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Protein

Gag-Pol polyprotein

Gene

gag-pol

Organism
Simian immunodeficiency virus (isolate PBj14/BCL-3) (SIV-sm) (Simian immunodeficiency virus sooty mangabey monkey)
Status
Reviewed-Annotation score: 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

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

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)DescriptionActionsGraphical viewLength
Sitei222 – 223Cis/trans isomerization of proline peptide bond; by human PPIA/CYPABy similarity2
Active sitei523For protease activity; shared with dimeric partnerPROSITE-ProRule annotation1
Metal bindingi707Magnesium; catalytic; for reverse transcriptase activityBy similarity1
Metal bindingi782Magnesium; catalytic; for reverse transcriptase activityBy similarity1
Metal bindingi783Magnesium; catalytic; for reverse transcriptase activityBy similarity1
Sitei997Essential for RT p66/p51 heterodimerizationBy similarity1
Sitei1010Essential for RT p66/p51 heterodimerizationBy similarity1
Metal bindingi1039Magnesium; catalytic; for RNase H activityBy similarity1
Metal bindingi1074Magnesium; catalytic; for RNase H activityBy similarity1
Metal bindingi1094Magnesium; catalytic; for RNase H activityBy similarity1
Metal bindingi1145Magnesium; catalytic; for RNase H activityBy similarity1
Metal bindingi1220Magnesium; catalytic; for integrase activityBy similarity1
Metal bindingi1272Magnesium; catalytic; for integrase activityBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri392 – 409CCHC-type 1PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri413 – 430CCHC-type 2PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri1159 – 1200Integrase-typePROSITE-ProRule annotationAdd BLAST42
DNA bindingi1379 – 1426Integrase-typePROSITE-ProRule annotationAdd BLAST48

GO - Molecular functioni

GO - Biological processi

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 (EC:2.7.7.-By similarity, EC:3.1.-.-By similarity)
Short name:
IN
Gene namesi
Name:gag-pol
OrganismiSimian immunodeficiency virus (isolate PBj14/BCL-3) (SIV-sm) (Simian immunodeficiency virus sooty mangabey monkey)
Taxonomic identifieri11738 [NCBI]
Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeLentivirusPrimate lentivirus group
Virus hostiCercopithecidae (Old World monkeys) [TaxID: 9527]
Proteomesi
  • UP000007221 Componenti: Genome

Subcellular locationi

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
Integrase :

GO - Cellular componenti

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)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved; by hostBy similarity
ChainiPRO_00003060652 – 1449Gag-Pol polyproteinAdd BLAST1448
ChainiPRO_00003060662 – 135Matrix protein p17By similarityAdd BLAST134
ChainiPRO_0000306067136 – 365Capsid protein p24By similarityAdd BLAST230
ChainiPRO_0000306068366 – 434Nucleocapsid protein p7By similarityAdd BLAST69
ChainiPRO_0000306069435 – 501p6-polSequence analysisAdd BLAST67
ChainiPRO_0000306070502 – 597ProteaseBy similarityAdd BLAST96
ChainiPRO_0000306071598 – 1156Reverse transcriptase/ribonuclease HBy similarityAdd BLAST559
ChainiPRO_0000306072598 – 1036p51 RTBy similarityAdd BLAST439
ChainiPRO_00003060731037 – 1156p15By similarityAdd BLAST120
ChainiPRO_00003060741157 – 1449IntegraseBy similarityAdd BLAST293

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Lipidationi2N-myristoyl glycine; by hostBy similarity1

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.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei135 – 136Cleavage; by viral proteaseBy similarity2
Sitei365 – 366Cleavage; by viral proteaseBy similarity2
Sitei434 – 435Cleavage; by viral proteaseBy similarity2
Sitei501 – 502Cleavage; by viral proteaseBy similarity2
Sitei597 – 598Cleavage; by viral proteaseBy similarity2
Sitei1036 – 1037Cleavage; by viral proteaseBy similarity2
Sitei1156 – 1157Cleavage; by viral proteaseBy similarity2

Keywords - PTMi

Lipoprotein, Myristate, Phosphoprotein

Proteomic databases

PRIDEiP19505.

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

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JTSX-ray2.80C/F/I71-79[»]
ProteinModelPortaliP19505.
SMRiP19505.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini518 – 587Peptidase A2PROSITE-ProRule annotationAdd BLAST70
Domaini641 – 831Reverse transcriptasePROSITE-ProRule annotationAdd BLAST191
Domaini1030 – 1153RNase HPROSITE-ProRule annotationAdd BLAST124
Domaini1210 – 1360Integrase catalyticPROSITE-ProRule annotationAdd BLAST151

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni824 – 832RT 'primer grip'By similarity9

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi16 – 22Nuclear export signalBy similarity7
Motifi26 – 32Nuclear localization signalBy similarity7
Motifi994 – 1010Tryptophan repeat motifBy similarityAdd BLAST17

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)DescriptionActionsGraphical viewLength
Zinc fingeri392 – 409CCHC-type 1PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri413 – 430CCHC-type 2PROSITE-ProRule annotationAdd BLAST18
Zinc fingeri1159 – 1200Integrase-typePROSITE-ProRule annotationAdd BLAST42

