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P16088

- POL_FIVPE

UniProt

P16088 - POL_FIVPE

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Protein
Pol polyprotein
Gene
pol
Organism
Feline immunodeficiency virus (isolate Petaluma) (FIV)
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).

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei68 – 681For protease activity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri848 – 88942Integrase-type
Add
BLAST
DNA bindingi1067 – 111549Integrase-type
Add
BLAST

GO - Molecular functioni

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

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 (EC:3.4.23.-)
Alternative name(s):
Exoribonuclease H (EC:3.1.13.2)
Integrase
Short name:
IN
Gene namesi
Name:pol
OrganismiFeline immunodeficiency virus (isolate Petaluma) (FIV)
Taxonomic identifieri11674 [NCBI]
Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeLentivirusFeline lentivirus group
Virus hostiFelidae (cat family) [TaxID: 9681]

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 154154Protease
PRO_0000038841Add
BLAST
Chaini155 – 690536Reverse transcriptase/ribonuclease H
PRO_0000038842Add
BLAST
Chaini691 – 843153Deoxyuridine 5'-triphosphate nucleotidohydrolase
PRO_0000038843Add
BLAST
Chaini844 – 1124281Integrase
PRO_0000038844Add
BLAST

Post-translational modificationi

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

Proteomic databases

PRIDEiP16088.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi48 – 503
Beta strandi53 – 586
Beta strandi61 – 677
Beta strandi71 – 733
Beta strandi75 – 773
Helixi78 – 803
Beta strandi87 – 9610
Beta strandi99 – 11315
Turni115 – 1173
Beta strandi121 – 13010
Beta strandi136 – 1405
Helixi142 – 1454
Turni146 – 1494
Beta strandi151 – 1533
Beta strandi713 – 7186
Beta strandi726 – 7316
Beta strandi736 – 7383
Beta strandi743 – 7475
Beta strandi751 – 7533
Beta strandi758 – 7636
Helixi766 – 7694
Turni770 – 7723
Beta strandi773 – 7764
Beta strandi778 – 7803
Beta strandi789 – 7946
Beta strandi796 – 7983
Beta strandi800 – 8023
Beta strandi807 – 8159
Beta strandi830 – 8323

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1B11X-ray1.90A42-154[»]
1DUTX-ray1.90A/B711-843[»]
1F7DX-ray1.40A/B711-846[»]
1F7KX-ray2.20A/B711-846[»]
1F7NX-ray2.20A/B711-846[»]
1F7OX-ray2.20A/B/C711-846[»]
1F7PX-ray2.30A/B/C711-846[»]
1F7QX-ray2.26A/B/C711-846[»]
1F7RX-ray2.50A711-846[»]
1FIVX-ray2.00A42-154[»]
2FIVX-ray2.00A/B39-154[»]
2HAHX-ray1.70A39-154[»]
3FIVX-ray1.85A/B39-154[»]
3OGPX-ray1.70A/B39-154[»]
3OGQX-ray1.80A/B39-154[»]
4FIVX-ray1.80A42-154[»]
5FIVX-ray1.90A42-154[»]
6FIVX-ray1.90A42-154[»]
ProteinModelPortaliP16088.
SMRiP16088. Positions 42-154, 711-843.

Miscellaneous databases

EvolutionaryTraceiP16088.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini63 – 14482Peptidase A2
Add
BLAST
Domaini200 – 389190Reverse transcriptase
Add
BLAST
Domaini592 – 712121RNase H
Add
BLAST
Domaini899 – 1049151Integrase catalytic
Add
BLAST

Sequence similaritiesi

Contains 1 RNase H domain.

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.

