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Protein

Gag-Pol polyprotein

Gene

gag-pol

Organism
Human immunodeficiency virus type 1 group M subtype B (isolate YU-2) (HIV-1)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Gag-Pol polyprotein: Mediates, with Gag polyrotein, the essential events in virion assembly, including binding the plasma membrane, making the protein-protein interactions necessary to create spherical particles, recruiting the viral Env proteins, and packaging the genomic RNA via direct interactions with the RNA packaging sequence (Psi). Gag-Pol polyprotein may regulate its own translation, by the binding genomic RNA in the 5'-UTR. At low concentration, the polyprotein would promote translation, whereas at high concentration, the polyprotein would encapsidate genomic RNA and then shutt off translation.By similarity
Matrix protein p17: Targets the polyprotein to the plasma membrane via a multipartite membrane-binding signal, that includes its myristoylated N-terminus. Matrix protein is part of the pre-integration complex. Implicated in the release from host cell mediated by Vpu. Binds to RNA.By similarity
Capsid protein p24: Forms the conical core that encapsulates the genomic RNA-nucleocapsid complex in the virion. Most core are conical, with only 7% tubular. The core is constituted by capsid protein hexamer subunits. The core is disassembled soon after virion entry (By similarity). Host restriction factors such as TRIM5-alpha or TRIMCyp bind retroviral capsids and cause premature capsid disassembly, leading to blocks in reverse transcription. Capsid restriction by TRIM5 is one of the factors which restricts HIV-1 to the human species. Host PIN1 apparently facilitates the virion uncoating. On the other hand, interactions with PDZD8 or CYPA stabilize the capsid.By similarity
Nucleocapsid protein p7: Encapsulates and protects viral dimeric unspliced genomic RNA (gRNA). Binds these RNAs through its zinc fingers. Acts as a nucleic acid chaperone which is involved in rearangement of nucleic acid secondary structure during gRNA retrotranscription. Also facilitates template switch leading to recombination. As part of the polyprotein, participates to gRNA dimerization, packaging, tRNA incorporation and virion assembly.By similarity
Protease: 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. Also cleaves Nef and Vif, probably concomitantly with viral structural proteins on maturation of virus particles. Hydrolyzes host EIF4GI and PABP1 in order to shut off the capped cellular mRNA translation. The resulting inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response (By similarity).PROSITE-ProRule annotationBy similarity
Reverse transcriptase/ribonuclease H: 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(3)-Lys 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 two polypurine tracts (PPTs) situated at the 5'-end and near the center 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 PPTs that have not been removed by RNase H as primers. PPTs 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: 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, Vpr 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, the PIC enters cell nucleus. This process is mediated through integrase and Vpr proteins, and allows the virus to infect a non dividing cell. This ability to enter the nucleus is specific of lentiviruses, other retroviruses cannot and rely on cell division to access cell chromosomes. 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 5'-ends are produced by integrase-catalyzed staggered cuts, 5 bp apart. A Y-shaped, gapped, recombination intermediate results, with the 5'-ends of the viral DNA strands and the 3' ends of target DNA strands remaining unjoined, flanking a gap of 5 bp. The last step is viral DNA integration into host chromosome. This involves host DNA repair synthesis in which the 5 bp gaps between the unjoined strands are filled in and then ligated. Since this process occurs at both cuts flanking the HIV genome, a 5 bp duplication of host DNA is produced at the ends of HIV-1 integration. Alternatively, Integrase may catalyze the excision of viral DNA just after strand transfer, this is termed disintegration.By similarity

Catalytic activityi

Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.PROSITE-ProRule annotation
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.By similarity
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid.By similarity
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).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: Magnesium ions are required for integrase activity. Binds at least 1, maybe 2 magnesium ions.By similarity

