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P35956

- POL_VILVK

UniProt

P35956 - POL_VILVK

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Protein

Pol polyprotein

Gene

pol

Organism
Maedi visna virus (strain KV1772) (MVV) (Visna lentivirus)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

During replicative cycle of retroviruses, the reverse-transcribed viral DNA is integrated into the host chromosome by the viral integrase enzyme. RNase H activity is associated with the reverse transcriptase.

Catalytic activityi

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.
dUTP + H2O = dUMP + diphosphate.
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).PROSITE-ProRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei59 – 591PROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri823 – 86442Integrase-typePROSITE-ProRule annotationAdd
BLAST
DNA bindingi1042 – 109453Integrase-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. aspartic-type endopeptidase activity Source: UniProtKB-KW
  2. DNA binding Source: UniProtKB-KW
  3. dUTP diphosphatase activity Source: UniProtKB-EC
  4. exoribonuclease H activity Source: UniProtKB-EC
  5. RNA-directed DNA polymerase activity Source: UniProtKB-KW
  6. RNA-DNA hybrid ribonuclease activity Source: InterPro
  7. zinc ion binding Source: InterPro

GO - Biological processi

  1. DNA integration Source: UniProtKB-KW
  2. DNA recombination Source: UniProtKB-KW
  3. dUTP metabolic process Source: InterPro
  4. establishment of integrated proviral latency Source: UniProtKB-KW
  5. viral entry into host cell Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Aspartyl protease, Endonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Protease, RNA-directed DNA polymerase, Transferase

Keywords - Biological processi

DNA integration, DNA recombination, Nucleotide metabolism, Viral genome integration, Virus entry into host cell

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Protein family/group databases

MEROPSiA02.006.

Names & Taxonomyi

Protein namesi
Recommended name:
Pol polyprotein
Cleaved into the following 4 chains:
Alternative name(s):
Retropepsin
Alternative name(s):
Exoribonuclease H (EC:3.1.13.2)
Integrase
Short name:
IN
Gene namesi
Name:pol
OrganismiMaedi visna virus (strain KV1772) (MVV) (Visna lentivirus)
Taxonomic identifieri36374 [NCBI]
Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeLentivirusOvine/caprine lentivirus group
Virus hostiOvis aries (Sheep) [TaxID: 9940]

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 135135ProteaseBy similarityPRO_0000038869Add
BLAST
Chaini136 – 686551Reverse transcriptase/ribonuclease HBy similarityPRO_0000038870Add
BLAST
Chaini687 – 820134Deoxyuridine 5'-triphosphate nucleotidohydrolaseBy similarityPRO_0000038871Add
BLAST
Chaini821 – 1101281IntegraseBy similarityPRO_0000038872Add
BLAST

Post-translational modificationi

Cleavage sites that yield the mature proteins remain to be determined.

Structurei

Secondary structure

1
1101
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi825 – 83511Combined sources
Helixi839 – 8457Combined sources
Helixi850 – 8578Combined sources
Helixi861 – 8644Combined sources
Beta strandi882 – 8909Combined sources
Beta strandi893 – 9008Combined sources
Turni901 – 9033Combined sources
Beta strandi906 – 9127Combined sources
Helixi916 – 93015Combined sources
Beta strandi934 – 9374Combined sources
Helixi941 – 9444Combined sources
Helixi946 – 95510Combined sources
Beta strandi958 – 9625Combined sources
Helixi967 – 98721Combined sources
Helixi988 – 9903Combined sources
Helixi994 – 100613Combined sources
Turni1012 – 10143Combined sources
Helixi1017 – 103216Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3HPGX-ray3.28A/B/C/D/E/F823-1039[»]
3HPHX-ray2.64A/B/C/D823-1039[»]
ProteinModelPortaliP35956.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP35956.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini54 – 12572Peptidase A2PROSITE-ProRule annotationAdd
BLAST
Domaini182 – 371190Reverse transcriptasePROSITE-ProRule annotationAdd
BLAST
Domaini566 – 688123RNase HPROSITE-ProRule annotationAdd
BLAST
Domaini865 – 1025161Integrase catalyticPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the retroviral Pol polyprotein family.Curated
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 fingeri823 – 86442Integrase-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Family and domain databases

