O92815 · POL_WDSV
- ProteinGag-Pol polyprotein
- Genegag-pol
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids1752 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
function
Matrix protein p10
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 pre-integration complex (By similarity).
Capsid protein p25 forms the spherical core of the virion that encapsulates the genomic RNA-nucleocapsid complex.
Nucleocapsid protein p14
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 (By similarity).
Protease p15
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).
Reverse transcriptase/ribonuclease H p90
Is a multifunctional enzyme that converts the viral dimeric RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell. This enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3' to 5' endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires many steps. A tRNA binds to the primer-binding site (PBS) situated at the 5' end of the viral RNA. RT uses the 3' end of the tRNA primer to perform a short round of RNA-dependent minus-strand DNA synthesis. The reading proceeds through the U5 region and ends after the repeated (R) region which is present at both ends of viral RNA. The portion of the RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA hybridizes with the identical R region situated at the 3' end of viral RNA. This template exchange, known as minus-strand DNA strong stop transfer, can be either intra- or intermolecular. RT uses the 3' end of this newly synthesized short ssDNA to perform the RNA-dependent minus-strand DNA synthesis of the whole template. RNase H digests the RNA template except for a polypurine tract (PPT) situated at the 5' end of the genome. It is not clear if both polymerase and RNase H activities are simultaneous. RNase H probably can proceed both in a polymerase-dependent (RNA cut into small fragments by the same RT performing DNA synthesis) and a polymerase-independent mode (cleavage of remaining RNA fragments by free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis using the PPT that has not been removed by RNase H as primers. PPT and tRNA primers are then removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. Strand displacement synthesis by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA copy of the viral genome that includes long terminal repeats (LTRs) at both ends (By similarity).
Integrase p46
Catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising the viral genome, matrix protein and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from each 3' end of the viral DNA, leaving recessed CA OH's at the 3' ends. In the second step that requires cell division, the PIC enters cell nucleus. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. The last step is viral DNA integration into host chromosome.
Gag-Pol polyprotein
Plays a role in budding and is processed by the viral protease during virion maturation outside the cell.
Miscellaneous
This protein is translated as a gag-pol fusion protein by episodic readthrough of the gag protein termination codon. Readthrough of the terminator codon TAG occurs between the codons for 582-Ala and 584-Asp (By similarity).
The nucleocapsid protein p14 released from Pol polyprotein (NC-pol) is a few amino acids longer than the nucleocapsid protein p14 released from Gag polyprotein (NC-gag).
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 swiching 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.
Catalytic activity
- a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1)
- a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1)
Cofactor
Protein has several cofactor binding sites:
Note: Binds 2 magnesium ions for reverse transcriptase polymerase activity.
Note: Binds 2 magnesium ions for ribonuclease H (RNase H) activity.
Note: Magnesium ions are required for integrase activity. Binds at least 1, maybe 2 magnesium ions.
pH Dependence
Optimum pH is 7.0 for protease p14.