Enzyme regulationi

Protease: The viral protease is inhibited by many synthetic protease inhibitors (PIs), such as amprenavir, atazanavir, indinavir, loprinavir, nelfinavir, ritonavir and saquinavir. Use of protease inhibitors in tritherapy regimens permit more ambitious therapeutic strategies. Reverse transcriptase/ribonuclease H: RT can be inhibited either by nucleoside RT inhibitors (NRTIs) or by non nucleoside RT inhibitors (NNRTIs). NRTIs act as chain terminators, whereas NNRTIs inhibit DNA polymerization by binding a small hydrophobic pocket near the RT active site and inducing an allosteric change in this region. Classical NRTIs are abacavir, adefovir (PMEA), didanosine (ddI), lamivudine (3TC), stavudine (d4T), tenofovir (PMPA), zalcitabine (ddC), and zidovudine (AZT). Classical NNRTIs are atevirdine (BHAP U-87201E), delavirdine, efavirenz (DMP-266), emivirine (I-EBU), and nevirapine (BI-RG-587). The tritherapies used as a basic effective treatment of AIDS associate two NRTIs and one NNRTI.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei132 – 1332Cleavage; by viral proteaseBy similarity
Sitei221 – 2222Cis/trans isomerization of proline peptide bond; by human PPIA/CYPABy similarity
Sitei363 – 3642Cleavage; by viral proteaseBy similarity
Sitei377 – 3782Cleavage; by viral proteaseBy similarity
Sitei432 – 4332Cleavage; by viral proteaseSequence Analysis
Sitei440 – 4412Cleavage; by viral proteaseBy similarity
Sitei488 – 4892Cleavage; by viral proteaseBy similarity
Active sitei513 – 5131For protease activity; shared with dimeric partnerPROSITE-ProRule annotation
Sitei587 – 5882Cleavage; by viral proteaseBy similarity
Metal bindingi697 – 6971Magnesium; catalytic; for reverse transcriptase activityBy similarity
Metal bindingi772 – 7721Magnesium; catalytic; for reverse transcriptase activityBy similarity
Metal bindingi773 – 7731Magnesium; catalytic; for reverse transcriptase activityBy similarity
Sitei988 – 9881Essential for RT p66/p51 heterodimerizationBy similarity
Sitei1001 – 10011Essential for RT p66/p51 heterodimerizationBy similarity
Sitei1027 – 10282Cleavage; by viral protease; partialBy similarity
Metal bindingi1030 – 10301Magnesium; catalytic; for RNase H activityBy similarity
Metal bindingi1065 – 10651Magnesium; catalytic; for RNase H activityBy similarity
Metal bindingi1085 – 10851Magnesium; catalytic; for RNase H activityBy similarity
Metal bindingi1136 – 11361Magnesium; catalytic; for RNase H activityBy similarity
Sitei1147 – 11482Cleavage; by viral proteaseBy similarity
Metal bindingi1211 – 12111Magnesium; catalytic; for integrase activityBy similarity
Metal bindingi1263 – 12631Magnesium; catalytic; for integrase activityBy similarity
Metal bindingi1299 – 12991Magnesium; catalytic; for integrase activityBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri390 – 40718CCHC-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri411 – 42818CCHC-type 2PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri1150 – 119142Integrase-typePROSITE-ProRule annotationAdd
BLAST
DNA bindingi1370 – 141748Integrase-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. aspartic-type endopeptidase activity Source: UniProtKB-KW
  2. DNA binding Source: UniProtKB-KW
  3. DNA-directed DNA polymerase activity Source: UniProtKB-KW
  4. exoribonuclease H activity Source: UniProtKB-EC
  5. lipid binding Source: UniProtKB-KW
  6. RNA binding Source: UniProtKB-KW
  7. RNA-directed DNA polymerase activity Source: UniProtKB-KW
  8. RNA-DNA hybrid ribonuclease activity Source: InterPro
  9. structural molecule activity Source: InterPro
  10. zinc ion binding Source: InterPro

GO - Biological processi

  1. DNA integration Source: UniProtKB-KW
  2. DNA recombination Source: UniProtKB-KW
  3. establishment of integrated proviral latency Source: UniProtKB-KW
  4. induction by virus of host cysteine-type endopeptidase activity involved in apoptotic process Source: UniProtKB-KW
  5. suppression by virus of host gene expression Source: UniProtKB-KW
  6. viral entry into host cell Source: UniProtKB-KW
  7. viral penetration into host nucleus Source: UniProtKB-KW
  8. viral release from host cell Source: UniProtKB-KW
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