Gene3Di1.10.10.200. 1 hit.
2.30.30.10. 1 hit.
2.40.70.10. 1 hit.
2.70.40.10. 1 hit.
3.30.420.10. 2 hits.
InterProiIPR001969. Aspartic_peptidase_AS.
IPR029054. dUTPase-like.
IPR008180. dUTPase/dCTP_deaminase.
IPR001037. Integrase_C_retrovir.
IPR001584. Integrase_cat-core.
IPR017856. Integrase_Zn-bd_dom-like_N.
IPR003308. Integrase_Zn-bd_dom_N.
IPR018061. Pept_A2A_retrovirus_sg.
IPR001995. Peptidase_A2_cat.
IPR021109. Peptidase_aspartic_dom.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR000477. RT_dom.
IPR010659. RVT_connect.
IPR010661. RVT_thumb.
[Graphical view]
PfamiPF00692. dUTPase. 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.
[Graphical view]
SUPFAMiSSF46919. SSF46919. 1 hit.
SSF50122. SSF50122. 1 hit.
SSF50630. SSF50630. 1 hit.
SSF51283. SSF51283. 1 hit.
SSF53098. SSF53098. 2 hits.
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.
PS50876. ZF_INTEGRASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P35956-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MPSLWKKRTY AKGLPAEETA GKQQEGATCG AVRAPYVVTE APPKIEIKVG
60 70 80 90 100
TRWKKLLVDT GADKTIVTSH DMSGIPKGRI ILQGIGGIIE GEKWEQVHLQ
110 120 130 140 150
YKDKIIRGTI VVLATSPVEV LGRDNMRELG IGLIMANLEE KKIPSTRVRL
160 170 180 190 200
KEGCKGPHIA QWPLTQEKLE GLKEIVDRLE KEGKVGRAPP HWTCNTPIFC
210 220 230 240 250
IKKKSGKWRM LIDFRELNKQ TEDLAEAQLG LPHPGGLQRK KHVTILDIGD
260 270 280 290 300
AYFTIPLYEP YRQYTCFTML SPNNLGPCVR YYWKVLPQGW KLSPAVYQFT
310 320 330 340 350
MQKILRGWIE EHPMIQFGIY MDDIYIGSDL GLEEHRGIVN ELASYIAQYG
360 370 380 390 400
FMLPEDKRQE GYPAKWLGFE LHPEKWKFQK HTLPEITEGP ITLNKLQKLV
410 420 430 440 450
GDLVWRQSLI GKSIPNILKL MEGDRALQSE RYIESIHVRE WEACRQKLKE
460 470 480 490 500
MEGNYYDEEK DIYGQLDWGN KAIEYIVFQE KGKPLWVNVV HSIKNLSQAQ
510 520 530 540 550
QIIKAAQKLT QEVIIRTGKI PWILLPGREE DWILELQMGN INWMPSFWSC
560 570 580 590 600
YKGSVRWKKR NVIAEVVPGP TYYTDGGKKN GRGSLGYITS TGEKFRIHEE
610 620 630 640 650
GTNQQLELRA IEEACKQGPE KMNIVTDSRY AYEFMLRNWD EEVIRNPIQA
660 670 680 690 700
RIMELVHNKE KIGVHWVPGH KGIPQNEEID RYISEIFLAK EGRGILQKRA
710 720 730 740 750
EDAGYDLICP QEISIPAGQV KRIAIDLKIN LKKDQWAMIG TKSSFANKGV
760 770 780 790 800
FVQGGIIDSG YQGTIQVVIY NSNNKEVVIP QGRKFAQLIL MPLIHEELEP
810 820 830 840 850
WGETRKTERG EQGFGSTGMY WIENIPLAEE EHNKWHQDAV SLHLEFGIPR
860 870 880 890 900
TAAEDIVQQC DVCQENKMPS TLRGSNKRGI DHWQVDYTHY EDKIILVWVE
910 920 930 940 950
TNSGLIYAER VKGETGQEFR VQTMKWYAMF APKSLQSDNG PAFVAESTQL
960 970 980 990 1000
LMKYLGIEHT TGIPWNPQSQ ALVERTHQTL KNTLEKLIPM FNAFESALAG
1010 1020 1030 1040 1050
TLITLNIKRK GGLGTSPMDI FIFNKEQQRI QQQSKSKQEK IRFCYYRTRK
1060 1070 1080 1090 1100
RGHPGEWQGP TQVLWGGDGA IVVKDRGTDR YLVIANKDVK FIPPPKEIQK

