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P19028

- POL_FIVSD

UniProt

P19028 - POL_FIVSD

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Protein

Pol polyprotein

Gene

pol

Organism
Feline immunodeficiency virus (strain San Diego) (FIV)
Status
Reviewed - 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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei68 – 681For protease activityPROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri848 – 88942Integrase-typePROSITE-ProRule annotationAdd
BLAST
DNA bindingi1067 – 111549Integrase-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

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
OrganismiFeline immunodeficiency virus (strain San Diego) (FIV)
Taxonomic identifieri11675 [NCBI]
Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeLentivirusFeline lentivirus group
Virus hostiFelidae (cat family) [TaxID: 9681]

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 154154ProteaseBy similarityPRO_0000038845Add
BLAST
Chaini155 – 710556Reverse transcriptase/ribonuclease HBy similarityPRO_0000038846Add
BLAST
Chaini711 – 843133Deoxyuridine 5'-triphosphate nucleotidohydrolaseBy similarityPRO_0000038847Add
BLAST
Chaini844 – 1124281IntegraseBy similarityPRO_0000038848Add
BLAST

Post-translational modificationi

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

Structurei

3D structure databases

ProteinModelPortaliP19028.
SMRiP19028. Positions 42-154, 711-843.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini63 – 14482Peptidase A2PROSITE-ProRule annotationAdd
BLAST
Domaini200 – 389190Reverse transcriptasePROSITE-ProRule annotationAdd
BLAST
Domaini592 – 712121RNase HPROSITE-ProRule annotationAdd
BLAST
Domaini899 – 1049151Integrase 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 fingeri848 – 88942Integrase-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.
IPR008181. dUTPase_1.
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.
TIGRFAMsiTIGR00576. dut. 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.
PS50876. ZF_INTEGRASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P19028-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
KKFGKLEGGA SCSPSESSAA NSNAICTSNG GKIIGFINYN KVGTTTSLEK
60 70 80 90 100
RPEILIFVNG YPIKFLLDTG ADITILNRRD FQVKNSIENG RQNMIGVGGG
110 120 130 140 150
KRGTNYINVH LEIRDENYKT QCIFGNVCVL EDNSLIQPLL GRDNMIKFNI
160 170 180 190 200
RLVMAQISDK IPIVKVKMKD PNKGPQIKQW PLSNEKIEAL TEIVERLERE
210 220 230 240 250
GKVKRADPNN PWNTPVFAIK KKSGKWRMLI DFRELNKLTE KGAEVQLGLP
260 270 280 290 300
HPAGLQMKKQ ITVLDIGDAY FTNPLDPDYA PYTAFTLPRK NNAGPGRRFV
310 320 330 340 350
WCSLPQGWIL SPLIYQSTLD NIIQPFIRQN PQLDIYQYMD DIYIGSNLSK
360 370 380 390 400
KEHKEKVEEL RKLLLWWGFE TPEDKLQEEP PYKWMGYELH PLTWTIQQKQ
410 420 430 440 450
LEIPEKPTLN ELQKLAGKIN WASQTIPELS IKSLTNMTRG NQNLNSTREW
460 470 480 490 500
TEEARLEVQK AKRAIEEQVQ LGYYDPSKEL YAKLSLVGPH QISYQVYQKC
510 520 530 540 550
PEKILWYGKM SRQKKKAENT CDIALRACYK IREESIIRIG KEPRYEIPTS
560 570 580 590 600
REAWESNLIN SPYLKAPPPE VDYIHAALNI KRALSMIKDP PISGAETWYI
610 620 630 640 650
DGGRKLGKAA KAAYWTDTGK WQVMELEGSN QKAEIQALLL ALKAGPEEMN
660 670 680 690 700
IITDSQYMIN ILSQQPDKME GIWQEVLEEL EKKTAIFIDW VPGHKGIPGN
710 720 730 740 750
EEVDKLCQTM MIIEGDGILD KRTEDAGYDL LAAKEIHLLP GEVKVIPTGV
760 770 780 790 800
KLMLPKGHWG LIMGKSSIGS KGLDVLGGVI DEGYRGEIGV IMINLSKKSI
810 820 830 840 850
TLLEQQKIAQ LIILPHKHEA LEQGKVVMDS ERGEKGYGST GVFSSWVDRI
860 870 880 890 900
EEAETNHEKF HSDPQYLRTE FNLPKMVAEE IRRKCPVCRI RGEQVGGQLK
910 920 930 940 950
IGPGIWQMDC THFDGKIILV AIHVESGYIW AQIISQETAD CTVKAVLQLL
960 970 980 990 1000
SAHIVTELQT DNGPNFKNQK MEGVLNYMGV KHKFGIPGNP QSQALVENVN
1010 1020 1030 1040 1050
QTLKVWVHKF LPETTSLDNA LALAVHCLNF KQRGRIGGMA PYELLAQQES
1060 1070 1080 1090 1100
LRIQDYFSAI PQKLQAQWIY YKDQKDKKWK GPMRVEYWGQ GSVLLKDEEK
1110 1120
GYFLIPRRHV KRVPEPCALP EGDE
Length:1,124
Mass (Da):127,605
Last modified:November 1, 1990 - v1
Checksum:i1A4706685CFDA8CF
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M36968 Genomic RNA. Translation: AAA43076.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M36968 Genomic RNA. Translation: AAA43076.1 .

3D structure databases

ProteinModelPortali P19028.
SMRi P19028. Positions 42-154, 711-843.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

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.
IPR008181. dUTPase_1.
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.
TIGRFAMsi TIGR00576. dut. 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.
PS50876. ZF_INTEGRASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Comparison of two host cell range variants of feline immunodeficiency virus."
    Phillips T.R., Talbott R.L., Lamont C., Muir S., Lovelace K.M., Elder J.H.
    J. Virol. 64:4605-4613(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
    Strain: Isolate PPR.

Entry informationi

Entry nameiPOL_FIVSD
AccessioniPrimary (citable) accession number: P19028
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1990
Last sequence update: November 1, 1990
Last modified: October 29, 2014
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

Caution

The N-terminus of the polypeptide is uncertain.Curated

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

External Data

Dasty 3