Activation of host caspases by virus, DNA integration, DNA recombination, Eukaryotic host gene expression shutoff by virus, Eukaryotic host translation shutoff by virus, Host gene expression shutoff by virus, Host-virus interaction, Modulation of host cell apoptosis by virus, Viral genome integration, Viral penetration into host nucleus, Virion maturation, Virus entry into host cell, Virus exit from host cell

Keywords - Ligandi

DNA-binding, Lipid-binding, Magnesium, Metal-binding, RNA-binding, Viral nucleoprotein, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Gag-Pol polyprotein
Alternative name(s):
Pr160Gag-Pol
Cleaved into the following 11 chains:
Matrix protein p17
Short name:
MA
Capsid protein p24
Short name:
CA
Spacer peptide 1By similarity
Short name:
SP1
Alternative name(s):
p2
Transframe peptide
Short name:
TF
p6-pol
Short name:
p6*
Alternative name(s):
PR
Retropepsin
Alternative name(s):
Exoribonuclease H (EC:3.1.13.2)
p66 RT
Integrase
Short name:
IN
Gene namesi
Name:gag-pol
OrganismiHuman immunodeficiency virus type 1 group M subtype B (isolate YU-2) (HIV-1)
Taxonomic identifieri362651 [NCBI]
Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeLentivirusPrimate lentivirus group
Virus hostiHomo sapiens (Human) [TaxID: 9606]
ProteomesiUP000007419 Componenti: Genome

Subcellular locationi

Chain Gag-Pol polyprotein : Host cell membrane; Lipid-anchor. Host endosomehost multivesicular body
Note: These locations are linked to virus assembly sites. The main location is the cell membrane, but under some circumstances, late endosomal compartments can serve as productive sites for virion assembly.By similarity
Chain Integrase : Virion Curated. Host nucleus Curated. Host cytoplasm Curated
Note: Nuclear at initial phase, cytoplasmic at assembly.Curated

GO - Cellular componenti

  1. host cell nucleus Source: UniProtKB-SubCell
  2. host cell plasma membrane Source: UniProtKB-SubCell
  3. host multivesicular body Source: UniProtKB-SubCell
  4. intracellular Source: GOC
  5. viral nucleocapsid Source: UniProtKB-KW
  6. virion membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Host cell membrane, Host cytoplasm, Host endosome, Host membrane, Host nucleus, Membrane, Virion

Pathology & Biotechi

Keywords - Diseasei

AIDS

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed; by hostBy similarity
Chaini2 – 14351434Gag-Pol polyproteinPRO_0000261287Add
BLAST
Chaini2 – 132131Matrix protein p17By similarityPRO_0000042303Add
BLAST
Chaini133 – 363231Capsid protein p24By similarityPRO_0000042304Add
BLAST
Peptidei364 – 37714Spacer peptide 1By similarityPRO_0000042305Add
BLAST
Chaini378 – 43255Nucleocapsid protein p7By similarityPRO_0000042306Add
BLAST
Peptidei433 – 4408Transframe peptideSequence AnalysisPRO_0000246737
Chaini441 – 48848p6-polSequence AnalysisPRO_0000042307Add
BLAST
Chaini489 – 58799ProteaseBy similarityPRO_0000038649Add
BLAST
Chaini588 – 1147560Reverse transcriptase/ribonuclease HBy similarityPRO_0000042308Add
BLAST
Chaini588 – 1027440p51 RTBy similarityPRO_0000042309Add
BLAST
Chaini1028 – 1147120p15By similarityPRO_0000042310Add
BLAST
Chaini1148 – 1435288IntegraseBy similarityPRO_0000042311Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Lipidationi2 – 21N-myristoyl glycine; by hostBy similarity
Modified residuei132 – 1321Phosphotyrosine; by hostBy similarity

