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Pol polyprotein [Cleaved into: Protease (Retropepsin) (EC 3.4.23.-); Reverse transcriptase/ribonuclease H (RT) (EC 2.7.7.49) (EC 3.1.26.13) (Exoribonuclease H) (EC 3.1.13.2); Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) (EC 3.6.1.23); Integrase (IN) (EC 2.7.7.-) (EC 3.1.-.-)]

 POL_FIVPE               Reviewed;        1124 AA.
P16088;
01-APR-1990, integrated into UniProtKB/Swiss-Prot.
01-APR-1990, sequence version 1.
10-MAY-2017, entry version 151.
RecName: Full=Pol polyprotein;
Contains:
RecName: Full=Protease;
AltName: Full=Retropepsin;
EC=3.4.23.-;
Contains:
RecName: Full=Reverse transcriptase/ribonuclease H;
Short=RT;
EC=2.7.7.49;
EC=3.1.26.13;
AltName: Full=Exoribonuclease H;
EC=3.1.13.2;
Contains:
RecName: Full=Deoxyuridine 5'-triphosphate nucleotidohydrolase;
Short=dUTPase;
EC=3.6.1.23;
Contains:
RecName: Full=Integrase;
Short=IN;
EC=2.7.7.- {ECO:0000250|UniProtKB:P04585};
EC=3.1.-.- {ECO:0000250|UniProtKB:P04585};
Name=pol;
Feline immunodeficiency virus (isolate Petaluma) (FIV).
Viruses; Retro-transcribing viruses; Retroviridae; Orthoretrovirinae;
Lentivirus; Feline lentivirus group.
NCBI_TaxID=11674;
NCBI_TaxID=9681; Felidae (cat family).
[1]
NUCLEOTIDE SEQUENCE [GENOMIC RNA].
STRAIN=Clone 34TF10;
PubMed=2762293; DOI=10.1073/pnas.86.15.5743;
Talbott R.L., Sparger E.E., Lovelace K.M., Fitch W.M., Pedersen N.C.,
Luciw P.A., Elder J.H.;
"Nucleotide sequence and genomic organization of feline
immunodeficiency virus.";
Proc. Natl. Acad. Sci. U.S.A. 86:5743-5747(1989).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC RNA].
STRAIN=Clone FIV-14;
PubMed=2813380; DOI=10.1073/pnas.86.20.8088;
Olmsted R.A., Hirsch V.M., Purcell R.H., Johnson P.R.;
"Nucleotide sequence analysis of feline immunodeficiency virus: genome
organization and relationship to other lentiviruses.";
Proc. Natl. Acad. Sci. U.S.A. 86:8088-8092(1989).
[3]
PROTEOLYTIC PROCESSING OF POLYPROTEIN.
PubMed=8383214;
Elder J.H., Schnoelzer M., Hasselkus-Light C.S., Henson M.,
Lerner D.A., Phillips T.R., Wagaman P.C., Kent S.B.H.;
"Identification of proteolytic processing sites within the Gag and Pol
polyproteins of feline immunodeficiency virus.";
J. Virol. 67:1869-1876(1993).
[4]
X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 42-154.
PubMed=7664111; DOI=10.1038/nsb0695-480;
Wlodawer A., Gustchina A., Reshetnikova L., Lubkowski J., Zdanov J.A.,
Hui K.Y., Angleton E.L., Farmerie W.G., Goodenow M.M., Bhatt D.,
Zhang L., Dunn B.M.;
"Structure of an inhibitor complex of the proteinase from feline
immunodeficiency virus.";
Nat. Struct. Biol. 2:480-488(1995).
[5]
X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 42-154.
PubMed=9271500; DOI=10.1021/bi9707436;
Laco G.S., Schalk-Hihi C., Lubkowski J., Morris G., Zdanov A.,
Olson A., Elder J.H., Wlodawer A., Gustchina A.;
"Crystal structures of the inactive D30N mutant of feline
immunodeficiency virus protease complexed with a substrate and an
inhibitor.";
Biochemistry 36:10696-10708(1997).