P16088-1 [UniParc]FASTAAdd to Basket

« Hide

KEFGKLEGGA SCSPSESNAA SSNAICTSNG GETIGFVNYN KVGTTTTLEK     50
RPEILIFVNG YPIKFLLDTG ADITILNRRD FQVKNSIENG RQNMIGVGGG 100
KRGTNYINVH LEIRDENYKT QCIFGNVCVL EDNSLIQPLL GRDNMIKFNI 150
RLVMAQISDK IPVVKVKMKD PNKGPQIKQW PLTNEKIEAL TEIVERLEKE 200
GKVKRADSNN PWNTPVFAIK KKSGKWRMLI DFRELNKLTE KGAEVQLGLP 250
HPAGLQIKKQ VTVLDIGDAY FTIPLDPDYA PYTAFTLPRK NNAGPGRRFV 300
WCSLPQGWIL SPLIYQSTLD NIIQPFIRQN PQLDIYQYMD DIYIGSNLSK 350
KEHKEKVEEL RKLLLWWGFE TPEDKLQEEP PYTWMGYELH PLTWTIQQKQ 400
LDIPEQPTLN ELQKLAGKIN WASQAIPDLS IKALTNMMRG NQNLNSTRQW 450
TKEARLEVQK AKKAIEEQVQ LGYYDPSKEL YAKLSLVGPH QISYQVYQKD 500
PEKILWYGKM SRQKKKAENT CDIALRACYK IREESIIRIG KEPRYEIPTS 550
REAWESNLIN SPYLKAPPPE VEYIHAALNI KRALSMIKDA PIPGAETWYI 600
DGGRKLGKAA KAAYWTDTGK WRVMDLEGSN QKAEIQALLL ALKAGSEEMN 650
IITDSQYVIN IILQQPDMME GIWQEVLEEL EKKTAIFIDW VPGHKGIPGN 700
EEVDKLCQTM MIIEGDGILD KRSEDAGYDL LAAKEIHLLP GEVKVIPTGV 750
KLMLPKGYWG LIIGKSSIGS KGLDVLGGVI DEGYRGEIGV IMINVSRKSI 800
TLMERQKIAQ LIILPCKHEV LEQGKVVMDS ERGDNGYGST GVFSSWVDRI 850
EEAEINHEKF HSDPQYLRTE FNLPKMVAEE IRRKCPVCRI IGEQVGGQLK 900
IGPGIWQMDC THFDGKIILV GIHVESGYIW AQIISQETAD CTVKAVLQLL 950
SAHNVTELQT DNGPNFKNQK MEGVLNYMGV KHKFGIPGNP QSQALVENVN 1000
HTLKVWIQKF LPETTSLDNA LSLAVHSLNF KRRGRIGGMA PYELLAQQES 1050
LRIQDYFSAI PQKLQAQWIY YKDQKDKKWK GPMRVEYWGQ GSVLLKDEEK 1100
GYFLIPRRHI RRVPEPCALP EGDE 1124
Length:1,124
Mass (Da):127,494
Last modified:April 1, 1990 - v1
Checksum:iEE8214169BE39CF9
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M25381 Genomic RNA. Translation: AAB59937.1. Sequence problems.
PIRiB33543. GNLJFP.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M25381 Genomic RNA. Translation: AAB59937.1 . Sequence problems.
PIRi B33543. GNLJFP.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1B11 X-ray 1.90 A 42-154 [» ]
1DUT X-ray 1.90 A/B 711-843 [» ]
1F7D X-ray 1.40 A/B 711-846 [» ]
1F7K X-ray 2.20 A/B 711-846 [» ]
1F7N X-ray 2.20 A/B 711-846 [» ]
1F7O X-ray 2.20 A/B/C 711-846 [» ]
1F7P X-ray 2.30 A/B/C 711-846 [» ]
1F7Q X-ray 2.26 A/B/C 711-846 [» ]
1F7R X-ray 2.50 A 711-846 [» ]
1FIV X-ray 2.00 A 42-154 [» ]
2FIV X-ray 2.00 A/B 39-154 [» ]
2HAH X-ray 1.70 A 39-154 [» ]
3FIV X-ray 1.85 A/B 39-154 [» ]
3OGP X-ray 1.70 A/B 39-154 [» ]
3OGQ X-ray 1.80 A/B 39-154 [» ]
4FIV X-ray 1.80 A 42-154 [» ]
5FIV X-ray 1.90 A 42-154 [» ]
6FIV X-ray 1.90 A 42-154 [» ]
ProteinModelPortali P16088.
SMRi P16088. Positions 42-154, 711-843.
ModBasei Search...

Proteomic databases

PRIDEi P16088.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Miscellaneous databases

EvolutionaryTracei P16088.

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. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
    Strain: Clone 34TF10.
  2. "Nucleotide sequence analysis of feline immunodeficiency virus: genome organization and relationship to other lentiviruses."
    Olmsted R.A., Hirsch V.M., Purcell R.H., Johnson P.R.
    Proc. Natl. Acad. Sci. U.S.A. 86:8088-8092(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
    Strain: Clone FIV-14.
  3. "Identification of proteolytic processing sites within the Gag and Pol polyproteins of feline immunodeficiency virus."
    Elder J.H., Schnoelzer M., Hasselkus-Light C.S., Henson M., Lerner D.A., Phillips T.R., Wagaman P.C., Kent S.B.H.
    J. Virol. 67:1869-1876(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEOLYTIC PROCESSING OF POLYPROTEIN.
  4. Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 42-154.
  5. "Crystal structures of the inactive D30N mutant of feline immunodeficiency virus protease complexed with a substrate and an inhibitor."
    Laco G.S., Schalk-Hihi C., Lubkowski J., Morris G., Zdanov A., Olson A., Elder J.H., Wlodawer A., Gustchina A.
    Biochemistry 36:10696-10708(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 42-154.
  6. "Crystal structure of dUTP pyrophosphatase from feline immunodeficiency virus."
    Prasad G.S., Stura E.A., McRee D.E., Laco G.S., Hasselkus-Light C., Elder J.H., Stout C.D.
    Protein Sci. 5:2429-2437(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 711-827.

Entry informationi

Entry nameiPOL_FIVPE
AccessioniPrimary (citable) accession number: P16088
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1990
Last sequence update: April 1, 1990
Last modified: July 9, 2014
This is version 135 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

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

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