Post-translational modificationi

Gag-Pol polyprotein: 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. Proteolytic cleavage of p66 RT removes the RNase H domain to yield the p51 RT subunit. Nucleocapsid protein p7 might be further cleaved after virus entry.PROSITE-ProRule annotationBy similarity
Matrix protein p17: Tyrosine phosphorylated presumably in the virion by a host kinase. Phosphorylation is apparently not a major regulator of membrane association.By similarity
Capsid protein p24: Phosphorylated possibly by host MAPK1; this phosphorylation is necessary for Pin1-mediated virion uncoating.By similarity
Nucleocapsid protein p7: Methylated by host PRMT6, impairing its function by reducing RNA annealing and the initiation of reverse transcription.By similarity

Keywords - PTMi

Lipoprotein, Myristate, Phosphoprotein

Interactioni

Subunit structurei

Matrix protein p17: Homotrimer; further assembles as hexamers of trimers (By similarity). Matrix protein p17: Interacts with gp41 (via C-terminus) (By similarity). Matrix protein p17: interacts with host CALM1; this interaction induces a conformational change in the Matrix protein, triggering exposure of the myristate group (By similarity). Matrix protein p17: interacts with host AP3D1; this interaction allows the polyprotein trafficking to multivesicular bodies during virus assembly (By similarity). Matrix protein p17: Part of the pre-integration complex (PIC) which is composed of viral genome, matrix protein, Vpr and integrase (By similarity). Capsid protein p24: Homodimer; the homodimer further multimerizes as homohexamers or homopentamers. Capsid protein p24: Interacts with human PPIA/CYPA (By similarity); This interaction stabilizes the capsid. Capsid protein p24: Interacts with human NUP153 (By similarity). Capsid protein p24: Interacts with host PDZD8; this interaction stabilizes the capsid (By similarity). Capsid protein p24: Interacts with monkey TRIM5; this interaction destabilizes the capsid (By similarity).Protease: Homodimer, whose active site consists of two apposed aspartic acid residues. Reverse transcriptase/ribonuclease H: Heterodimer of p66 RT and p51 RT (RT p66/p51). Heterodimerization of RT is essential for DNA polymerase activity. Despite the sequence identities, p66 RT and p51 RT have distinct folding. Integrase: Homodimer; possibly can form homotetramer. Integrase: Part of the pre-integration complex (PIC) which is composed of viral genome, matrix protein, Vpr and integrase. Integrase: Interacts with human SMARCB1/INI1 and human PSIP1/LEDGF isoform 1. Integrase: Interacts with human KPNA3; this interaction might play a role in nuclear import of the pre-integration complex (By similarity). Integrase: Interacts with human NUP153; this interaction might play a role in nuclear import of the pre-integration complex (By similarity).By similarity

Protein-protein interaction databases

DIPiDIP-45385N.
IntActiP35963. 1 interaction.