Features
Showing features for site, active site, binding site.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Site | 95-96 | Cleavage; by viral protease | ||||
Sequence: MT | ||||||
Site | 251-252 | Cleavage; by viral protease | ||||
Sequence: HP | ||||||
Site | 457-458 | Cleavage; by viral protease | ||||
Sequence: LA | ||||||
Site | 584-585 | Cleavage; by viral protease | ||||
Sequence: DP | ||||||
Active site | 623 | Protease; shared with dimeric partner | ||||
Sequence: D | ||||||
Site | 722-723 | Cleavage; by viral protease | ||||
Sequence: LS | ||||||
Binding site | 861 | Mg2+ 1 (UniProtKB | ChEBI); catalytic; for reverse transcriptase activity | ||||
Sequence: D | ||||||
Binding site | 928 | Mg2+ 1 (UniProtKB | ChEBI); catalytic; for reverse transcriptase activity | ||||
Sequence: D | ||||||
Binding site | 929 | Mg2+ 1 (UniProtKB | ChEBI); catalytic; for reverse transcriptase activity | ||||
Sequence: D | ||||||
Binding site | 1231 | Mg2+ (UniProtKB | ChEBI); for RNase H activity | ||||
Sequence: D | ||||||
Binding site | 1269 | Mg2+ (UniProtKB | ChEBI); for RNase H activity | ||||
Sequence: E | ||||||
Binding site | 1290 | Mg2+ (UniProtKB | ChEBI); for RNase H activity | ||||
Sequence: D | ||||||
Binding site | 1360 | Mg2+ (UniProtKB | ChEBI); for RNase H activity | ||||
Sequence: D | ||||||
Site | 1372-1373 | Cleavage; by viral protease | ||||
Sequence: RV | ||||||
Binding site | 1493 | Mg2+ 3 (UniProtKB | ChEBI); catalytic; for integrase activity | ||||
Sequence: D | ||||||
Binding site | 1550 | Mg2+ 3 (UniProtKB | ChEBI); catalytic; for integrase activity | ||||
Sequence: D |
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | host cell plasma membrane | |
Cellular Component | membrane | |
Cellular Component | viral nucleocapsid | |
Molecular Function | aspartic-type endopeptidase activity | |
Molecular Function | DNA binding | |
Molecular Function | DNA-directed DNA polymerase activity | |
Molecular Function | RNA binding | |
Molecular Function | RNA-directed DNA polymerase activity | |
Molecular Function | RNA-DNA hybrid ribonuclease activity | |
Molecular Function | structural constituent of virion | |
Molecular Function | zinc ion binding | |
Biological Process | DNA integration | |
Biological Process | DNA recombination | |
Biological Process | proteolysis |
Keywords
- Molecular function
- Biological process
- Ligand
Protein family/group databases
Names & Taxonomy
Protein names
- Recommended nameGag-Pol polyprotein
