P16088 (POL_FIVPE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Pol polyprotein

Cleaved into the following 4 chains:

1. Protease
   Alternative name(s):
   Retropepsin
   EC=3.4.23.-
2. Reverse transcriptase/ribonuclease H
   Short name=RT
   EC=2.7.7.49
   EC=3.1.26.13
   Alternative name(s):
   Exoribonuclease H
   EC=3.1.13.2
3. Deoxyuridine 5'-triphosphate nucleotidohydrolase
   Short name=dUTPase
   EC=3.6.1.23
4. Integrase
   Short name=IN

Gene names

Name:

pol

Organism

Feline immunodeficiency virus (isolate Petaluma) (FIV)

Taxonomic identifier

11674 [NCBI]

Taxonomic lineage

Viruses › Retro-transcribing viruses › Retroviridae › Orthoretrovirinae › Lentivirus › Feline lentivirus group › Feline immunodeficiency virus

Virus host

Felidae (cat family) [TaxID: 9681]

Protein attributes

Sequence length	1124 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

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. 3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid. dUTP + H2O = dUMP + diphosphate. Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
Post-translational modification	Cleavage sites that yield the mature proteins remain to be determined.
Sequence similarities	Belongs to the retroviral Pol polyprotein family. Contains 1 integrase catalytic domain. Contains 1 integrase-type DNA-binding domain. Contains 1 integrase-type zinc finger. Contains 1 peptidase A2 domain. Contains 1 reverse transcriptase domain. Contains 1 RNase H domain.

Ontologies

Keywords
Biological process	DNA integration DNA recombination Nucleotide metabolism Viral genome integration Virus entry into host cell
Domain	Zinc-finger
Ligand	DNA-binding Metal-binding Zinc
Molecular function	Aspartyl protease Endonuclease Hydrolase Nuclease Nucleotidyltransferase Protease RNA-directed DNA polymerase Transferase
Technical term	3D-structure Multifunctional enzyme
Gene Ontology (GO)
Biological_process	DNA integration Inferred from electronic annotation. Source: UniProtKB-KW DNA recombination Inferred from electronic annotation. Source: UniProtKB-KW RNA-dependent DNA replication Inferred from electronic annotation. Source: InterPro dUTP metabolic process Inferred from electronic annotation. Source: InterPro establishment of integrated proviral latency Inferred from electronic annotation. Source: UniProtKB-KW nucleic acid phosphodiester bond hydrolysis Inferred from electronic annotation. Source: GOC proteolysis Inferred from electronic annotation. Source: UniProtKB-KW viral entry into host cell Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW RNA binding Inferred from electronic annotation. Source: InterPro RNA-directed DNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW aspartic-type endopeptidase activity Inferred from electronic annotation. Source: UniProtKB-KW dUTP diphosphatase activity Inferred from electronic annotation. Source: EC exoribonuclease H activity Inferred from electronic annotation. Source: EC ribonuclease H activity Inferred from electronic annotation. Source: InterPro zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 154

154

Protease

PRO_0000038841

Chain

155 – 690

536

Reverse transcriptase/ribonuclease H

PRO_0000038842

Chain

691 – 843

153

Deoxyuridine 5'-triphosphate nucleotidohydrolase

PRO_0000038843

Chain

844 – 1124

281

Integrase

PRO_0000038844

Regions

Domain

63 – 144

82

Peptidase A2

Domain

200 – 389

190

Reverse transcriptase

Domain

592 – 712

121

RNase H

Domain

899 – 1049

151

Integrase catalytic

Zinc finger

848 – 889

42

Integrase-type

DNA binding

1067 – 1115

49

Integrase-type

Sites

Active site

68

1

For protease activity

Secondary structure

1

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1124

Helix Strand Turn

Details...