Structurei

Secondary structure

1
1435
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi282 – 2843Combined sources
Helixi293 – 30513Combined sources
Beta strandi307 – 3093Combined sources
Helixi311 – 32414Combined sources
Helixi328 – 33710Combined sources
Helixi343 – 3497Combined sources
Beta strandi352 – 3554Combined sources
Helixi381 – 3888Combined sources
Turni393 – 3953Combined sources
Beta strandi398 – 4003Combined sources
Helixi402 – 4043Combined sources
Beta strandi410 – 4134Combined sources
Turni414 – 4174Combined sources
Helixi423 – 4253Combined sources
Beta strandi493 – 4953Combined sources
Beta strandi498 – 5036Combined sources
Beta strandi506 – 5127Combined sources
Beta strandi517 – 5237Combined sources
Beta strandi531 – 5377Combined sources
Beta strandi540 – 55415Combined sources
Beta strandi557 – 56610Combined sources
Helixi575 – 5784Combined sources
Turni579 – 5824Combined sources
Beta strandi584 – 5863Combined sources
Helixi1149 – 11557Combined sources
Helixi1161 – 11644Combined sources
Helixi1166 – 11738Combined sources
Helixi1177 – 118610Combined sources
Helixi1188 – 11914Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1F6UNMR-A381-432[»]
1K6CX-ray2.20A/B489-587[»]
1K6PX-ray2.20A/B489-587[»]
1K6TX-ray2.25A/B489-587[»]
1K6VX-ray2.00A/B489-587[»]
1MFSNMR-A378-432[»]
1T7IX-ray1.35A/B489-587[»]
1T7JX-ray2.20A/B489-587[»]
1WJANMR-A/B1148-1194[»]
1WJCNMR-A/B1148-1194[»]
2JO0NMR-A278-363[»]
2L6ENMR-A280-363[»]
3OQ7X-ray1.71A489-587[»]
3OQAX-ray2.25A489-587[»]
3OQDX-ray1.71A489-587[»]
3OTSX-ray1.70A/B489-587[»]
P130-136[»]
3OTYX-ray1.75A/B489-587[»]
P1025-1031[»]
3OU1X-ray1.80A/B489-587[»]
P1145-1151[»]
3OU3X-ray1.70A/B489-587[»]
C585-591[»]
3OU4X-ray1.60A/B489-587[»]
C488-492[»]
3OUAX-ray1.70A/B489-587[»]
3OUBX-ray1.60A/B489-587[»]
3OUCX-ray2.00A/B489-587[»]
P375-381[»]
3OUDX-ray1.80A/B489-587[»]
3PJ6X-ray2.25A489-587[»]
3U7SX-ray2.05A/B489-587[»]
4A6BX-ray1.80A/B489-587[»]
4A6CX-ray1.50A/B489-587[»]
ProteinModelPortaliP35963.
SMRiP35963. Positions 2-432, 484-1144, 1148-1417.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP35963.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini508 – 57770Peptidase A2PROSITE-ProRule annotationAdd
BLAST
Domaini631 – 821191Reverse transcriptasePROSITE-ProRule annotationAdd
BLAST
Domaini1021 – 1144124RNase HPROSITE-ProRule annotationAdd
BLAST
Domaini1201 – 1351151Integrase catalyticPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni7 – 3125Interaction with Gp41By similarityAdd
BLAST
Regioni8 – 4336Interaction with host CALM1By similarityAdd
BLAST
Regioni12 – 198Interaction with host AP3D1By similarity
Regioni14 – 3320Interaction with membrane phosphatidylinositol 4,5-bisphosphate and RNABy similarityAdd
BLAST
Regioni73 – 775Interaction with membrane phosphatidylinositol 4,5-bisphosphateBy similarity
Regioni189 – 22739Interaction with human PPIA/CYPA and NUP153By similarityAdd
BLAST
Regioni277 – 36387Dimerization/Multimerization of capsid protein p24By similarityAdd
BLAST
Regioni489 – 4935Dimerization of proteaseBy similarity
Regioni537 – 5437Dimerization of proteaseBy similarity
Regioni576 – 58813Dimerization of proteaseBy similarityAdd
BLAST
Regioni814 – 8229RT 'primer grip'By similarity

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi16 – 227Nuclear export signalBy similarity
Motifi26 – 327Nuclear localization signalBy similarity
Motifi985 – 100117Tryptophan repeat motifBy similarityAdd
BLAST

Domaini

Reverse transcriptase/ribonuclease H: RT is structured in five subdomains: finger, palm, thumb, connection and RNase H. Within the palm subdomain, the 'primer grip' region is thought to be involved in the positioning of the primer terminus for accommodating the incoming nucleotide. The RNase H domain stabilizes the association of RT with primer-template.By similarity
Reverse transcriptase/ribonuclease H: The tryptophan repeat motif is involved in RT p66/p51 dimerization (By similarity).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

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)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri390 – 40718CCHC-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri411 – 42818CCHC-type 2PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri1150 – 119142Integrase-typePROSITE-ProRule annotationAdd
BLAST

