leukosis virus RSA (RSV-SRA) (Rous sarcoma virus (strain Schmidt-Ruppin A))
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Protein inferred from homologyi

Functioni

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.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: Binds 2 magnesium ions for reverse transcriptase polymerase activity.By similarity
  • 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
Active sitei614For protease activity; shared with dimeric partnerPROSITE-ProRule annotation1
Metal bindingi815Magnesium; catalytic; for reverse transcriptase activityBy similarity1
Metal bindingi890Magnesium; catalytic; for reverse transcriptase activityBy similarity1
Metal bindingi891Magnesium; catalytic; for reverse transcriptase activityBy similarity1
Metal bindingi1158Magnesium; catalytic; for RNase H activityBy similarity1
Metal bindingi1192Magnesium; catalytic; for RNase H activityBy similarity1
Metal bindingi1213Magnesium; catalytic; for RNase H activityBy similarity1
Metal bindingi1272Magnesium; catalytic; for RNase H activityBy similarity1
Metal bindingi1344Magnesium; catalytic; for integrase activityBy similarity1
Metal bindingi1401Magnesium; catalytic; for integrase activityBy similarity1
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

Complete GO annotation...

Keywords - Molecular functioni

Aspartyl protease, DNA-directed DNA polymerase, Endonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Protease, RNA-directed DNA polymerase, Transferase

Keywords - Biological processi

DNA integration, DNA recombination, Viral genome integration, Virus entry into host cell

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, RNA-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Gag-Pro-Pol polyprotein
Cleaved into the following 12 chains:
Integrase (EC:2.7.7.-1 Publication, EC:3.1.-.-1 Publication)
Short name:
IN
Alternative name(s):
pp32
Gene namesi
Name:gag-pro-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

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Virion

Pathology & Biotechi

Chemistry databases

DrugBankiDB02325. Isopropyl Alcohol.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003970481 – 155Matrix protein p19By similarityAdd BLAST155
ChainiPRO_0000397049156 – 166p2ABy similarityAdd BLAST11
ChainiPRO_0000397050167 – 177p2BBy similarityAdd BLAST11
ChainiPRO_0000397051178 – 239p10By similarityAdd BLAST62
ChainiPRO_0000397052240 – 479Capsid protein p27By similarityAdd BLAST240
ChainiPRO_0000397053480 – 488p3By similarity9
ChainiPRO_0000397054489 – 577Nucleocapsid protein p12By similarityAdd BLAST89
ChainiPRO_0000397055578 – 708Protease p15By similarityAdd BLAST131
ChainiPRO_0000397056709 – 1567Reverse transcriptase beta-subunitBy similarityAdd BLAST859
ChainiPRO_0000040982709 – 1280Reverse transcriptase alpha-subunitBy similarityAdd BLAST572
ChainiPRO_00000409831281 – 1567IntegraseBy similarityAdd BLAST287
ChainiPRO_00003970571568 – 1603p4By similarityAdd BLAST36

Post-translational modificationi

Specific enzymatic cleavages in vivo yield mature proteins.

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
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

Interactioni

Subunit structurei

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 (By similarity).By similarity

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

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi172 – 175PPXY motif4

Compositional bias

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

Domaini

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).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).By similarity

Sequence similaritiesi

Contains 2 CCHC-type zinc fingers.PROSITE-ProRule annotation
Contains 1 integrase catalytic domain.PROSITE-ProRule annotation
Contains 1 integrase-type DNA-binding domain.PROSITE-ProRule annotation
Contains 1 integrase-type zinc finger.PROSITE-ProRule annotation
Contains 1 peptidase A2 domain.PROSITE-ProRule annotation
Contains 1 reverse transcriptase domain.PROSITE-ProRule annotation
Contains 1 RNase H domain.PROSITE-ProRule annotation

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

Family and domain databases

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.
4.10.60.10. 1 hit.
InterProiIPR001969. Aspartic_peptidase_AS.
IPR004028. 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_HIV/RSV.
IPR001995. Peptidase_A2_cat.
IPR021109. Peptidase_aspartic_dom.
IPR018061. Retropepsins.
IPR008916. Retrov_capsid_C.
IPR008919. Retrov_capsid_N.
IPR010999. Retrovr_matrix.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR000477. RT_dom.
IPR010661. RVT_thumb.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF00607. 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.
[Graphical view]
ProDomiPD002871. Gag_M. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SMARTiSM00343. ZnF_C2HC. 2 hits.
[Graphical view]
SUPFAMiSSF46919. SSF46919. 1 hit.
SSF47353. SSF47353. 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.
PROSITEiPS50175. 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]

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-Pro. Ribosomal frameshifting at the gag-pro/pol genes boundary produces the Gag-Pro-Pol polyprotein.1 Publication
Isoform Gag-Pro-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.
Length:1,603
Mass (Da):173,933
Last modified:August 10, 2010 - v2
Checksum:i1F7CE50FE96A5283
GO
Isoform Gag-Pro 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.
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.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

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

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Chemistry databases

DrugBankiDB02325. Isopropyl Alcohol.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1491910.

Family and domain databases

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.
4.10.60.10. 1 hit.
InterProiIPR001969. Aspartic_peptidase_AS.
IPR004028. 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_HIV/RSV.
IPR001995. Peptidase_A2_cat.
IPR021109. Peptidase_aspartic_dom.
IPR018061. Retropepsins.
IPR008916. Retrov_capsid_C.
IPR008919. Retrov_capsid_N.
IPR010999. Retrovr_matrix.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR000477. RT_dom.
IPR010661. RVT_thumb.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF00607. 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.
[Graphical view]
ProDomiPD002871. Gag_M. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SMARTiSM00343. ZnF_C2HC. 2 hits.
[Graphical view]
SUPFAMiSSF46919. SSF46919. 1 hit.
SSF47353. SSF47353. 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.
PROSITEiPS50175. 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]
ProtoNetiSearch...

Entry informationi

Entry nameiPOL_RSVSA
AccessioniPrimary (citable) accession number: Q04095
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 27, 2004
Last sequence update: August 10, 2010
Last modified: November 30, 2016
This is version 101 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

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.

Keywords - Technical termi

Complete proteome, Multifunctional enzyme, Reference proteome

Documents

  1. Peptidase families
    Classification of peptidase families and list of entries
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.