E
Length:1,101
Mass (Da):126,178
Last modified:June 1, 1994 - v1
Checksum:iAB955654847267CF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L06906 Genomic RNA. Translation: AAA48359.1.
S55323 Genomic DNA. Translation: AAB25460.1.
RefSeqiNP_040840.1. NC_001452.1.

Genome annotation databases

GeneIDi1490013.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L06906 Genomic RNA. Translation: AAA48359.1 .
S55323 Genomic DNA. Translation: AAB25460.1 .
RefSeqi NP_040840.1. NC_001452.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3HPG X-ray 3.28 A/B/C/D/E/F 823-1039 [» ]
3HPH X-ray 2.64 A/B/C/D 823-1039 [» ]
ProteinModelPortali P35956.
ModBasei Search...
MobiDBi Search...

Protein family/group databases

MEROPSi A02.006.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 1490013.

Miscellaneous databases

EvolutionaryTracei P35956.

Family and domain databases

Gene3Di 1.10.10.200. 1 hit.
2.30.30.10. 1 hit.
2.40.70.10. 1 hit.
2.70.40.10. 1 hit.
3.30.420.10. 2 hits.
InterProi IPR001969. Aspartic_peptidase_AS.
IPR029054. dUTPase-like.
IPR008180. dUTPase/dCTP_deaminase.
IPR001037. Integrase_C_retrovir.
IPR001584. Integrase_cat-core.
IPR017856. Integrase_Zn-bd_dom-like_N.
IPR003308. Integrase_Zn-bd_dom_N.
IPR018061. Pept_A2A_retrovirus_sg.
IPR001995. Peptidase_A2_cat.
IPR021109. Peptidase_aspartic_dom.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR000477. RT_dom.
IPR010659. RVT_connect.
IPR010661. RVT_thumb.
[Graphical view ]
Pfami PF00692. dUTPase. 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.
[Graphical view ]
SUPFAMi SSF46919. SSF46919. 1 hit.
SSF50122. SSF50122. 1 hit.
SSF50630. SSF50630. 1 hit.
SSF51283. SSF51283. 1 hit.
SSF53098. SSF53098. 2 hits.
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.
PS50876. ZF_INTEGRASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Nucleotide sequence and biological properties of a pathogenic proviral molecular clone of neurovirulent visna virus."
    Andresson O.S., Elser J.E., Tobin G.J., Greenwood J.D., Gonda M.A., Georgsson G., Andresdottir V., Benediktsdottir E., Carlsdottir H.M., Maentylae E.O., Rafnar B., Palsson P.A., Casey J.W., Petursson G.
    Virology 193:89-105(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

Entry informationi

Entry nameiPOL_VILVK
AccessioniPrimary (citable) accession number: P35956
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: June 1, 1994
Last modified: November 26, 2014
This is version 115 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

This protein may be synthesized as a Gag-Pol polyprotein.

Keywords - Technical termi

3D-structure, 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