- Cleaved into 7 chains
Gene names
Organism names
- Taxonomic lineageViruses > Riboviria > Pararnavirae > Artverviricota > Revtraviricetes > Ortervirales > Retroviridae > Orthoretrovirinae > Epsilonretrovirus
- Virus hosts
Accessions
- Primary accessionO92815
Proteomes
Subcellular Location
UniProt Annotation
GO Annotation
Gag-Pol polyprotein
Host cell membrane ; Lipid-anchor
Matrix protein p10
Capsid protein p25
Nucleocapsid protein p14
Keywords
- Cellular component
PTM/Processing
Features
Showing features for initiator methionine, lipidation, chain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Initiator methionine | 1 | Removed | ||||
Sequence: M | ||||||
Lipidation | 2 | N-myristoyl glycine; by host | ||||
Sequence: G | ||||||
Chain | PRO_0000410593 | 2-95 | Matrix protein p10 | |||
Sequence: GNSSSTPPPSALKNSDLFKTMLRTQYSGSVKTRRINQDIKKQYPLWPDQGTCATKHWEQAVLIPLDSVSEETAKVLNFLRVKIQARKGETARQM | ||||||
Chain | PRO_0000410592 | 2-1752 | Gag-Pol polyprotein | |||
Sequence: GNSSSTPPPSALKNSDLFKTMLRTQYSGSVKTRRINQDIKKQYPLWPDQGTCATKHWEQAVLIPLDSVSEETAKVLNFLRVKIQARKGETARQMTAHTIKKLIVGTIDKNKQQTEILQKTDESDEEMDTTNTMLFIARNKRERIAQQQQADLAAQQQVLLLQREQQREQREKDIKKRDEKKKKLLPDTTQKVEQTDIGEASSSDASAQKPISTDNNPDLKVDGVLTRSQHTTVPSNITIKKDGTSVQYQHPIRNYPTGEGNLTAQVRNPFRPLELQQLRKDCPALPEGIPQLAEWLTQTMAIYNCDEADVEQLARVIFPTPVRQIAGVINGHAAANTAAKIQNYVTACRQHYPAVCDWGTIQAFTYKPPQTAHEYVKHAEIIFKNNSGLEWQHATVPFINMVVQGLPPKVTRSLMSGNPDWSTKTIPQIIPLMQHYLNLQSRQDAKIKQTPLVLQLAMPAQTMNGNKGYVGSYPTNEPYYSFQQQQRPAPRAPPGNVPSNTCFFCKQPGHWKADCPNKTRNLRNMGNMGRGGRMGGPPYRSQPYPAFIQPPQNHQNQYNGRMDRSQLQASAQEWLPGTYPAXDPIDCPYEKSGTKTTQDVITTKNAEIMVTVNHTKIPMLVDTGACLTAIGGAATVVPDLKLTNTEIIAVGISAEPVPHVLAKPTKIQIENTNIDISPWYNPDQTFHILGRDTLSKMRAIVSFEKNGEMTVLLPPTYHKQLSCQTKNTLNIDEYLLQFPDQLWASLPTDIGRMLVPPITIKIKDNASLPSIRQYPLPKDKTEGLRPLISSLENQGILIKCHSPCNTPIFPIKKAGRDEYRMIHDLRAINNIVAPLTAVVASPTTVLSNLAPSLHWFTVIDLSNAFFSVPIHKDSQYLFAFTFEGHQYTWTVLPQGFIHSPTLFSQALYQSLHKIKFKISSEICIYMDDVLIASKDRDTNLKDTAVMLQHLASEGHKVSKKKLQLCQQEVVYLGQLLTPEGRKILPDRKVTVSQFQQPTTIRQIRAFLGLVGYCRHWIPEFSIHSKFLEKQLKKDTAEPFQLDDQQVEAFNKLKHAITTAPVLVVPDPAKPFQLYTSHSEHASIAVLTQKHAGRTRPIAFLSSKFDAIESGLPPCLKACASIHRSLTQADSFILGAPLIIYTTHAICTLLQRDRSQLVTASRFSKWEADLLRPELTFVACSAVSPAHLYMQSCENNIPPHDCVLLTHTISRPRPDLSDLPIPDPDMTLFSDGSYTTGRGGAAVVMHRPVTDDFIIIHQQPGGASAQTAELLALAAACHLATDKTVNIYTDSRYAYGVVHDFGHLWMHRGFVTSAGTPIKNHKEIEYLLKQIMKPKQVSVIKIEAHTKGVSMEVRGNAAADEAAKNAVFLVQRVLKKGDALASTDLVMEYSETDEKFTAGAELHDGVFMRGDLIVPPLEMLHAILLAIHGVSHTHKGGIMSYFSKFWTHPKASQTIDLILGHCQICLKHNPKYKSRLQGHRPLPSRPFAHLQIDFVQMCVKKPMYALVIIDVFSKWPEIIPCNKEDAKTVCDILMKDIIPRWGLPDQIDSDQGTHFTAKISQELTHSIGVAWKLHCPGHPRSSGIVERTNRTLKSKIIKAQEQLQLSKWTEVLPYVLLEMRATPKKHGLSPHEIVMGRPMKTTYLSDMSPLWATDTLVTYMNKLTRQLSAYHQQVVDQWPSTSLPPGPEPGSWCMLRNPKKSSNWEGPFLILLSTPTAVKVEGRPTWIHLDHCKLLRSSLSSSLGGPVNQLLS | ||||||
