P03361 · POL_BLVJ

Function

function

Gag-Pro polyprotein: The matrix domain targets Gag, Gag-Pro and Gag-Pro-Pol polyproteins to the plasma membrane via a multipartite membrane binding signal, that includes its myristoylated N-terminus.

Matrix protein p15

Matrix protein.

Capsid protein p24

Forms the spherical core of the virus that encapsulates the genomic RNA-nucleocapsid complex.

Nucleocapsid protein p12-pro

Binds strongly to viral nucleic acids and promote their aggregation. Also destabilizes the nucleic acids duplexes via highly structured zinc-binding motifs.

Protease

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.

Reverse transcriptase/ribonuclease H

RT is a multifunctional enzyme that converts the viral 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-Pro 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 primer. 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.

Integrase

Catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions.

Miscellaneous

Reverse transcriptase/ribonuclease H

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

Mg2+ (UniProtKB | Rhea| CHEBI:18420 )

Note: The RT polymerase active site binds 2 magnesium ions.

Features

Showing features for site, active site, binding site, dna binding.

TypeIDPosition(s)Description
Site109-110Cleavage; by viral protease
Site322-323Cleavage; by viral protease
Site419-420Cleavage; by viral protease
Active site452Protease; shared with dimeric partner
Site544-545Cleavage; by viral protease
Binding site652Mg2+ 1 (UniProtKB | ChEBI); catalytic
Binding site727Mg2+ 1 (UniProtKB | ChEBI); catalytic
Binding site728Mg2+ 1 (UniProtKB | ChEBI); catalytic
Binding site1005Mg2+ 2 (UniProtKB | ChEBI)
Binding site1036Mg2+ 2 (UniProtKB | ChEBI)
Binding site1057Mg2+ 2 (UniProtKB | ChEBI)
Binding site1118Mg2+ 2 (UniProtKB | ChEBI)
Site1120-1121Cleavage; by viral protease
Binding site1190Mg2+ 3 (UniProtKB | ChEBI); catalytic
Binding site1247Mg2+ 3 (UniProtKB | ChEBI); catalytic
DNA binding1352-1400Integrase-type

GO annotations

AspectTerm
Cellular Componentviral nucleocapsid
Molecular Functionaspartic-type endopeptidase activity
Molecular FunctionDNA binding
Molecular FunctionDNA-directed DNA polymerase activity
Molecular FunctionRNA stem-loop 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 Processestablishment of integrated proviral latency
Biological Processproteolysis
Biological Processsymbiont entry into host cell
Biological Processviral budding via host ESCRT complex
Biological Processviral genome integration into host DNA
Biological Processviral translational frameshifting

Keywords

Names & Taxonomy

Protein names

Gene names

    • Name
      pol

Organism names

Accessions

  • Primary accession
    P03361

Subcellular Location

Matrix protein p15

Virion

Capsid protein p24

Virion

Nucleocapsid protein p12-pro

Virion

Keywords

PTM/Processing

Features

Showing features for initiator methionine, lipidation, chain.

TypeIDPosition(s)Description
Initiator methionine1Removed; by host
Lipidation2N-myristoyl glycine; by host
ChainPRO_00004425582-109Matrix protein p15
ChainPRO_00001254822-1416Gag-Pro-Pol polyprotein
ChainPRO_0000442559110-321Capsid protein p24
ChainPRO_0000442560322-419Nucleocapsid protein p12-pro
ChainPRO_0000442561420-545Protease
ChainPRO_0000442562546-1120Reverse transcriptase/ribonuclease H
ChainPRO_00004425631121-1416Integrase

Post-translational modification

Matrix protein p15

Phosphorylation of the matrix protein p15 by MAPK1 seems to play a role in budding.

Gag-Pro-Pol polyprotein

Myristoylated. Myristoylation of the matrix (MA) domain mediates the transport and binding of Gag polyproteins to the host plasma membrane and is required for the assembly of viral particles.

Gag-Pro-Pol polyprotein

Specific enzymatic cleavages by the viral protease yield mature proteins. The polyprotein is cleaved during and after budding, this process is termed maturation. The protease is autoproteolytically processed at its N- and C-termini.

Keywords

Interaction

Subunit

Gag-Pro-Pol polyprotein

Homodimer; the homodimers are part of the immature particles. Interacts with human TSG101 and NEDD4; these interactions are essential for budding and release of viral particles.

Matrix protein p15

Homodimer; further assembles as homohexamers.

Structure

3D structure databases

Family & Domains

Features

Showing features for motif, zinc finger, domain.

TypeIDPosition(s)Description
Motif100-103PPXY motif
Zinc finger345-362CCHC-type 1
Zinc finger370-387CCHC-type 2
Domain447-525Peptidase A2
Domain586-776Reverse transcriptase
Domain996-1126RNase H type-1
Domain1179-1343Integrase catalytic

Domain

Gag 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. Matrix protein p15 contains one L domain: a PPXY motif which binds to the WW domains of the ubiquitin ligase NEDD4.

