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P05896

- POL_SIVM1

UniProt

P05896 - POL_SIVM1

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Protein

Gag-Pol polyprotein

Gene

gag-pol

Organism
Simian immunodeficiency virus (isolate Mm142-83) (SIV-mac) (Simian immunodeficiency virus rhesus monkey)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Gag-Pol polyprotein and Gag polyprotein may regulate their own translation, by the binding genomic RNA in the 5'-UTR. At low concentration, Gag-Pol and Gag would promote translation, whereas at high concentration, the polyproteins encapsidate genomic RNA and then shutt off translation (By similarity).By similarity
Matrix protein p17 has two main functions: in infected cell, it targets Gag and Gag-pol polyproteins to the plasma membrane via a multipartite membrane-binding signal, that includes its myristointegration complex. The myristoylation signal and the NLS exert conflicting influences its subcellular localization. The key regulation of these motifs might be phosphorylation of a portion of MA molecules on the C-terminal tyrosine at the time of virus maturation, by virion-associated cellular tyrosine kinase. Implicated in the release from host cell mediated by Vpu (By similarity).By similarity
Capsid protein p24 forms the conical core that encapsulates the genomic RNA-nucleocapsid complex in the virion. The core is constituted by capsid protein hexamer subunits. The core is disassembled soon after virion entry. Interaction with host PPIA/CYPA protects the virus from restriction by host TRIM5-alpha and from an unknown antiviral activity in host cells. This capsid restriction by TRIM5 is one of the factors which restricts SIV to the simian species (By similarity).By similarity
Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers. Facilitates rearangement of nucleic acid secondary structure during retrotranscription of genomic RNA. This capability is referred to as nucleic acid chaperone activity (By similarity).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. 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 annotation
Reverse transcriptase/ribonuclease H (RT) 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 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 can probably 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).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 SIV genome, a 5 bp duplication of host DNA is produced at the ends of SIV integration. Alternatively, Integrase may catalyze the excision of viral DNA just after strand transfer, this is termed disintegration (By similarity).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.
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid.
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).PROSITE-ProRule annotation

Cofactori

Binds 2 magnesium ions for reverse transcriptase polymerase activity.By similarity
Binds 2 magnesium ions for ribonuclease H (RNase H) activity. Substrate-binding is a precondition for magnesium binding (By similarity).By similarity
Magnesium ions for integrase activity. Binds at least 1, maybe 2 magnesium ions (By similarity).By similarity

Enzyme regulationi

The viral protease is inhibited by many synthetic protease inhibitors (PIs), such as amprenavir, atazanavir, indinavir, loprinavir, nelfinavir, ritonavir and saquinavir. 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. Use of protease inhibitors in tritherapy regimens permit more ambitious therapeutic strategies.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei135 – 1362Cleavage; by viral proteaseBy similarity
Sitei364 – 3652Cleavage; by viral proteaseBy similarity
Sitei433 – 4342Cleavage; by viral proteaseBy similarity
Sitei500 – 5012Cleavage; by viral proteaseBy similarity
Active sitei522 – 5221For protease activity; shared with dimeric partnerPROSITE-ProRule annotation
Sitei596 – 5972Cleavage; by viral proteaseBy similarity
Metal bindingi706 – 7061Magnesium; catalytic; for reverse transcriptase activityBy similarity
Metal bindingi781 – 7811Magnesium; catalytic; for reverse transcriptase activityBy similarity
Metal bindingi782 – 7821Magnesium; catalytic; for reverse transcriptase activityBy similarity
Sitei996 – 9961Essential for RT p66/p51 heterodimerizationBy similarity
Sitei1009 – 10091Essential for RT p66/p51 heterodimerizationBy similarity
Sitei1035 – 10362Cleavage; by viral proteaseBy similarity
Metal bindingi1038 – 10381Magnesium; catalytic; for RNase H activityBy similarity
Metal bindingi1073 – 10731Magnesium; catalytic; for RNase H activityBy similarity
Metal bindingi1093 – 10931Magnesium; catalytic; for RNase H activityBy similarity
Metal bindingi1144 – 11441Magnesium; catalytic; for RNase H activityBy similarity
Sitei1155 – 11562Cleavage; by viral proteaseBy similarity
Metal bindingi1219 – 12191Magnesium; catalytic; for integrase activityBy similarity
Metal bindingi1271 – 12711Magnesium; catalytic; for integrase activityBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri391 – 40818CCHC-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri412 – 42918CCHC-type 2PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri1158 – 119942Integrase-typePROSITE-ProRule annotationAdd
BLAST
DNA bindingi1378 – 142548Integrase-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. RNA binding Source: UniProtKB-KW
  6. RNA-directed DNA polymerase activity Source: UniProtKB-KW
  7. RNA-DNA hybrid ribonuclease activity Source: InterPro
  8. structural molecule activity Source: InterPro
  9. 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. suppression by virus of host gene expression Source: UniProtKB-KW
  5. viral entry into host cell Source: UniProtKB-KW
  6. viral penetration into host nucleus Source: UniProtKB-KW
  7. 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