[6]
X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 711-827.
PubMed=8976551; DOI=10.1002/pro.5560051205;
Prasad G.S., Stura E.A., McRee D.E., Laco G.S., Hasselkus-Light C.,
Elder J.H., Stout C.D.;
"Crystal structure of dUTP pyrophosphatase from feline
immunodeficiency virus.";
Protein Sci. 5:2429-2437(1996).
-!- FUNCTION: 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 ACTIVITY: 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.
-!- CATALYTIC ACTIVITY: 3'-end directed exonucleolytic cleavage of
viral RNA-DNA hybrid.
-!- CATALYTIC ACTIVITY: dUTP + H(2)O = dUMP + diphosphate.
-!- CATALYTIC ACTIVITY: Deoxynucleoside triphosphate + DNA(n) =
diphosphate + DNA(n+1). {ECO:0000255|PROSITE-ProRule:PRU00405}.
-!- PTM: Cleavage sites that yield the mature proteins remain to be
determined.
-!- SIMILARITY: Belongs to the retroviral Pol polyprotein family.
{ECO:0000305}.
-----------------------------------------------------------------------
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Distributed under the Creative Commons Attribution-NoDerivs License
-----------------------------------------------------------------------
EMBL; M25381; AAB59937.1; ALT_SEQ; Genomic_RNA.
PIR; B33543; GNLJFP.
PDB; 1B11; X-ray; 1.90 A; A=42-154.
PDB; 1DUT; X-ray; 1.90 A; A/B=711-843.
PDB; 1F7D; X-ray; 1.40 A; A/B=711-846.
PDB; 1F7K; X-ray; 2.20 A; A/B=711-846.
PDB; 1F7N; X-ray; 2.20 A; A/B=711-846.
PDB; 1F7O; X-ray; 2.20 A; A/B/C=711-846.
PDB; 1F7P; X-ray; 2.30 A; A/B/C=711-846.
PDB; 1F7Q; X-ray; 2.26 A; A/B/C=711-846.
PDB; 1F7R; X-ray; 2.50 A; A=711-846.
PDB; 1FIV; X-ray; 2.00 A; A=42-154.
PDB; 2FIV; X-ray; 2.00 A; A/B=39-154.
PDB; 2HAH; X-ray; 1.70 A; A=39-154.
PDB; 3FIV; X-ray; 1.85 A; A/B=39-154.
PDB; 3OGP; X-ray; 1.70 A; A/B=39-154.
PDB; 3OGQ; X-ray; 1.80 A; A/B=39-154.
PDB; 4FIV; X-ray; 1.80 A; A=42-154.
PDB; 4MQ3; X-ray; 1.08 A; A=904-1029.
PDB; 4PA1; X-ray; 1.84 A; A=904-1052.
PDB; 5FIV; X-ray; 1.90 A; A=42-154.
PDB; 6FIV; X-ray; 1.90 A; A=42-154.
PDBsum; 1B11; -.
PDBsum; 1DUT; -.
PDBsum; 1F7D; -.
PDBsum; 1F7K; -.
PDBsum; 1F7N; -.
PDBsum; 1F7O; -.
PDBsum; 1F7P; -.
PDBsum; 1F7Q; -.
PDBsum; 1F7R; -.
PDBsum; 1FIV; -.
PDBsum; 2FIV; -.
PDBsum; 2HAH; -.
PDBsum; 3FIV; -.
PDBsum; 3OGP; -.
PDBsum; 3OGQ; -.
PDBsum; 4FIV; -.
PDBsum; 4MQ3; -.
PDBsum; 4PA1; -.
PDBsum; 5FIV; -.
PDBsum; 6FIV; -.
ProteinModelPortal; P16088; -.
SMR; P16088; -.
DrugBank; DB03800; 2'-deoxyuridylic acid.
