P19028 (POL_FIVSD) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Pol polyprotein

Cleaved into the following 4 chains:

1. Protease
   EC=3.4.23.-
   Alternative name(s):
   Retropepsin
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 (strain San Diego) (FIV)

Taxonomic identifier

11675 [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	Inferred from homology

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.
Caution	The N-terminus of the polypeptide is uncertain.

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	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 By similarity		PRO_0000038845
	Chain	155 – 710	556	Reverse transcriptase/ribonuclease H By similarity		PRO_0000038846
	Chain	711 – 843	133	Deoxyuridine 5'-triphosphate nucleotidohydrolase By similarity		PRO_0000038847
	Chain	844 – 1124	281	Integrase By similarity		PRO_0000038848
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 By similarity

Sequences

	Sequence		Length	Mass (Da)
	P19028 [UniParc]. Last modified November 1, 1990. Version 1. Checksum: 1A4706685CFDA8CF	FASTA	1,124	127,605
	10 20 30 40 50 60 KKFGKLEGGA SCSPSESSAA NSNAICTSNG GKIIGFINYN KVGTTTSLEK RPEILIFVNG 70 80 90 100 110 120 YPIKFLLDTG ADITILNRRD FQVKNSIENG RQNMIGVGGG KRGTNYINVH LEIRDENYKT 130 140 150 160 170 180 QCIFGNVCVL EDNSLIQPLL GRDNMIKFNI RLVMAQISDK IPIVKVKMKD PNKGPQIKQW 190 200 210 220 230 240 PLSNEKIEAL TEIVERLERE GKVKRADPNN PWNTPVFAIK KKSGKWRMLI DFRELNKLTE 250 260 270 280 290 300 KGAEVQLGLP HPAGLQMKKQ ITVLDIGDAY FTNPLDPDYA PYTAFTLPRK NNAGPGRRFV 310 320 330 340 350 360 WCSLPQGWIL SPLIYQSTLD NIIQPFIRQN PQLDIYQYMD DIYIGSNLSK KEHKEKVEEL 370 380 390 400 410 420 RKLLLWWGFE TPEDKLQEEP PYKWMGYELH PLTWTIQQKQ LEIPEKPTLN ELQKLAGKIN 430 440 450 460 470 480 WASQTIPELS IKSLTNMTRG NQNLNSTREW TEEARLEVQK AKRAIEEQVQ LGYYDPSKEL 490 500 510 520 530 540 YAKLSLVGPH QISYQVYQKC PEKILWYGKM SRQKKKAENT CDIALRACYK IREESIIRIG 550 560 570 580 590 600 KEPRYEIPTS REAWESNLIN SPYLKAPPPE VDYIHAALNI KRALSMIKDP PISGAETWYI 610 620 630 640 650 660 DGGRKLGKAA KAAYWTDTGK WQVMELEGSN QKAEIQALLL ALKAGPEEMN IITDSQYMIN 670 680 690 700 710 720 ILSQQPDKME GIWQEVLEEL EKKTAIFIDW VPGHKGIPGN EEVDKLCQTM MIIEGDGILD 730 740 750 760 770 780 KRTEDAGYDL LAAKEIHLLP GEVKVIPTGV KLMLPKGHWG LIMGKSSIGS KGLDVLGGVI 790 800 810 820 830 840 DEGYRGEIGV IMINLSKKSI TLLEQQKIAQ LIILPHKHEA LEQGKVVMDS ERGEKGYGST 850 860 870 880 890 900 GVFSSWVDRI EEAETNHEKF HSDPQYLRTE FNLPKMVAEE IRRKCPVCRI RGEQVGGQLK 910 920 930 940 950 960 IGPGIWQMDC THFDGKIILV AIHVESGYIW AQIISQETAD CTVKAVLQLL SAHIVTELQT 970 980 990 1000 1010 1020 DNGPNFKNQK MEGVLNYMGV KHKFGIPGNP QSQALVENVN QTLKVWVHKF LPETTSLDNA 1030 1040 1050 1060 1070 1080 LALAVHCLNF KQRGRIGGMA PYELLAQQES LRIQDYFSAI PQKLQAQWIY YKDQKDKKWK 1090 1100 1110 1120 GPMRVEYWGQ GSVLLKDEEK GYFLIPRRHV KRVPEPCALP EGDE

References

[1]	"Comparison of two host cell range variants of feline immunodeficiency virus." Phillips T.R., Talbott R.L., Lamont C., Muir S., Lovelace K.M., Elder J.H. J. Virol. 64:4605-4613(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate PPR.

Cross-references

Sequence databases
EMBL GenBank DDBJ	M36968 Genomic RNA. Translation: AAA43076.1.
3D structure databases
ProteinModelPortal	P19028.
SMR	P19028. 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...

Entry information

Entry name

POL_FIVSD

Accession

Primary (citable) accession number: P19028

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1990
Last sequence update:	November 1, 1990
Last modified:	April 3, 2013
This is version 112 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program