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Protein

Pol polyprotein

Gene

pol

Organism
Feline immunodeficiency virus (isolate Petaluma) (FIV)
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 sitei68For protease activity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri848 – 889Integrase-typePROSITE-ProRule annotationAdd BLAST42
DNA bindingi1067 – 1115Integrase-typePROSITE-ProRule annotationAdd BLAST49

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

Enzyme and pathway databases

BRENDAi3.4.23.B4. 2231.

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
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)DescriptionActionsGraphical viewLength
ChainiPRO_00000388411 – 154ProteaseAdd BLAST154
ChainiPRO_0000038842155 – 690Reverse transcriptase/ribonuclease HAdd BLAST536
ChainiPRO_0000038843691 – 843Deoxyuridine 5'-triphosphate nucleotidohydrolaseAdd BLAST153
ChainiPRO_0000038844844 – 1124IntegraseAdd BLAST281

Post-translational modificationi

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

Proteomic databases

PRIDEiP16088.

Structurei

Secondary structure

11124
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi48 – 50Combined sources3
Beta strandi53 – 58Combined sources6
Beta strandi61 – 67Combined sources7
Beta strandi71 – 73Combined sources3
Beta strandi75 – 77Combined sources3
Helixi78 – 80Combined sources3
Beta strandi87 – 96Combined sources10
Beta strandi99 – 113Combined sources15
Turni115 – 117Combined sources3
Beta strandi121 – 130Combined sources10
Beta strandi136 – 140Combined sources5
Helixi142 – 145Combined sources4
Turni146 – 149Combined sources4
Beta strandi151 – 153Combined sources3
Beta strandi713 – 718Combined sources6
Beta strandi726 – 731Combined sources6
Beta strandi736 – 738Combined sources3
Beta strandi743 – 747Combined sources5
Beta strandi751 – 753Combined sources3
Beta strandi758 – 763Combined sources6
Helixi766 – 769Combined sources4
Turni770 – 772Combined sources3
Beta strandi773 – 776Combined sources4
Beta strandi778 – 780Combined sources3
Beta strandi789 – 794Combined sources6
Beta strandi796 – 798Combined sources3
Beta strandi800 – 802Combined sources3
Beta strandi807 – 815Combined sources9
Beta strandi830 – 832Combined sources3
Beta strandi905 – 913Combined sources9
Beta strandi916 – 923Combined sources8
Turni924 – 926Combined sources3
Beta strandi929 – 935Combined sources7
Helixi939 – 952Combined sources14
Beta strandi956 – 961Combined sources6
Turni964 – 966Combined sources3
Helixi969 – 978Combined sources10
Beta strandi981 – 986Combined sources6
Turni990 – 992Combined sources3
Helixi994 – 1010Combined sources17
Helixi1011 – 1013Combined sources3
Beta strandi1014 – 1016Combined sources3
Helixi1017 – 1029Combined sources13
Helixi1041 – 1051Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP16088.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini63 – 144Peptidase A2PROSITE-ProRule annotationAdd BLAST82
Domaini200 – 389Reverse transcriptasePROSITE-ProRule annotationAdd BLAST190
Domaini592 – 712RNase HPROSITE-ProRule annotationAdd BLAST121
Domaini899 – 1049Integrase catalyticPROSITE-ProRule annotationAdd BLAST151

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 fingeri848 – 889Integrase-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.
IPR008181. dUTPase_1.
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.
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.
PIRiB33543. GNLJFP.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiP16088.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

BRENDAi3.4.23.B4. 2231.

Miscellaneous databases

EvolutionaryTraceiP16088.

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.
IPR008181. dUTPase_1.
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.
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]
ProtoNetiSearch...

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 2, 2016
This is version 147 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

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.