O92815 · POL_WDSV

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

Cofactor

Protein has several cofactor binding sites:
Mg2+ (UniProtKB | Rhea| CHEBI:18420 )

Note: Binds 2 magnesium ions for reverse transcriptase polymerase activity.
Mg2+ (UniProtKB | Rhea| CHEBI:18420 )

Note: Binds 2 magnesium ions for ribonuclease H (RNase H) activity.
Mg2+ (UniProtKB | Rhea| CHEBI:18420 )

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.

TypeIDPosition(s)Description
Site95-96Cleavage; by viral protease
Site251-252Cleavage; by viral protease
Site457-458Cleavage; by viral protease
Site584-585Cleavage; by viral protease
Active site623Protease; shared with dimeric partner
Site722-723Cleavage; by viral protease
Binding site861Mg2+ 1 (UniProtKB | ChEBI); catalytic; for reverse transcriptase activity
Binding site928Mg2+ 1 (UniProtKB | ChEBI); catalytic; for reverse transcriptase activity
Binding site929Mg2+ 1 (UniProtKB | ChEBI); catalytic; for reverse transcriptase activity
Binding site1231Mg2+ (UniProtKB | ChEBI); for RNase H activity
Binding site1269Mg2+ (UniProtKB | ChEBI); for RNase H activity
Binding site1290Mg2+ (UniProtKB | ChEBI); for RNase H activity
Binding site1360Mg2+ (UniProtKB | ChEBI); for RNase H activity
Site1372-1373Cleavage; by viral protease
Binding site1493Mg2+ 3 (UniProtKB | ChEBI); catalytic; for integrase activity
Binding site1550Mg2+ 3 (UniProtKB | ChEBI); catalytic; for integrase activity

GO annotations

AspectTerm
Cellular Componenthost cell plasma membrane
Cellular Componentmembrane
Cellular Componentviral nucleocapsid
Molecular Functionaspartic-type endopeptidase activity
Molecular FunctionDNA binding
Molecular FunctionDNA-directed DNA polymerase activity
Molecular FunctionRNA binding
Molecular FunctionRNA-directed DNA polymerase activity
Molecular FunctionRNA-DNA hybrid ribonuclease activity
Molecular Functionstructural constituent of virion
Molecular Functionzinc ion binding
Biological ProcessDNA integration
Biological ProcessDNA recombination
Biological Processproteolysis

Keywords

Protein family/group databases

Names & Taxonomy

Protein names

Gene names

    • Name
      gag-pol

Organism names

Accessions

  • Primary accession
    O92815

Proteomes

Subcellular Location

Gag-Pol polyprotein

Host cell membrane
; Lipid-anchor

Matrix protein p10

Virion

Capsid protein p25

Virion

Nucleocapsid protein p14

Virion

Keywords

PTM/Processing

Features

Showing features for initiator methionine, lipidation, chain.

TypeIDPosition(s)Description
Initiator methionine1Removed
Lipidation2N-myristoyl glycine; by host
ChainPRO_00004105932-95Matrix protein p10
ChainPRO_00004105922-1752Gag-Pol polyprotein
ChainPRO_000041059496-251p20
ChainPRO_0000410595252-457Capsid protein p25
ChainPRO_0000410596458-584Nucleocapsid protein p14
ChainPRO_0000410597585-722Protease p15
ChainPRO_0000410598723-1372Reverse transcriptase/ribonuclease H p90
ChainPRO_00004105991373-1752Integrase p46

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

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).

Family & Domains

Features

Showing features for coiled coil, compositional bias, region, zinc finger, domain.

TypeIDPosition(s)Description
Coiled coil154-185
Compositional bias171-190Basic and acidic residues
Region171-222Disordered
Compositional bias191-216Polar residues
Zinc finger501-518CCHC-type
Region517-560Disordered
Domain618-694Peptidase A2
Domain793-977Reverse transcriptase
Domain1222-1368RNase H type-1
Domain1482-1638Integrase catalytic