Chain | PRO_0000410594 | 96-251 | p20 | |||
Sequence: TAHTIKKLIVGTIDKNKQQTEILQKTDESDEEMDTTNTMLFIARNKRERIAQQQQADLAAQQQVLLLQREQQREQREKDIKKRDEKKKKLLPDTTQKVEQTDIGEASSSDASAQKPISTDNNPDLKVDGVLTRSQHTTVPSNITIKKDGTSVQYQH | ||||||
Chain | PRO_0000410595 | 252-457 | Capsid protein p25 | |||
Sequence: PIRNYPTGEGNLTAQVRNPFRPLELQQLRKDCPALPEGIPQLAEWLTQTMAIYNCDEADVEQLARVIFPTPVRQIAGVINGHAAANTAAKIQNYVTACRQHYPAVCDWGTIQAFTYKPPQTAHEYVKHAEIIFKNNSGLEWQHATVPFINMVVQGLPPKVTRSLMSGNPDWSTKTIPQIIPLMQHYLNLQSRQDAKIKQTPLVLQL | ||||||
Chain | PRO_0000410596 | 458-584 | Nucleocapsid protein p14 | |||
Sequence: AMPAQTMNGNKGYVGSYPTNEPYYSFQQQQRPAPRAPPGNVPSNTCFFCKQPGHWKADCPNKTRNLRNMGNMGRGGRMGGPPYRSQPYPAFIQPPQNHQNQYNGRMDRSQLQASAQEWLPGTYPAXD | ||||||
Chain | PRO_0000410597 | 585-722 | Protease p15 | |||
Sequence: PIDCPYEKSGTKTTQDVITTKNAEIMVTVNHTKIPMLVDTGACLTAIGGAATVVPDLKLTNTEIIAVGISAEPVPHVLAKPTKIQIENTNIDISPWYNPDQTFHILGRDTLSKMRAIVSFEKNGEMTVLLPPTYHKQL | ||||||
Chain | PRO_0000410598 | 723-1372 | Reverse transcriptase/ribonuclease H p90 | |||
Sequence: SCQTKNTLNIDEYLLQFPDQLWASLPTDIGRMLVPPITIKIKDNASLPSIRQYPLPKDKTEGLRPLISSLENQGILIKCHSPCNTPIFPIKKAGRDEYRMIHDLRAINNIVAPLTAVVASPTTVLSNLAPSLHWFTVIDLSNAFFSVPIHKDSQYLFAFTFEGHQYTWTVLPQGFIHSPTLFSQALYQSLHKIKFKISSEICIYMDDVLIASKDRDTNLKDTAVMLQHLASEGHKVSKKKLQLCQQEVVYLGQLLTPEGRKILPDRKVTVSQFQQPTTIRQIRAFLGLVGYCRHWIPEFSIHSKFLEKQLKKDTAEPFQLDDQQVEAFNKLKHAITTAPVLVVPDPAKPFQLYTSHSEHASIAVLTQKHAGRTRPIAFLSSKFDAIESGLPPCLKACASIHRSLTQADSFILGAPLIIYTTHAICTLLQRDRSQLVTASRFSKWEADLLRPELTFVACSAVSPAHLYMQSCENNIPPHDCVLLTHTISRPRPDLSDLPIPDPDMTLFSDGSYTTGRGGAAVVMHRPVTDDFIIIHQQPGGASAQTAELLALAAACHLATDKTVNIYTDSRYAYGVVHDFGHLWMHRGFVTSAGTPIKNHKEIEYLLKQIMKPKQVSVIKIEAHTKGVSMEVRGNAAADEAAKNAVFLVQR | ||||||
Chain | PRO_0000410599 | 1373-1752 | Integrase p46 | |||
Sequence: VLKKGDALASTDLVMEYSETDEKFTAGAELHDGVFMRGDLIVPPLEMLHAILLAIHGVSHTHKGGIMSYFSKFWTHPKASQTIDLILGHCQICLKHNPKYKSRLQGHRPLPSRPFAHLQIDFVQMCVKKPMYALVIIDVFSKWPEIIPCNKEDAKTVCDILMKDIIPRWGLPDQIDSDQGTHFTAKISQELTHSIGVAWKLHCPGHPRSSGIVERTNRTLKSKIIKAQEQLQLSKWTEVLPYVLLEMRATPKKHGLSPHEIVMGRPMKTTYLSDMSPLWATDTLVTYMNKLTRQLSAYHQQVVDQWPSTSLPPGPEPGSWCMLRNPKKSSNWEGPFLILLSTPTAVKVEGRPTWIHLDHCKLLRSSLSSSLGGPVNQLLS |
Post-translational modification
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).