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.
IPR000721. Gag_p24.
IPR001037. Integrase_C_retrovir.
IPR001584. Integrase_cat-core.
IPR017856. Integrase_Zn-bd_dom-like_N.
IPR003308. Integrase_Zn-bd_dom_N.
IPR000071. Lentvrl_matrix_N.
IPR012344. Matrix_HIV/RSV.
IPR018061. Pept_A2A_retrovirus_sg.
IPR001995. Peptidase_A2_cat.
IPR021109. Peptidase_aspartic_dom.
IPR008916. Retrov_capsid_C.
IPR008919. Retrov_capsid_N.
IPR010999. Retrovr_matrix.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR000477. RT_dom.
IPR010659. RVT_connect.
IPR010661. RVT_thumb.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF00540. Gag_p17. 1 hit.
PF00607. Gag_p24. 1 hit.
PF00552. IN_DBD_C. 1 hit.
PF02022. Integrase_Zn. 1 hit.
PF00075. RNase_H. 1 hit.
PF00665. rve. 1 hit.
PF00077. RVP. 1 hit.
PF00078. RVT_1. 1 hit.
PF06815. RVT_connect. 1 hit.
PF06817. RVT_thumb. 1 hit.
PF00098. zf-CCHC. 2 hits.
[Graphical view]
PRINTSiPR00234. HIV1MATRIX.
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. 2 hits.
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 polyprotein most of the time. Ribosomal frameshifting at the gag-pol genes boundary occurs at low frequency and produces the Gag-Pol polyprotein. This strategy of translation probably allows the virus to modulate the quantity of each viral protein. Maintenance of a correct Gag to Gag-Pol ratio is essential for RNA dimerization and viral infectivity.

Isoform Gag-Pol polyprotein (identifier: P35963-1) [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
MGARASVLSA GELDKWEKIR LRPGGKKQYR LKHIVWASRE LERFAVDPGL
60 70 80 90 100
LETSEGCRQI LGQLQPSLQT GSEELRSLYN TVATLYCVHQ KIEVKDTKEA
110 120 130 140 150
LEKIEEEQNK SKKKAQQAAA DTGNSSQVSQ NYPIVQNLQG QMVHQAISPR
160 170 180 190 200
TLNAWVKVVE EKAFSPEVIP MFSALSEGAT PQDLNTMLNT VGGHQAAMQM
210 220 230 240 250
LKETINEEAA EWDRLHPVHA GPIAPGQMRE PRGSDIAGTT STLQEQIGWM
260 270 280 290 300
TNNPPIPVGE IYKRWIILGL NKIVRMYSPT SILDIRQGPK EPFRDYVDRF
310 320 330 340 350
YKTLRAEQAS QEVKNWMTET LLVQNANPDC KTILKALGPA ATLEEMMTAC
360 370 380 390 400
QGVGGPGHKA RVLAEAMSQV TNSATIMMQR GNFRNQRKTV KCFNCGKEGH
410 420 430 440 450
IAKNCRAPRK KGCWKCGKEG HQMKDCTERQ ANFLREDLAF PQGKARKFSS
460 470 480 490 500
EQTRANSPIR RERQVWRRDN NSLSEAGADR QGTVSFSFPQ ITLWQRPLVT
510 520 530 540 550
IKIGGQLKEA LLDTGADDTV LEEMNLPGRW KPKMIGGIGG FIKVRQYDQI
560 570 580 590 600
PIEICGHKAI GTVLVGPTPV NIIGRNLLTQ IGCTLNFPIS PIETVPVKLK
610 620 630 640 650
PGMDGPKVKQ WPLTEEKIKA LVEICTEMEK EGKISKIGPE NPYNTPVFAI
660 670 680 690 700
KKKDSTKWRK LVDFRELNKR TQDFWEVQLG IPHPAGLKKK KSVTVLDVGD
710 720 730 740 750
AYFSVPLHED FRKYTAFTIP SINNETPGTR YQYNVLPQGW KGSPAIFQSS
760 770 780 790 800
MTTILEPFRK QNPDLVIYQY MDDLYVGSDL EIGQHRTKIE ELRQHLLRWG
810 820 830 840 850
FTTPDKKHQK EPPFLWMGYE LHPDKWTVQP IVLPEKDSWT VNDIQKLVGK
860 870 880 890 900
LNWASQIYAG IKVRQLCKLL RGTKALTEVI PLTEEAELEL AENREILKEP
910 920 930 940 950
VHGVYYDPSK DLIAEIQKQG QGQWTYQIYQ EPFKNLKTGK YARTRGAHTN
960 970 980 990 1000
DVKQLTEAVQ KIATESIVIW GKTPKFKLPI QKETWETWWT EYWQATWIPE
1010 1020 1030 1040 1050
WEFVNTPPLV KLWYQLEKEP IIGAETFYVD GAANRETKLG KAGYVTNKGR
1060 1070 1080 1090 1100
QKVVSLTDTT NQKTELQAIY LALQDSGLEV NIVTDSQYAL GIIQAQPDRS
1110 1120 1130 1140 1150
ESELVSQIIE QLIKKEKVYL AWVPAHKGIG GNEQVDKLVS AGIRKVLFLD
1160 1170 1180 1190 1200
GIDKAQEEHE KYHSNWRAMA SDFNLPPVVA KEIVASCDKC QLKGEAMHGQ
1210 1220 1230 1240 1250
VDCSPGIWQL DCTHLEGKVI LVAVHVASGY IEAEVIPAET GQETAYFLLK
1260 1270 1280 1290 1300
LAGRWPVTTI HTDNGSNFTS ATVKAACWWA GIKQEFGIPY NPQSQGVVES
1310 1320 1330 1340 1350
MNKELKKIIG QVRDQAEHLK TAVQMAVFIH NFKRKGGIGG YSAGERIVDI
1360 1370 1380 1390 1400
IATDIQTKEL QKQITKIQNF RVYYRDSRDP LWKGPAKLLW KGEGAVVIQD
1410 1420 1430
NSDIKVVPRR KAKIIRDYGK QMAGDDCVAG RQDED