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.
IPR001995. Peptidase_A2_cat.
IPR021109. Peptidase_aspartic_dom.
IPR018061. Retropepsins.
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. 1 hit.
[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: P19505-1) [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 LRPGGKKRYQ LKHIVWAANE LDRFGLAESL
60 70 80 90 100
LENKEGCQKI LSVLAPLVPT GSENLKSLYN TVCVLWCIHA EEKVKHTEEA
110 120 130 140 150
KQIVQRHLVV ETGTADKMPA TSRPTAPPSG KGGNYPVQQI GGNYTHLPLS
160 170 180 190 200
PRTLNAWVKL IEEKKFGAEV VPGFQALSEG CTPYDINQML NCVGEHQAAM
210 220 230 240 250
QIIREIINEE AADWDLQHPQ PGPIPPGQLR EPRGSDIAGT TSTVDEQIQW
260 270 280 290 300
MYRQQNPIPV GNIYRRWIQL GLQKCVRMYN PTNILDVKQG PKEPFQSYVD
310 320 330 340 350
RFYKSLRAEQ TDPAVKNWMT QTLLIQNANP DCKLVLKGLG INPTLEEMLT
360 370 380 390 400
ACQGVGGPGQ KARLMAEALK DALTQGPLPF AAVQQKGQRK IIKCWNCGKE
410 420 430 440 450
GHSARQCRAP RRQGCWKCGK AGHVMAKCPE RQAGFFRAWP MGKEAPQFPH
460 470 480 490 500
GPDASGADTN CSPRGSSCGS TEELHEDGQK AEGEQRETLQ GGNGGFAAPQ
510 520 530 540 550
FSLWRRPIVT AYIEEQPVEV LLDTGADDSI VAGIELGPNY TPKIVGGIGG
560 570 580 590 600
FINTKEYKDV KIKVLGKVIK GTIMTGDTPI NIFGRNLLTA MGMSLNLPIA
610 620 630 640 650
KVEPIKVTLK PGKDGPKLRQ WPLSKEKIIA LREICEKMEK DGQLEEAPPT
660 670 680 690 700
NPYNTPTFAI KKKDKNKWRM LIDFRELNKV TQDFTEVQLG IPHPAGLAKR
710 720 730 740 750
RRITVLDVGD AYFSIPLDEE FRQYTAFTLP SVNNAEPGKR YIYKVLPQGW
760 770 780 790 800
KGSPAIFQHT MRNVLEPFRK ANPDVTLIQY MDDILIASDR TDLEHDRVVL
810 820 830 840 850
QLKELLNSIG FSTPEEKFQK DPPFQWMGYE LWPTKWKLQK IELPQRETWT
860 870 880 890 900
VNDIQKLVGV LNWAAQIYPG IKTKHLCRLI RGKMTLTEEV QWTEMAEAEY
910 920 930 940 950
EENKIILSQE QEGCYYQEGK PLEATVIKSQ DNQWSYKIHQ EDKILKVGKF
960 970 980 990 1000
AKIKNTHTNG VRLLAHVVQK IGKEAIVIWG QVPRFHLPVE REIWEQWWTD
1010 1020 1030 1040 1050
YWQVTWIPEW DFVSTPPLVR LVFNLVKEPI QGAETFYVDG SCNRQSREGK
1060 1070 1080 1090 1100
AGYVTDRGRD KAKLLEQTTN QQAELEAFYL ALADSGPKAN IIVDSQYVMG
1110 1120 1130 1140 1150
IVAGQPTESE SRLVNQIIEE MIKKEAIYVA WVPAHKGIGG NQEVDHLVSQ
1160 1170 1180 1190 1200
GIRQVLFLEK IEPAQEEHEK YHSNVKELVF KFGLPRLVAK QIVDTCDKCH
1210 1220 1230 1240 1250
QKGEAIHGQV NAELGTWQMD CTHLEGKIII VAVHVASGFI EAEVIPQETG
1260 1270 1280 1290 1300
RQTALFLLKL ASRWPITHLH TDNGANFTSQ EVKMVAWWAG IEQTFGVPYN
1310 1320 1330 1340 1350
PQSQGVVEAM NHHLKTQIDR IREQANSIET IVLMAVHCMN FKRRGGIGDM
1360 1370 1380 1390 1400
TPAERLVNMI TTEQEIQFQQ SKNSKFKNFR VYYREGRDQL WKGPGELLWK
1410 1420 1430 1440
GEGAVILKVG TEIKVVPRRK AKIIKDYGGG KELDSGSHLE DTGEAREVA
Note: Produced by -1 ribosomal frameshifting.
Length:1,449
Mass (Da):163,326
Last modified:October 2, 2007 - v2
Checksum:i9552AA34B6D21028
GO
Isoform Gag polyprotein (identifier: P19504-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry P19504.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by conventional translation.
Length:507
Mass (Da):56,667
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M31325 Genomic RNA. Translation: AAA47753.1.
L03298 Genomic RNA. Translation: AAA47777.1.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M31325 Genomic RNA. Translation: AAA47753.1.
L03298 Genomic RNA. Translation: AAA47777.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JTSX-ray2.80C/F/I71-79[»]
ProteinModelPortaliP19505.
SMRiP19505.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiP19505.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

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.
IPR001995. Peptidase_A2_cat.
IPR021109. Peptidase_aspartic_dom.
IPR018061. Retropepsins.
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. 1 hit.
[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.
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Entry informationi

Entry nameiPOL_SIVSP
AccessioniPrimary (citable) accession number: P19505
Secondary accession number(s): Q88140
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1991
Last sequence update: October 2, 2007
Last modified: November 30, 2016
This is version 141 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

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

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 one 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.