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Protein

Pol polyprotein

Gene

pol

Organism
Maedi visna virus (strain 1514 / clone LV1-1KS1) (MVV) (Visna lentivirus)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Protein inferred from homologyi

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 sitei63PROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri827 – 868Integrase-typePROSITE-ProRule annotationAdd BLAST42
DNA bindingi1046 – 1098Integrase-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

Names & Taxonomyi

Protein namesi
Recommended name:
Pol polyprotein
Cleaved into the following 4 chains:
Alternative name(s):
Retropepsin (EC:3.4.23.-)
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 1514 / clone LV1-1KS1) (MVV) (Visna lentivirus)
Taxonomic identifieri11743 [NCBI]
Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeLentivirusOvine/caprine lentivirus group
Virus hostiOvis aries (Sheep) [TaxID: 9940]

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000388611 – 139ProteaseBy similarityAdd BLAST139
ChainiPRO_0000038862140 – 690Reverse transcriptase/ribonuclease HBy similarityAdd BLAST551
ChainiPRO_0000038863691 – 824Deoxyuridine 5'-triphosphate nucleotidohydrolaseBy similarityAdd BLAST134
ChainiPRO_0000038864825 – 1105IntegraseBy similarityAdd BLAST281

Post-translational modificationi

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

Structurei

3D structure databases

ProteinModelPortaliP23426.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini58 – 129Peptidase A2PROSITE-ProRule annotationAdd BLAST72
Domaini186 – 375Reverse transcriptasePROSITE-ProRule annotationAdd BLAST190
Domaini570 – 692RNase HPROSITE-ProRule annotationAdd BLAST123
Domaini869 – 1029Integrase 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 fingeri827 – 868Integrase-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.

P23426-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
TRNNMPSLWK KRTYAKGLPA EETAGKQQEG ATCGAVRAPY VVTEAPPKIE
60 70 80 90 100
IKVGTRWKKL LVDTGADKTI VTSHDMSGIP KGRIILQGIG GIIEGEKWEQ
110 120 130 140 150
VHLQYKDKII RGTIVVLATS PVEVLGRDNM SELGIGLIMA NLEEKKIPIT
160 170 180 190 200
EVRLKEGCKG PHIAQWPLTQ EKLEGLKEIV DRLEKEGKVG RAPPHWTCNT
210 220 230 240 250
PIFCIKKKSG KWRMLIDFRE LNKQTEDLAE AQLGLPHPGG LQRKKHVTIL
260 270 280 290 300
DIGDAYFTIP LYEPYRQYTC FTMLSPNNLG PCVRYYWKVL PQGWKLSPSV
310 320 330 340 350
YQFTMQKILR GWIEEHPMIQ FGIYMDDIYI GSDLGLEEHR GIVNELASYI
360 370 380 390 400
AQYGFMLPED KRQEGYPAKW LGFELHPEKW KFQKHTLPEI TEGPITLNKL
410 420 430 440 450
QKLVGDLVWR QSLIGKSIPN ILKLMEGDRA LQSERYIESI HVREWEACRQ
460 470 480 490 500
KLKEMEGNYY DEEKDIYGQL DWGNKAIEYI VFQEKGKPLW VNVVHSIKNL
510 520 530 540 550
SQAQQIIKAA QKLTQEVIIR TGKIPWILLP GREEDWILEL QMGNINWMPS
560 570 580 590 600
FWSCYKGSVR WKKRNVIAEV VSGPTYYTDG GKKNGRGSLG YIASTGEKFR
610 620 630 640 650
IYEEGTNQQL ELRAIEEACK QGPEKMNIVT DSRYAYEFML RNWDEEVIRN
660 670 680 690 700
PIQARIMELM HNKEKIGVHW VPGHKGIPQN EEIDRYISEI FLAKEGRGIL
710 720 730 740 750
QKRAEDAGYD LICPQEISIP AGQVKRIAID LKINLKKDQW AMIGTKSSFA
760 770 780 790 800
NKGVFVQGGI IDSGYQGTIQ VVIYNSNNKE VVIPQGRKFA QLILMPLIHE
810 820 830 840 850
ELEPWGETRK TERGEQGFGS TGMYWIENIP LAEEEHNKWH QDAVSLHLEF
860 870 880 890 900
GIPRTAAEDI VQQCDVCQEN KMPSTLRGSN KRGIDHWQVD YTHYEDKIIL
910 920 930 940 950
VWVETNSGLI YAERVKGETG QEFRVQTMKW YAMFAPKSLQ SDNGPAFVAE
960 970 980 990 1000
STQLLMKYLG IEHTTGIPWN PQSQALVERT HQTLKNTLEK LIPMFNAFES
1010 1020 1030 1040 1050
ALAGTLITLN IKRKGGLGTS PMDIFIFNKE QQRIQQQSKS KQEKIRFCYY
1060 1070 1080 1090 1100
RTRKRGHPGE WQGPTQVLWG GDGAIVVKDR GTDRYLVIAN KDVKFIPPPK

EIQKE
Length:1,105
Mass (Da):126,628
Last modified:November 1, 1991 - v1
Checksum:i3CD012675D163839
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M60609 Unassigned RNA. Translation: AAA17524.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M60609 Unassigned RNA. Translation: AAA17524.1.

3D structure databases

ProteinModelPortaliP23426.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

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_VILV1
AccessioniPrimary (citable) accession number: P23426
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1991
Last sequence update: November 1, 1991
Last modified: September 7, 2016
This is version 118 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

Multifunctional enzyme

Documents

  1. Peptidase families
    Classification of peptidase families and list of entries
  2. 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.