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, Viral genome integration, Viral penetration into host nucleus, Virion maturation, Virus entry into host cell, Virus exit from host cell

Keywords - Ligandi

DNA-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 9 chains:
Matrix protein p17
Short name:
MA
Capsid protein p24
Short name:
CA
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
OrganismiSimian immunodeficiency virus (isolate Mm142-83) (SIV-mac) (Simian immunodeficiency virus rhesus monkey)
Taxonomic identifieri11733 [NCBI]
Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeLentivirusPrimate lentivirus group
Virus hostiCercopithecidae (Old World monkeys) [TaxID: 9527]
ProteomesiUP000007220: Genome

Subcellular locationi

Chain Matrix protein p17 : Virion Curated. Host nucleus By similarity. Host cytoplasm By similarity. Host cell membrane Curated; Lipid-anchor Curated
Note: Following virus entry, the nuclear localization signal (NLS) of the matrix protein participates with Vpr to the nuclear localization of the viral genome. During virus production, the nuclear export activity of the matrix protein counteracts the NLS to maintain the Gag and Gag-Pol polyproteins in the cytoplasm, thereby directing unspliced RNA to the plasma membrane (By similarity).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 cytoplasm Source: UniProtKB-KW
  2. host cell nucleus Source: UniProtKB-KW
  3. host cell plasma membrane Source: UniProtKB-KW
  4. intracellular Source: GOC
  5. membrane Source: UniProtKB-KW
  6. viral nucleocapsid Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed; by hostBy similarity
Chaini2 – 14481447Gag-Pol polyproteinPRO_0000306035Add
BLAST
Chaini2 – 135134Matrix protein p17By similarityPRO_0000306036Add
BLAST
Chaini136 – 364229Capsid protein p24By similarityPRO_0000306037Add
BLAST
Chaini365 – 43369Nucleocapsid protein p7By similarityPRO_0000306038Add
BLAST
Chaini434 – 50067p6-polSequence AnalysisPRO_0000306039Add
BLAST
Chaini501 – 59696ProteaseBy similarityPRO_0000306040Add
BLAST
Chaini597 – 1155559Reverse transcriptase/ribonuclease HBy similarityPRO_0000306041Add
BLAST
Chaini597 – 1035439p51 RTBy similarityPRO_0000306042Add
BLAST
Chaini1036 – 1155120p15By similarityPRO_0000306043Add
BLAST
Chaini1156 – 1448293IntegraseBy similarityPRO_0000306044Add
BLAST

Amino acid modifications

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

Post-translational modificationi

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.PROSITE-ProRule annotation
Capsid protein p24 is phosphorylated.

Keywords - PTMi

Lipoprotein, Myristate, Phosphoprotein

Interactioni

Subunit structurei

Matrix protein p17 is a trimer. Interacts with gp120. The protease is a homodimer, whose active site consists of two apposed aspartic acid residues. The reverse transcriptase is a 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. The integrase is a homodimer and possibly a homotetramer (By similarity).By similarity

Structurei

Secondary structure

1
1448
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi502 – 5043
Beta strandi507 – 5126
Beta strandi515 – 5217
Beta strandi525 – 5273
Beta strandi540 – 5445
Beta strandi551 – 56313
Beta strandi566 – 57510
Helixi584 – 5896
Beta strandi593 – 5953
Beta strandi1215 – 12239
Beta strandi1226 – 12327
Beta strandi1239 – 12435
Helixi1249 – 126012
Beta strandi1267 – 12693
Helixi1280 – 12889
Beta strandi1291 – 12933
Turni1309 – 13113
Helixi1312 – 13187
Turni1319 – 13224
Beta strandi1323 – 13253
Helixi1327 – 133913
Beta strandi1344 – 13474
Helixi1351 – 136313

