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Protein

Pol polyprotein

Gene

pol

Organism
Maedi visna virus (strain KV1772) (MVV) (Visna lentivirus)
Status
Reviewed-Annotation score: 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)DescriptionActionsGraphical viewLength
Active sitei59PROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri823 – 864Integrase-typePROSITE-ProRule annotationAdd BLAST42
DNA bindingi1042 – 1094Integrase-typePROSITE-ProRule annotationAdd BLAST53

GO - Molecular functioni

GO - Biological processi

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 (EC:2.7.7.-By similarity, EC:3.1.-.-By similarity)
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)DescriptionActionsGraphical viewLength
ChainiPRO_00000388691 – 135ProteaseBy similarityAdd BLAST135
ChainiPRO_0000038870136 – 686Reverse transcriptase/ribonuclease HBy similarityAdd BLAST551
ChainiPRO_0000038871687 – 820Deoxyuridine 5'-triphosphate nucleotidohydrolaseBy similarityAdd BLAST134
ChainiPRO_0000038872821 – 1101IntegraseBy similarityAdd BLAST281

Post-translational modificationi

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

Structurei

Secondary structure

11101
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi825 – 835Combined sources11
Helixi839 – 845Combined sources7
Helixi850 – 857Combined sources8
Helixi861 – 864Combined sources4
Beta strandi882 – 890Combined sources9
Beta strandi893 – 900Combined sources8
Turni901 – 903Combined sources3
Beta strandi906 – 912Combined sources7
Helixi916 – 930Combined sources15
Beta strandi934 – 937Combined sources4
Helixi941 – 944Combined sources4
Helixi946 – 955Combined sources10
Beta strandi958 – 962Combined sources5
Helixi967 – 987Combined sources21
Helixi988 – 990Combined sources3
Helixi994 – 1006Combined sources13
Turni1012 – 1014Combined sources3
Helixi1017 – 1032Combined sources16

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3HPGX-ray3.28A/B/C/D/E/F823-1039[»]
3HPHX-ray2.64A/B/C/D823-1039[»]
ProteinModelPortaliP35956.
SMRiP35956.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP35956.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini54 – 125Peptidase A2PROSITE-ProRule annotationAdd BLAST72
Domaini182 – 371Reverse transcriptasePROSITE-ProRule annotationAdd BLAST190
Domaini566 – 688RNase HPROSITE-ProRule annotationAdd BLAST123
Domaini865 – 1025Integrase catalyticPROSITE-ProRule annotationAdd BLAST161

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)DescriptionActionsGraphical viewLength
Zinc fingeri823 – 864Integrase-typePROSITE-ProRule annotationAdd BLAST42

Keywords - Domaini

Zinc-finger

Family and domain databases

CDDicd07557. trimeric_dUTPase. 1 hit.
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.
IPR033704. dUTPase_trimeric.
IPR001037. Integrase_C_retrovir.
IPR001584. Integrase_cat-core.
IPR017856. Integrase_Zn-bd_dom-like_N.
IPR003308. Integrase_Zn-bd_dom_N.
IPR001995. Peptidase_A2_cat.
IPR021109. Peptidase_aspartic_dom.
IPR018061. Retropepsins.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR000477. RT_dom.
IPR010659. RVT_connect.
IPR010661. RVT_thumb.
[Graphical view]
PfamiPF00692. dUTPase. 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.
KEGGivg:1490013.

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.
RefSeqiNP_040840.1. NC_001452.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3HPGX-ray3.28A/B/C/D/E/F823-1039[»]
3HPHX-ray2.64A/B/C/D823-1039[»]
ProteinModelPortaliP35956.
SMRiP35956.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

MEROPSiA02.006.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1490013.
KEGGivg:1490013.

Miscellaneous databases

EvolutionaryTraceiP35956.

Family and domain databases

CDDicd07557. trimeric_dUTPase. 1 hit.
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.
IPR033704. dUTPase_trimeric.
IPR001037. Integrase_C_retrovir.
IPR001584. Integrase_cat-core.
IPR017856. Integrase_Zn-bd_dom-like_N.
IPR003308. Integrase_Zn-bd_dom_N.
IPR001995. Peptidase_A2_cat.
IPR021109. Peptidase_aspartic_dom.
IPR018061. Retropepsins.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR000477. RT_dom.
IPR010659. RVT_connect.
IPR010661. RVT_thumb.
[Graphical view]
PfamiPF00692. dUTPase. 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]
ProtoNetiSearch...

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 2, 2016
This is version 121 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

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.