DrugBank; DB02333; Deoxyuridine-5'-Triphosphate.
DrugBank; DB08253; NAM NAPTHYLAMINOALANINE.
DrugBank; DB07365; NAPHTHALEN-2-YL-3-ALANINE.
DrugBank; DB01891; Tl-3-093.
DrugBank; DB03435; Uridine-5'-Diphosphate.
PRIDE; P16088; -.
BRENDA; 3.4.23.B4; 2231.
EvolutionaryTrace; P16088; -.
GO; GO:0004190; F:aspartic-type endopeptidase activity; IEA:UniProtKB-KW.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0004170; F:dUTP diphosphatase activity; IEA:UniProtKB-EC.
GO; GO:0004533; F:exoribonuclease H activity; IEA:UniProtKB-EC.
GO; GO:0003964; F:RNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
GO; GO:0004523; F:RNA-DNA hybrid ribonuclease activity; IEA:InterPro.
GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
GO; GO:0015074; P:DNA integration; IEA:UniProtKB-KW.
GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
GO; GO:0046080; P:dUTP metabolic process; IEA:InterPro.
GO; GO:0075713; P:establishment of integrated proviral latency; IEA:UniProtKB-KW.
GO; GO:0046718; P:viral entry into host cell; IEA:UniProtKB-KW.
GO; GO:0044826; P:viral genome integration into host DNA; IEA:UniProtKB-KW.
CDD; cd05482; HIV_retropepsin_like; 1.
CDD; cd07557; trimeric_dUTPase; 1.
Gene3D; 1.10.10.200; -; 1.
Gene3D; 2.30.30.10; -; 1.
Gene3D; 2.40.70.10; -; 1.
Gene3D; 3.30.420.10; -; 2.
InterPro; IPR001969; Aspartic_peptidase_AS.
InterPro; IPR029054; dUTPase-like.
InterPro; IPR008181; dUTPase_1.
InterPro; IPR033704; dUTPase_trimeric.
InterPro; IPR001037; Integrase_C_retrovir.
InterPro; IPR001584; Integrase_cat-core.
InterPro; IPR017856; Integrase_Zn-bd_dom-like_N.
InterPro; IPR003308; Integrase_Zn-bd_dom_N.
InterPro; IPR001995; Peptidase_A2_cat.
InterPro; IPR021109; Peptidase_aspartic_dom.
InterPro; IPR034170; Retropepsin-like_cat_dom.
InterPro; IPR018061; Retropepsins.
InterPro; IPR012337; RNaseH-like_dom.
InterPro; IPR002156; RNaseH_domain.
InterPro; IPR000477; RT_dom.
InterPro; IPR010659; RVT_connect.
InterPro; IPR010661; RVT_thumb.
Pfam; PF00692; dUTPase; 1.
Pfam; PF00552; IN_DBD_C; 1.
Pfam; PF02022; Integrase_Zn; 1.
Pfam; PF00075; RNase_H; 1.
Pfam; PF00665; rve; 1.
Pfam; PF00077; RVP; 1.
Pfam; PF00078; RVT_1; 1.
Pfam; PF06815; RVT_connect; 1.
Pfam; PF06817; RVT_thumb; 1.
SUPFAM; SSF46919; SSF46919; 1.
SUPFAM; SSF50122; SSF50122; 1.
SUPFAM; SSF50630; SSF50630; 1.
SUPFAM; SSF51283; SSF51283; 1.
SUPFAM; SSF53098; SSF53098; 2.
TIGRFAMs; TIGR00576; dut; 1.
PROSITE; PS50175; ASP_PROT_RETROV; 1.
PROSITE; PS00141; ASP_PROTEASE; 1.
PROSITE; PS50994; INTEGRASE; 1.
PROSITE; PS51027; INTEGRASE_DBD; 1.
PROSITE; PS50879; RNASE_H; 1.
PROSITE; PS50878; RT_POL; 1.