Note: Produced by -1 ribosomal frameshifting.

Length:1,435
Mass (Da):161,980
Last modified:January 23, 2007 - v3
Checksum:i8EF29043F867979E
GO
Isoform Gag polyprotein (identifier: P35962-1) [UniParc]FASTAAdd to basket

The sequence of this isoform can be found in the external entry P35962.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Note: Produced by conventional translation.

Length:500
Mass (Da):55,792
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M93258 Genomic RNA. No translation available.
PIRiB44001.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Web resourcesi

HIV drug resistance mutations
hivdb

HIV drug resistance database

BioAfrica: HIV bioinformatics in Africa

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M93258 Genomic RNA. No translation available.
PIRiB44001.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1F6UNMR-A381-432[»]
1K6CX-ray2.20A/B489-587[»]
1K6PX-ray2.20A/B489-587[»]
1K6TX-ray2.25A/B489-587[»]
1K6VX-ray2.00A/B489-587[»]
1MFSNMR-A378-432[»]
1T7IX-ray1.35A/B489-587[»]
1T7JX-ray2.20A/B489-587[»]
1WJANMR-A/B1148-1194[»]
1WJCNMR-A/B1148-1194[»]
2JO0NMR-A278-363[»]
2L6ENMR-A280-363[»]
3OQ7X-ray1.71A489-587[»]
3OQAX-ray2.25A489-587[»]
3OQDX-ray1.71A489-587[»]
3OTSX-ray1.70A/B489-587[»]
P130-136[»]
3OTYX-ray1.75A/B489-587[»]
P1025-1031[»]
3OU1X-ray1.80A/B489-587[»]
P1145-1151[»]
3OU3X-ray1.70A/B489-587[»]
C585-591[»]
3OU4X-ray1.60A/B489-587[»]
C488-492[»]
3OUAX-ray1.70A/B489-587[»]
3OUBX-ray1.60A/B489-587[»]
3OUCX-ray2.00A/B489-587[»]
P375-381[»]
3OUDX-ray1.80A/B489-587[»]
3PJ6X-ray2.25A489-587[»]
3U7SX-ray2.05A/B489-587[»]
4A6BX-ray1.80A/B489-587[»]
4A6CX-ray1.50A/B489-587[»]
ProteinModelPortaliP35963.
SMRiP35963. Positions 2-432, 484-1144, 1148-1417.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-45385N.
IntActiP35963. 1 interaction.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP35963.