Beta strand

48 – 50

3

Beta strand

53 – 58

6

Beta strand

61 – 67

7

Beta strand

71 – 73

3

Beta strand

75 – 77

3

Helix

78 – 80

3

Beta strand

87 – 96

10

Beta strand

99 – 113

15

Turn

115 – 117

3

Beta strand

121 – 130

10

Beta strand

136 – 140

5

Helix

142 – 145

4

Turn

146 – 149

4

Beta strand

151 – 153

3

Beta strand

713 – 718

6

Beta strand

726 – 731

6

Beta strand

736 – 738

3

Beta strand

743 – 747

5

Beta strand

751 – 753

3

Beta strand

758 – 763

6

Helix

766 – 769

4

Turn

770 – 772

3

Beta strand

773 – 776

4

Beta strand

778 – 780

3

Beta strand

789 – 794

6

Beta strand

796 – 798

3

Beta strand

800 – 802

3

Beta strand

807 – 815

9

Beta strand

830 – 832

3

Sequences

	Sequence		Length	Mass (Da)
	P16088 [UniParc]. Last modified April 1, 1990. Version 1. Checksum: EE8214169BE39CF9	FASTA	1,124	127,494
	10 20 30 40 50 60 KEFGKLEGGA SCSPSESNAA SSNAICTSNG GETIGFVNYN KVGTTTTLEK RPEILIFVNG 70 80 90 100 110 120 YPIKFLLDTG ADITILNRRD FQVKNSIENG RQNMIGVGGG KRGTNYINVH LEIRDENYKT 130 140 150 160 170 180 QCIFGNVCVL EDNSLIQPLL GRDNMIKFNI RLVMAQISDK IPVVKVKMKD PNKGPQIKQW 190 200 210 220 230 240 PLTNEKIEAL TEIVERLEKE GKVKRADSNN PWNTPVFAIK KKSGKWRMLI DFRELNKLTE 250 260 270 280 290 300 KGAEVQLGLP HPAGLQIKKQ VTVLDIGDAY FTIPLDPDYA PYTAFTLPRK NNAGPGRRFV 310 320 330 340 350 360 WCSLPQGWIL SPLIYQSTLD NIIQPFIRQN PQLDIYQYMD DIYIGSNLSK KEHKEKVEEL 370 380 390 400 410 420 RKLLLWWGFE TPEDKLQEEP PYTWMGYELH PLTWTIQQKQ LDIPEQPTLN ELQKLAGKIN 430 440 450 460 470 480 WASQAIPDLS IKALTNMMRG NQNLNSTRQW TKEARLEVQK AKKAIEEQVQ LGYYDPSKEL 490 500 510 520 530 540 YAKLSLVGPH QISYQVYQKD PEKILWYGKM SRQKKKAENT CDIALRACYK IREESIIRIG 550 560 570 580 590 600 KEPRYEIPTS REAWESNLIN SPYLKAPPPE VEYIHAALNI KRALSMIKDA PIPGAETWYI 610 620 630 640 650 660 DGGRKLGKAA KAAYWTDTGK WRVMDLEGSN QKAEIQALLL ALKAGSEEMN IITDSQYVIN 670 680 690 700 710 720 IILQQPDMME GIWQEVLEEL EKKTAIFIDW VPGHKGIPGN EEVDKLCQTM MIIEGDGILD 730 740 750 760 770 780 KRSEDAGYDL LAAKEIHLLP GEVKVIPTGV KLMLPKGYWG LIIGKSSIGS KGLDVLGGVI 790 800 810 820 830 840 DEGYRGEIGV IMINVSRKSI TLMERQKIAQ LIILPCKHEV LEQGKVVMDS ERGDNGYGST 850 860 870 880 890 900 GVFSSWVDRI EEAEINHEKF HSDPQYLRTE FNLPKMVAEE IRRKCPVCRI IGEQVGGQLK 910 920 930 940 950 960 IGPGIWQMDC THFDGKIILV GIHVESGYIW AQIISQETAD CTVKAVLQLL SAHNVTELQT 970 980 990 1000 1010 1020 DNGPNFKNQK MEGVLNYMGV KHKFGIPGNP QSQALVENVN HTLKVWIQKF LPETTSLDNA 1030 1040 1050 1060 1070 1080 LSLAVHSLNF KRRGRIGGMA PYELLAQQES LRIQDYFSAI PQKLQAQWIY YKDQKDKKWK 1090 1100 1110 1120 GPMRVEYWGQ GSVLLKDEEK GYFLIPRRHI RRVPEPCALP EGDE

References

[1]	"Nucleotide sequence and genomic organization of feline immunodeficiency virus." Talbott R.L., Sparger E.E., Lovelace K.M., Fitch W.M., Pedersen N.C., Luciw P.A., Elder J.H. Proc. Natl. Acad. Sci. U.S.A. 86:5743-5747(1989) [PubMed] [Europe PMC] [Abstract] 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]	"Structure of an inhibitor complex of the proteinase from feline immunodeficiency virus." 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. Nat. Struct. Biol. 2:480-488(1995) [PubMed] [Europe PMC] [Abstract] 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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M25381 Genomic RNA. Translation: AAB59937.1. Sequence problems.

PIR

GNLJFP. B33543.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P16088.

SMR

P16088. Positions 42-154, 711-843.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

Gene3D

1.10.10.200. 1 hit.
2.30.30.10. 1 hit.
2.40.70.10. 1 hit.

InterPro

IPR008180. dUTP_pyroPase.
IPR008181. dUTP_pyroPase_sf.
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.
IPR001969. Peptidase_aspartic_AS.
IPR012337. RNaseH-like_dom.
IPR002156. RNaseH_domain.
IPR000477. RVT.
IPR010659. RVT_connect.
IPR010661. RVT_thumb.
[Graphical view]

Pfam

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]

SUPFAM

SSF50122. Integrase_C. 1 hit.
SSF46919. Integrase_Zn_N. 1 hit.
SSF50630. Pept_Aspartic. 1 hit.
SSF53098. RNaseH_fold. 2 hits.

TIGRFAMs

TIGR00576. dut. 1 hit.

PROSITE

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]

ProtoNet

Search...

Other

EvolutionaryTrace

P16088.

Entry information

Entry name

POL_FIVPE

Accession

Primary (citable) accession number: P16088

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1990
Last sequence update:	April 1, 1990
Last modified:	April 3, 2013
This is version 126 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program