PROSITE; PS50876; ZF_INTEGRASE; 1.
1: Evidence at protein level;
3D-structure; Aspartyl protease; DNA integration; DNA recombination;
DNA-binding; Endonuclease; Hydrolase; Metal-binding;
Multifunctional enzyme; Nuclease; Nucleotide metabolism;
Nucleotidyltransferase; Protease; RNA-directed DNA polymerase;
Transferase; Viral genome integration; Virus entry into host cell;
Zinc; Zinc-finger.
CHAIN 1 154 Protease.
/FTId=PRO_0000038841.
CHAIN 155 690 Reverse transcriptase/ribonuclease H.
/FTId=PRO_0000038842.
CHAIN 691 843 Deoxyuridine 5'-triphosphate
nucleotidohydrolase.
/FTId=PRO_0000038843.
CHAIN 844 1124 Integrase.
/FTId=PRO_0000038844.
DOMAIN 63 144 Peptidase A2. {ECO:0000255|PROSITE-
ProRule:PRU00275}.
DOMAIN 200 389 Reverse transcriptase.
{ECO:0000255|PROSITE-ProRule:PRU00405}.
DOMAIN 592 712 RNase H. {ECO:0000255|PROSITE-
ProRule:PRU00408}.
DOMAIN 899 1049 Integrase catalytic.
{ECO:0000255|PROSITE-ProRule:PRU00457}.
ZN_FING 848 889 Integrase-type. {ECO:0000255|PROSITE-
ProRule:PRU00450}.
DNA_BIND 1067 1115 Integrase-type. {ECO:0000255|PROSITE-
ProRule:PRU00506}.
ACT_SITE 68 68 For protease activity.
STRAND 48 50 {ECO:0000244|PDB:3OGP}.
STRAND 53 58 {ECO:0000244|PDB:3OGP}.
STRAND 61 67 {ECO:0000244|PDB:3OGP}.
STRAND 71 73 {ECO:0000244|PDB:3FIV}.
STRAND 75 77 {ECO:0000244|PDB:3OGP}.
HELIX 78 80 {ECO:0000244|PDB:3OGP}.
STRAND 87 96 {ECO:0000244|PDB:3OGP}.
STRAND 99 113 {ECO:0000244|PDB:3OGP}.
TURN 115 117 {ECO:0000244|PDB:3OGP}.
STRAND 121 130 {ECO:0000244|PDB:3OGP}.
STRAND 136 140 {ECO:0000244|PDB:3OGP}.
HELIX 142 145 {ECO:0000244|PDB:3OGP}.
TURN 146 149 {ECO:0000244|PDB:3OGP}.
STRAND 151 153 {ECO:0000244|PDB:3OGP}.
STRAND 713 718 {ECO:0000244|PDB:1F7D}.
STRAND 726 731 {ECO:0000244|PDB:1F7D}.
STRAND 736 738 {ECO:0000244|PDB:1F7D}.
STRAND 743 747 {ECO:0000244|PDB:1F7D}.
STRAND 751 753 {ECO:0000244|PDB:1F7N}.
STRAND 758 763 {ECO:0000244|PDB:1F7D}.
HELIX 766 769 {ECO:0000244|PDB:1F7D}.
TURN 770 772 {ECO:0000244|PDB:1F7D}.
STRAND 773 776 {ECO:0000244|PDB:1F7D}.
STRAND 778 780 {ECO:0000244|PDB:1F7O}.
STRAND 789 794 {ECO:0000244|PDB:1F7D}.
STRAND 796 798 {ECO:0000244|PDB:1F7D}.
STRAND 800 802 {ECO:0000244|PDB:1F7D}.
STRAND 807 815 {ECO:0000244|PDB:1F7D}.
STRAND 830 832 {ECO:0000244|PDB:1F7R}.
STRAND 905 913 {ECO:0000244|PDB:4MQ3}.