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.
IPR000721. Gag_p24.
IPR001037. Integrase_C_retrovir.
IPR001584. Integrase_cat-core.
IPR017856. Integrase_Zn-bd_dom-like_N.
IPR003308. Integrase_Zn-bd_dom_N.
IPR000071. Lentvrl_matrix_N.
IPR012344. Matrix_HIV/RSV.
IPR018061. Pept_A2A_retrovirus_sg.
IPR001995. Peptidase_A2_cat.
IPR021109. Peptidase_aspartic_dom.
IPR008916. Retrov_capsid_C.
IPR008919. Retrov_capsid_N.
IPR010999. Retrovr_matrix.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR000477. RT_dom.
IPR010659. RVT_connect.
IPR010661. RVT_thumb.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF00540. Gag_p17. 1 hit.
PF00607. Gag_p24. 1 hit.
PF00552. IN_DBD_C. 1 hit.
PF02022. Integrase_Zn. 1 hit.
PF00075. RNase_H. 1 hit.
PF00665. rve. 1 hit.
PF00077. RVP. 1 hit.
PF00078. RVT_1. 1 hit.
PF06815. RVT_connect. 1 hit.
PF06817. RVT_thumb. 1 hit.
PF00098. zf-CCHC. 2 hits.
[Graphical view]
PRINTSiPR00234. HIV1MATRIX.
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. 2 hits.
PS50876. ZF_INTEGRASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Complete nucleotide sequence, genome organization, and biological properties of human immunodeficiency virus type 1 in vivo: evidence for limited defectiveness and complementation."
    Li Y., Hui H., Burgess C.J., Price R.W., Sharp P.M., Hahn B.H., Shaw G.M.
    J. Virol. 66:6587-6600(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
  2. "Proteolytic processing and particle maturation."
    Vogt V.M.
    Curr. Top. Microbiol. Immunol. 214:95-131(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  3. Cited for: REVIEW.
  4. "Mechanisms of retroviral recombination."
    Negroni M., Buc H.
    Annu. Rev. Genet. 35:275-302(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  5. Cited for: REVIEW.
  6. "Role of HIV-1 Gag domains in viral assembly."
    Scarlata S., Carter C.
    Biochim. Biophys. Acta 1614:62-72(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  7. "Solution structure of the N-terminal zinc binding domain of HIV-1 integrase."
    Cai M., Zheng R., Caffrey M., Craigie R., Clore G.M., Gronenborn A.M.
    Nat. Struct. Biol. 4:567-577(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 1148-1194.
  8. "NMR structure of the HIV-1 nucleocapsid protein bound to stem-loop SL2 of the psi-RNA packaging signal. Implications for genome recognition."
    Amarasinghe G.K., De Guzman R.N., Turner R.B., Chancellor K.J., Wu Z.R., Summers M.F.
    J. Mol. Biol. 301:491-511(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 379-432.
  9. "Lack of synergy for inhibitors targeting a multi-drug-resistant HIV-1 protease."
    King N.M., Melnick L., Prabu-Jeyabalan M., Nalivaika E.A., Yang S.S., Gao Y., Nie X., Zepp C., Heefner D.L., Schiffer C.A.
    Protein Sci. 11:418-429(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 489-587 IN COMPLEX WITH INDINAVIR ANALOGS.
  10. Cited for: X-RAY CRYSTALLOGRAPHY (1.35 ANGSTROMS) OF 489-587.

Entry informationi

Entry nameiPOL_HV1Y2
AccessioniPrimary (citable) accession number: P35963
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: January 23, 2007
Last modified: April 1, 2015
This is version 161 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

Reverse transcriptase/ribonuclease H: 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.By similarity
HIV-1 lineages are divided in three main groups, M (for Major), O (for Outlier), and N (for New, or Non-M, Non-O). The vast majority of strains found worldwide belong to the group M. Group O seems to be endemic to and largely confined to Cameroon and neighboring countries in West Central Africa, where these viruses represent a small minority of HIV-1 strains. The group N is represented by a limited number of isolates from Cameroonian persons. The group M is further subdivided in 9 clades or subtypes (A to D, F to H, J and K).
Resistance to inhibitors associated with mutations are observed both in viral protease and in reverse transcriptase. Most of the time, single mutations confer only a modest reduction in drug susceptibility. Combination of several mutations is usually required to develop a high-level drug resistance. These mutations are predominantly found in clade B viruses and not in other genotypes. They are listed in the clade B representative isolate HXB2 (AC P04585).

Keywords - Technical termi

3D-structure, Complete proteome, Multifunctional enzyme

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.