Keywords
- PTM
Interaction
Subunit
Capsid protein p25
Homohexamer. Further associates as homomultimer. The virus core is composed of a lattice formed from hexagonal rings, each containing six capsid monomers. The protease is a homodimer, whose active site consists of two apposed aspartic acid residues. The reverse transcriptase is a monomer (By similarity).
Structure
Family & Domains
Features
Showing features for coiled coil, compositional bias, region, zinc finger, domain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Coiled coil | 154-185 | |||||
Sequence: AAQQQVLLLQREQQREQREKDIKKRDEKKKKL | ||||||
Compositional bias | 171-190 | Basic and acidic residues | ||||
Sequence: REKDIKKRDEKKKKLLPDTT | ||||||
Region | 171-222 | Disordered | ||||
Sequence: REKDIKKRDEKKKKLLPDTTQKVEQTDIGEASSSDASAQKPISTDNNPDLKV | ||||||
Compositional bias | 191-216 | Polar residues | ||||
Sequence: QKVEQTDIGEASSSDASAQKPISTDN | ||||||
Zinc finger | 501-518 | CCHC-type | ||||
Sequence: NTCFFCKQPGHWKADCPN | ||||||
Region | 517-560 | Disordered | ||||
Sequence: PNKTRNLRNMGNMGRGGRMGGPPYRSQPYPAFIQPPQNHQNQYN | ||||||
Domain | 618-694 | Peptidase A2 | ||||
Sequence: IPMLVDTGACLTAIGGAATVVPDLKLTNTEIIAVGISAEPVPHVLAKPTKIQIENTNIDISPWYNPDQTFHILGRDT | ||||||
Domain | 793-977 | Reverse transcriptase | ||||
Sequence: ENQGILIKCHSPCNTPIFPIKKAGRDEYRMIHDLRAINNIVAPLTAVVASPTTVLSNLAPSLHWFTVIDLSNAFFSVPIHKDSQYLFAFTFEGHQYTWTVLPQGFIHSPTLFSQALYQSLHKIKFKISSEICIYMDDVLIASKDRDTNLKDTAVMLQHLASEGHKVSKKKLQLCQQEVVYLGQLL | ||||||
Domain | 1222-1368 | RNase H type-1 | ||||
Sequence: PDPDMTLFSDGSYTTGRGGAAVVMHRPVTDDFIIIHQQPGGASAQTAELLALAAACHLATDKTVNIYTDSRYAYGVVHDFGHLWMHRGFVTSAGTPIKNHKEIEYLLKQIMKPKQVSVIKIEAHTKGVSMEVRGNAAADEAAKNAVF | ||||||
Domain | 1482-1638 | Integrase catalytic | ||||
Sequence: LPSRPFAHLQIDFVQMCVKKPMYALVIIDVFSKWPEIIPCNKEDAKTVCDILMKDIIPRWGLPDQIDSDQGTHFTAKISQELTHSIGVAWKLHCPGHPRSSGIVERTNRTLKSKIIKAQEQLQLSKWTEVLPYVLLEMRATPKKHGLSPHEIVMGRP |
Keywords
- Domain
Family and domain databases
Sequence
- Sequence statusComplete
- Length1,752
- Mass (Da)196,265
- Last updated2011-06-28 v2
- ChecksumA9DEF76316FBE4E0
Features
Showing features for compositional bias.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Compositional bias | 171-190 | Basic and acidic residues | ||||
Sequence: REKDIKKRDEKKKKLLPDTT | ||||||
Compositional bias | 191-216 | Polar residues | ||||
Sequence: QKVEQTDIGEASSSDASAQKPISTDN |
Keywords
- Coding sequence diversity
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
L41838 EMBL· GenBank· DDBJ | - | Genomic RNA | No translation available. | |
AF033822 EMBL· GenBank· DDBJ | AAC82611.2 EMBL· GenBank· DDBJ | Genomic RNA |