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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).PROSITE-ProRule annotation

Sites

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

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 (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 – 154154ProteasePRO_0000038841Add
BLAST
Chaini155 – 690536Reverse transcriptase/ribonuclease HPRO_0000038842Add
BLAST
Chaini691 – 843153Deoxyuridine 5'-triphosphate nucleotidohydrolasePRO_0000038843Add
BLAST
Chaini844 – 1124281IntegrasePRO_0000038844Add
BLAST

Post-translational modificationi

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

Proteomic databases

PRIDEiP16088.

Structurei

Secondary structure

1
1124
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi48 – 503Combined sources
Beta strandi53 – 586Combined sources
Beta strandi61 – 677Combined sources
Beta strandi71 – 733Combined sources
Beta strandi75 – 773Combined sources
Helixi78 – 803Combined sources
Beta strandi87 – 9610Combined sources
Beta strandi99 – 11315Combined sources
Turni115 – 1173Combined sources
Beta strandi121 – 13010Combined sources
Beta strandi136 – 1405Combined sources
Helixi142 – 1454Combined sources
Turni146 – 1494Combined sources
Beta strandi151 – 1533Combined sources
Beta strandi713 – 7186Combined sources
Beta strandi726 – 7316Combined sources
Beta strandi736 – 7383Combined sources
Beta strandi743 – 7475Combined sources
Beta strandi751 – 7533Combined sources
Beta strandi758 – 7636Combined sources
Helixi766 – 7694Combined sources
Turni770 – 7723Combined sources
Beta strandi773 – 7764Combined sources
Beta strandi778 – 7803Combined sources
Beta strandi789 – 7946Combined sources
Beta strandi796 – 7983Combined sources
Beta strandi800 – 8023Combined sources
Beta strandi807 – 8159Combined sources
Beta strandi830 – 8323Combined sources
Beta strandi905 – 9139Combined sources
Beta strandi916 – 9238Combined sources
Turni924 – 9263Combined sources
Beta strandi929 – 9357Combined sources
Helixi939 – 95214Combined sources
Beta strandi956 – 9616Combined sources
Turni964 – 9663Combined sources
Helixi969 – 97810Combined sources
Beta strandi981 – 9866Combined sources
Turni990 – 9923Combined sources
Helixi994 – 101017Combined sources
Helixi1011 – 10133Combined sources
Beta strandi1014 – 10163Combined sources
Helixi1017 – 102913Combined sources
Helixi1041 – 105111Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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[»]
4MQ3X-ray1.08A904-1029[»]
4PA1X-ray1.84A904-1052[»]
5FIVX-ray1.90A42-154[»]
6FIVX-ray1.90A42-154[»]
ProteinModelPortaliP16088.
SMRiP16088. Positions 42-154, 711-843.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP16088.

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.

P16088-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
KEFGKLEGGA SCSPSESNAA SSNAICTSNG GETIGFVNYN KVGTTTTLEK
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 IPVVKVKMKD PNKGPQIKQW PLTNEKIEAL TEIVERLEKE
210 220 230 240 250
GKVKRADSNN PWNTPVFAIK KKSGKWRMLI DFRELNKLTE KGAEVQLGLP
260 270 280 290 300
HPAGLQIKKQ VTVLDIGDAY FTIPLDPDYA PYTAFTLPRK NNAGPGRRFV
310 320 330 340 350
WCSLPQGWIL SPLIYQSTLD NIIQPFIRQN PQLDIYQYMD DIYIGSNLSK
360 370 380 390 400
KEHKEKVEEL RKLLLWWGFE TPEDKLQEEP PYTWMGYELH PLTWTIQQKQ
410 420 430 440 450
LDIPEQPTLN ELQKLAGKIN WASQAIPDLS IKALTNMMRG NQNLNSTRQW
460 470 480 490 500
TKEARLEVQK AKKAIEEQVQ LGYYDPSKEL YAKLSLVGPH QISYQVYQKD
510 520 530 540 550
PEKILWYGKM SRQKKKAENT CDIALRACYK IREESIIRIG KEPRYEIPTS
560 570 580 590 600
REAWESNLIN SPYLKAPPPE VEYIHAALNI KRALSMIKDA PIPGAETWYI
610 620 630 640 650
DGGRKLGKAA KAAYWTDTGK WRVMDLEGSN QKAEIQALLL ALKAGSEEMN
660 670 680 690 700
IITDSQYVIN IILQQPDMME GIWQEVLEEL EKKTAIFIDW VPGHKGIPGN
710 720 730 740 750
EEVDKLCQTM MIIEGDGILD KRSEDAGYDL LAAKEIHLLP GEVKVIPTGV
760 770 780 790 800
KLMLPKGYWG LIIGKSSIGS KGLDVLGGVI DEGYRGEIGV IMINVSRKSI
810 820 830 840 850
TLMERQKIAQ LIILPCKHEV LEQGKVVMDS ERGDNGYGST GVFSSWVDRI
860 870 880 890 900
EEAEINHEKF HSDPQYLRTE FNLPKMVAEE IRRKCPVCRI IGEQVGGQLK
910 920 930 940 950
IGPGIWQMDC THFDGKIILV GIHVESGYIW AQIISQETAD CTVKAVLQLL
960 970 980 990 1000
SAHNVTELQT DNGPNFKNQK MEGVLNYMGV KHKFGIPGNP QSQALVENVN
1010 1020 1030 1040 1050
HTLKVWIQKF LPETTSLDNA LSLAVHSLNF KRRGRIGGMA PYELLAQQES
1060 1070 1080 1090 1100
LRIQDYFSAI PQKLQAQWIY YKDQKDKKWK GPMRVEYWGQ GSVLLKDEEK
1110 1120
GYFLIPRRHI RRVPEPCALP EGDE
Length:1,124
Mass (Da):127,494
Last modified:April 1, 1990 - v1
Checksum:iEE8214169BE39CF9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M25381 Genomic RNA. Translation: AAB59937.1. Sequence problems.
PIRiB33543. GNLJFP.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M25381 Genomic RNA. Translation: AAB59937.1 . Sequence problems.
PIRi B33543. GNLJFP.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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 [» ]
4MQ3 X-ray 1.08 A 904-1029 [» ]
4PA1 X-ray 1.84 A 904-1052 [» ]
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...
MobiDBi 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: November 26, 2014
This is version 138 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