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1AZ5X-ray2.00A498-595[»]
1C6VX-ray3.00A/B/C/D1205-1368[»]
1SIVX-ray2.50A/B498-596[»]
1TCWX-ray2.40A/B498-596[»]
1YTIX-ray2.20A498-595[»]
1YTJX-ray2.50A498-595[»]
ProteinModelPortaliP05896.
SMRiP05896. Positions 2-135, 146-352, 383-432, 498-596, 599-1151, 1156-1201, 1210-1368, 1371-1425.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP05896.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini517 – 58670Peptidase A2PROSITE-ProRule annotationAdd
BLAST
Domaini640 – 830191Reverse transcriptasePROSITE-ProRule annotationAdd
BLAST
Domaini1029 – 1152124RNase HPROSITE-ProRule annotationAdd
BLAST
Domaini1209 – 1359151Integrase catalyticPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni823 – 8319RT 'primer grip'By similarity

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi16 – 227Nuclear export signalBy similarity
Motifi26 – 327Nuclear localization signalBy similarity
Motifi993 – 100917Tryptophan repeat motifBy similarityAdd
BLAST

Domaini

The p66 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).By similarity
The tryptophan repeat motif is involved in RT p66/p51 dimerization.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 fingeri391 – 40818CCHC-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri412 – 42918CCHC-type 2PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri1158 – 119942Integrase-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_N_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_N.
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. Align

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: P05896-1) [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
MGARNSVLSG KKADELEKIR LRPGGKKKYM LKHVVWAANE LDRFGLAESL
60 70 80 90 100
LENKEGCQKI LSVLAPLVPT GSENLKSLYN TVCVIWCIHA EEKVKHTEEA
110 120 130 140 150
KQIVQRHLVM ETGTAETMPK TSRPTAPFSG RGGNYPVQQI GGNYTHLPLS
160 170 180 190 200
PRTLNAWVKL IEEKKFGAEV VSGFQALSEG CLPYDINQML NCVGDHQAAM
210 220 230 240 250
QIIRDIINEE AADWDLQHPQ QAPQQGQLRE PSGSDIAGTT STVEEQIQWM
260 270 280 290 300
YRQQNPIPVG NIYRRWIQLG LQKCVRMYNP TNILDVKQGP KEPFQSYVDR
310 320 330 340 350
FYKSLRAEQT DPAVKNWMTQ TLLIQNANPD CKLVLKGLGT NPTLEEMLTA
360 370 380 390 400
CQGVGGPGQK ARLMAEALKE ALAPAPIPFA AAQQKGPRKP IKCWNCGKEG
410 420 430 440 450
HSARQCRAPR RQGCWKCGKM DHVMAKCPNR QAGFFRPWPL GKEAPQFPHG
460 470 480 490 500
SSASGADANC SPRRTSCGSA KELHALGQAA ERKQREALQG GDRGFAAPQF
510 520 530 540 550
SLWRRPVVTA HIEGQPVEVL LDTGADDSIV TGIELGPHYT PKIVGGIGGF
560 570 580 590 600
INTKEYKNVE IEVLGKRIKG TIMTGDTPIN IFGRNLLTAL GMSLNLPIAK
610 620 630 640 650
VEPVKSPLKP GKDGPKLKQW PLSKEKIVAL REICEKMEKD GQLEEAPPTN
660 670 680 690 700
PYNTPTFAIK KKDKNKWRML IDFRELNRVT QDFTEVQLGI PHPAGLAKRK
710 720 730 740 750
RITVLDIGDA YFSIPLDEEF RQYTAFTLPS VNNAEPGKRY IYKVLPQGWK
760 770 780 790 800
GSPAIFQYTM RHVLEPFRKA NPDVTLVQYM DDILIASDRT DLEHDRVVLQ
810 820 830 840 850
LKELLNSIGF SSPEEKFQKD PPFQWMGYEL WPTKWKLQKI ELPQRETWTV
860 870 880 890 900
NDIQKLVGVL NWAAQIYPGI KTKHLCRLIR GKMTLTEEVQ WTEMAEAEYE
910 920 930 940 950
ENKIILSQEQ EGCYYQESKP LEATVIKSQD NQWSYKIHQE DKILKVGKFA
960 970 980 990 1000
KIKNTHTNGV RLLAHVIQKI GKEAIVIWGQ VPKFHLPVEK DVWEQWWTDY
1010 1020 1030 1040 1050
WQVTWIPEWD FISTPPLVRL VFNLVKDPIE GEETYYVDGS CSKQSKEGKA
1060 1070 1080 1090 1100
GYITDRGKDK VKVLEQTTNQ QAELEAFLMA LTDSGPKANI IVDSQYVMGI
1110 1120 1130 1140 1150
ITGCPTESES RLVNQIIEEM IKKTEIYVAW VPAHKGIGGN QEIDHLVSQG
1160 1170 1180 1190 1200
IRQVLFLEKI EPAQEEHSKY HSNIKELVFK FGLPRLVAKQ IVDTCDKCHQ
1210 1220 1230 1240 1250
KGEAIHGQVN SDLGTWQMDC THLEGKIVIV AVHVASGFIE AEVIPQETGR
1260 1270 1280 1290 1300
QTALFLLKLA SRWPITHLHT DNGANFASQE VKMVAWWAGI EHTFGVPYNP
1310 1320 1330 1340 1350
QSQGVVEAMN HHLKNQIDRI REQANSVETI VLMAVHCMNF KRRGGIGDMT
1360 1370 1380 1390 1400
PAERLINMIT TEQEIQFQQS KNSKFKNFRV YYREGRDQLW KGPGELLWKG
1410 1420 1430 1440
EGAVILKVGT DIKVVPRRKA KIIKDYGGGK EMDSSSHMED TGEAREVA