Sequence similarities

Belongs to the retroviral Pol polyprotein family.

Keywords

Family and domain databases

Sequence & Isoforms

Align isoforms (3)
  • Sequence status
    Complete

This entry describes 3 isoforms produced by Ribosomal frameshifting.

P03361-1

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.

  • Name
    Gag-Pro-Pol polyprotein
  • Note
    Produced by -1 ribosomal frameshiftings between gag-pro and pro-pol.
  • See also
    sequence in UniParc or sequence clusters in UniRef
  • Length
    1,416
  • Mass (Da)
    156,397
  • Last updated
    2017-12-20 v2
  • Checksum
    4840617B29D4A098
MGNSPSYNPPAGISPSDWLNLLQSAQRLNPRPSPSDFTDLKNYIHWFHKTQKKPWTFTSGGPTSCPPGRFGRVPLVLATLNEVLSNEGGAPGASAPEEQPPPYDPPAILPIISEGNRNRHRAWALRELQDIKKEIENKAPGSQVWIQTLRLAILQADPTPADLEQLCQYIASPVDQTAHMTSLTAAIAAAEAANTLQGFNPKTGTLTQQSAQPNAGDLRSQYQNLWLQAGKNLPTRPSAPWSTIVQGPAESSVEFVNRLQISLADNLPDGVPKEPIIDSLSYANANRECQQILQGRGPVAAVGQKLQACAQWAPKNKQPALLVHTPGPKMPGPRQPAPKRPPPGPCYRCLKEGHWARDCPTKATGPPPGPCPICKDPSHWKRDCPTLKSKNKLIEGGLSAPQTITPITDSLSEAELECLLSIPLARSRPSVAVYLSGPWLQPSQNQALMLVDTGAENTVLPQNWLVRDYPRIPAAVLGAGGVSRNRYNWLQGPLTLALKPEGPFITIPKILVDTSDKWQILGRDVPSRLQASISIPEEVRPPVVGVLDTPPSHIGLEHLPPPPEVPQFPLNLERLQALQDLVHRSLEAGYISPWDGPGNNPVFPVRKPNGAWRFVHDLRATNALTKPIPALSPGPPDLTAIPTHPPHIICLDLKDAFFQIPVEDRFRFYLSFTLPSPGGLQPHRRFAWRVLPQGFINSPALFERALQEPLRQVSAAFSQSLLVSYMDDILYASPTEEQRSQCYQALAARLRDLGFQVASEKTSQTPSPVPFLGQMVHEQIVTYQSLPTLQISSPISLHQLQAVLGDLQWVSRGTPTTRRPLQLLYSSLKRHHDPRAIIQLSPEQLQGIAELRQALSHNARSRYNEQEPLLAYVHLTRAGSTLVLFQKGAQFPLAYFQTPLTDNQASPWGLLLLLGCQYLQTQALSSYAKPILKYYHNLPKTSLDNWIQSSEDPRVQELLQLWPQISSQGIQPPGPWKTLITRAEVFLTPQFSPDPIPAALCLFSDGATGRGAYCLWKDHLLDFQAVPAPESAQKGELAGLLAGLAAAPPEPVNIWVDSKYLYSLLRTLVLGAWLQPDPVPSYALLYKSLLRHPAIVVGHVRSHSSASHPIASLNNYVDQLLPLETPEQWHKLTHCNSRALSRWPNPRISAWDPRSPATLCETCQKLNPTGGGKMRTIQRGWAPNHIWQADITHYKYKQFTYALHVFVDTYSGATHASAKRGLTTQTTIEGLLEAIVHLGRPKKLNTDQGANYTSKTFVRFCQQFGVSLSHHVPYNPTSSGLDERTNGLLKLLLSKYHLDEPHLPMTQALSRALWTHNQINLLPILKTRWELHHSPPLAVISEGGETPKGSDKLFLYLLPGQNNRRWLGPLPALVEASGGALLATDPPVWVPWRLLKAFKCLKNDGPEDAHNRSSDG

P03344-1

The sequence of this isoform can be found in the external entry linked below. Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

View isoform
  • Name
    Gag polyprotein
  • See also
    sequence in UniParc or sequence clusters in UniRef

P0DOI0-1

The sequence of this isoform can be found in the external entry linked below. Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

View isoform
  • Name
    Gag-Pro polyprotein
  • See also
    sequence in UniParc or sequence clusters in UniRef

Sequence caution

The sequence AAA42785.1 differs from that shown. Reason: Erroneous gene model prediction

Keywords

Sequence databases

Nucleotide SequenceProtein SequenceMolecule TypeStatus
K02120
EMBL· GenBank· DDBJ
AAA42785.1
EMBL· GenBank· DDBJ
Genomic RNA Sequence problems.

Similar Proteins

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