STRAND 916 923 {ECO:0000244|PDB:4MQ3}.
TURN 924 926 {ECO:0000244|PDB:4MQ3}.
STRAND 929 935 {ECO:0000244|PDB:4MQ3}.
HELIX 939 952 {ECO:0000244|PDB:4MQ3}.
STRAND 956 961 {ECO:0000244|PDB:4MQ3}.
TURN 964 966 {ECO:0000244|PDB:4MQ3}.
HELIX 969 978 {ECO:0000244|PDB:4MQ3}.
STRAND 981 986 {ECO:0000244|PDB:4MQ3}.
TURN 990 992 {ECO:0000244|PDB:4MQ3}.
HELIX 994 1010 {ECO:0000244|PDB:4MQ3}.
HELIX 1011 1013 {ECO:0000244|PDB:4MQ3}.
STRAND 1014 1016 {ECO:0000244|PDB:4MQ3}.
HELIX 1017 1029 {ECO:0000244|PDB:4MQ3}.
HELIX 1041 1051 {ECO:0000244|PDB:4PA1}.
SEQUENCE 1124 AA; 127494 MW; EE8214169BE39CF9 CRC64;
KEFGKLEGGA SCSPSESNAA SSNAICTSNG GETIGFVNYN KVGTTTTLEK RPEILIFVNG
YPIKFLLDTG ADITILNRRD FQVKNSIENG RQNMIGVGGG KRGTNYINVH LEIRDENYKT
QCIFGNVCVL EDNSLIQPLL GRDNMIKFNI RLVMAQISDK IPVVKVKMKD PNKGPQIKQW
PLTNEKIEAL TEIVERLEKE GKVKRADSNN PWNTPVFAIK KKSGKWRMLI DFRELNKLTE
KGAEVQLGLP HPAGLQIKKQ VTVLDIGDAY FTIPLDPDYA PYTAFTLPRK NNAGPGRRFV
WCSLPQGWIL SPLIYQSTLD NIIQPFIRQN PQLDIYQYMD DIYIGSNLSK KEHKEKVEEL
RKLLLWWGFE TPEDKLQEEP PYTWMGYELH PLTWTIQQKQ LDIPEQPTLN ELQKLAGKIN
WASQAIPDLS IKALTNMMRG NQNLNSTRQW TKEARLEVQK AKKAIEEQVQ LGYYDPSKEL
YAKLSLVGPH QISYQVYQKD PEKILWYGKM SRQKKKAENT CDIALRACYK IREESIIRIG
KEPRYEIPTS REAWESNLIN SPYLKAPPPE VEYIHAALNI KRALSMIKDA PIPGAETWYI
DGGRKLGKAA KAAYWTDTGK WRVMDLEGSN QKAEIQALLL ALKAGSEEMN IITDSQYVIN
IILQQPDMME GIWQEVLEEL EKKTAIFIDW VPGHKGIPGN EEVDKLCQTM MIIEGDGILD
KRSEDAGYDL LAAKEIHLLP GEVKVIPTGV KLMLPKGYWG LIIGKSSIGS KGLDVLGGVI
DEGYRGEIGV IMINVSRKSI TLMERQKIAQ LIILPCKHEV LEQGKVVMDS ERGDNGYGST
GVFSSWVDRI EEAEINHEKF HSDPQYLRTE FNLPKMVAEE IRRKCPVCRI IGEQVGGQLK
IGPGIWQMDC THFDGKIILV GIHVESGYIW AQIISQETAD CTVKAVLQLL SAHNVTELQT
DNGPNFKNQK MEGVLNYMGV KHKFGIPGNP QSQALVENVN HTLKVWIQKF LPETTSLDNA
LSLAVHSLNF KRRGRIGGMA PYELLAQQES LRIQDYFSAI PQKLQAQWIY YKDQKDKKWK
GPMRVEYWGQ GSVLLKDEEK GYFLIPRRHI RRVPEPCALP EGDE


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