Keywords

Family and domain databases

Sequence

  • Sequence status
    Complete
  • Length
    1,752
  • Mass (Da)
    196,265
  • Last updated
    2011-06-28 v2
  • Checksum
    A9DEF76316FBE4E0
MGNSSSTPPPSALKNSDLFKTMLRTQYSGSVKTRRINQDIKKQYPLWPDQGTCATKHWEQAVLIPLDSVSEETAKVLNFLRVKIQARKGETARQMTAHTIKKLIVGTIDKNKQQTEILQKTDESDEEMDTTNTMLFIARNKRERIAQQQQADLAAQQQVLLLQREQQREQREKDIKKRDEKKKKLLPDTTQKVEQTDIGEASSSDASAQKPISTDNNPDLKVDGVLTRSQHTTVPSNITIKKDGTSVQYQHPIRNYPTGEGNLTAQVRNPFRPLELQQLRKDCPALPEGIPQLAEWLTQTMAIYNCDEADVEQLARVIFPTPVRQIAGVINGHAAANTAAKIQNYVTACRQHYPAVCDWGTIQAFTYKPPQTAHEYVKHAEIIFKNNSGLEWQHATVPFINMVVQGLPPKVTRSLMSGNPDWSTKTIPQIIPLMQHYLNLQSRQDAKIKQTPLVLQLAMPAQTMNGNKGYVGSYPTNEPYYSFQQQQRPAPRAPPGNVPSNTCFFCKQPGHWKADCPNKTRNLRNMGNMGRGGRMGGPPYRSQPYPAFIQPPQNHQNQYNGRMDRSQLQASAQEWLPGTYPAXDPIDCPYEKSGTKTTQDVITTKNAEIMVTVNHTKIPMLVDTGACLTAIGGAATVVPDLKLTNTEIIAVGISAEPVPHVLAKPTKIQIENTNIDISPWYNPDQTFHILGRDTLSKMRAIVSFEKNGEMTVLLPPTYHKQLSCQTKNTLNIDEYLLQFPDQLWASLPTDIGRMLVPPITIKIKDNASLPSIRQYPLPKDKTEGLRPLISSLENQGILIKCHSPCNTPIFPIKKAGRDEYRMIHDLRAINNIVAPLTAVVASPTTVLSNLAPSLHWFTVIDLSNAFFSVPIHKDSQYLFAFTFEGHQYTWTVLPQGFIHSPTLFSQALYQSLHKIKFKISSEICIYMDDVLIASKDRDTNLKDTAVMLQHLASEGHKVSKKKLQLCQQEVVYLGQLLTPEGRKILPDRKVTVSQFQQPTTIRQIRAFLGLVGYCRHWIPEFSIHSKFLEKQLKKDTAEPFQLDDQQVEAFNKLKHAITTAPVLVVPDPAKPFQLYTSHSEHASIAVLTQKHAGRTRPIAFLSSKFDAIESGLPPCLKACASIHRSLTQADSFILGAPLIIYTTHAICTLLQRDRSQLVTASRFSKWEADLLRPELTFVACSAVSPAHLYMQSCENNIPPHDCVLLTHTISRPRPDLSDLPIPDPDMTLFSDGSYTTGRGGAAVVMHRPVTDDFIIIHQQPGGASAQTAELLALAAACHLATDKTVNIYTDSRYAYGVVHDFGHLWMHRGFVTSAGTPIKNHKEIEYLLKQIMKPKQVSVIKIEAHTKGVSMEVRGNAAADEAAKNAVFLVQRVLKKGDALASTDLVMEYSETDEKFTAGAELHDGVFMRGDLIVPPLEMLHAILLAIHGVSHTHKGGIMSYFSKFWTHPKASQTIDLILGHCQICLKHNPKYKSRLQGHRPLPSRPFAHLQIDFVQMCVKKPMYALVIIDVFSKWPEIIPCNKEDAKTVCDILMKDIIPRWGLPDQIDSDQGTHFTAKISQELTHSIGVAWKLHCPGHPRSSGIVERTNRTLKSKIIKAQEQLQLSKWTEVLPYVLLEMRATPKKHGLSPHEIVMGRPMKTTYLSDMSPLWATDTLVTYMNKLTRQLSAYHQQVVDQWPSTSLPPGPEPGSWCMLRNPKKSSNWEGPFLILLSTPTAVKVEGRPTWIHLDHCKLLRSSLSSSLGGPVNQLLS

Features

Showing features for compositional bias.

TypeIDPosition(s)Description
Compositional bias171-190Basic and acidic residues
Compositional bias191-216Polar residues

Keywords

Sequence databases

Nucleotide SequenceProtein SequenceMolecule TypeStatus
L41838
EMBL· GenBank· DDBJ
-Genomic RNA No translation available.
AF033822
EMBL· GenBank· DDBJ
AAC82611.2
EMBL· GenBank· DDBJ
Genomic RNA

Genome annotation databases

Similar Proteins

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