Note: Produced by -1 ribosomal frameshifting.

Length:1,448
Mass (Da):163,372
Last modified:October 2, 2007 - v2
Checksum:i460D13331B3E68E5
GO
Isoform Gag polyprotein (identifier: P05894-1) [UniParc]FASTAAdd to Basket

The sequence of this isoform can be found in the external entry P05894.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Note: Produced by conventional translation.

Length:506
Mass (Da):56,436
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
Y00277 Genomic DNA. Translation: CAA68380.1.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
Y00277 Genomic DNA. Translation: CAA68380.1 .

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1AZ5 X-ray 2.00 A 498-595 [» ]
1C6V X-ray 3.00 A/B/C/D 1205-1368 [» ]
1SIV X-ray 2.50 A/B 498-596 [» ]
1TCW X-ray 2.40 A/B 498-596 [» ]
1YTI X-ray 2.20 A 498-595 [» ]
1YTJ X-ray 2.50 A 498-595 [» ]
ProteinModelPortali P05896.
SMRi P05896. Positions 2-135, 146-352, 383-432, 498-596, 599-1151, 1156-1201, 1210-1368, 1371-1425.
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Protocols and materials databases

Structural Biology Knowledgebase Search...

Miscellaneous databases

EvolutionaryTracei P05896.

Family and domain databases

Gene3Di 1.10.10.200. 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.
InterProi IPR001969. 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_N_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_N.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR000477. RT_dom.
IPR010659. RVT_connect.
IPR010661. RVT_thumb.
IPR001878. Znf_CCHC.
[Graphical view ]
Pfami PF00540. 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 ]
PRINTSi PR00234. HIV1MATRIX.
SMARTi SM00343. ZnF_C2HC. 2 hits.
[Graphical view ]
SUPFAMi SSF46919. 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.
PROSITEi PS50175. 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 ]
ProtoNeti Search...

Publicationsi

  1. "Sequence of simian immunodeficiency virus from macaque and its relationship to other human and simian retroviruses."
    Chakrabarti L., Guyader M., Alizon M., Daniel M.D., Desrosiers R.C., Tiollais P., Sonigo P.
    Nature 328:543-547(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Domain flexibility in retroviral proteases: structural implications for drug resistant mutations."
    Rose R.B., Craik C.S., Stroud R.M.
    Biochemistry 37:2607-2621(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 498-595.

Entry informationi

Entry nameiPOL_SIVM1
AccessioniPrimary (citable) accession number: P05896
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1988
Last sequence update: October 2, 2007
Last modified: October 29, 2014
This is version 138 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

This is a macaque isolate.
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

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