Pol polyprotein - Feline immunodeficiency virus (isolate Petaluma) (FIV)

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Reviewed, UniProtKB/Swiss-Prot P16088 (POL_FIVPE)

Last modified November 25, 2008. Version 96. History...

Clusters with 100%, 90%, 50% identity |

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    Pol polyprotein
Cleaved into the following 4 chains:
    1- Recommended name:
            Protease
        Alternative name(s):
            Retropepsin
            EC=3.4.23.-
    2- Recommended name:
            Reverse transcriptase/ribonuclease H
                Short name=RT
              EC=2.7.7.49
              EC=3.1.26.4
    3- Recommended name:
            Deoxyuridine 5'-triphosphate nucleotidohydrolase
                Short name=dUTPase
              EC=3.6.1.23
    4- Recommended name:
            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

Virus host

Felidae (cat family) [TaxID: 9681]

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Protein attributes

Sequence length	1124 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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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	Endonucleolytic cleavage to 5'-phosphomonoester. dUTP + H(2)O = 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.

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Ontologies

Keywords
Biological process	DNA integration DNA recombination Nucleotide metabolism
Domain	Zinc-finger
Ligand	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: InterPro 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 proteolysis Inferred from electronic annotation. Source: InterPro transposition Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	DNA binding Inferred from electronic annotation. Source: InterPro RNA binding Inferred from electronic annotation. Source: InterPro RNA-directed DNA polymerase activity Inferred from electronic annotation. Source: InterPro aspartic-type endopeptidase activity Inferred from electronic annotation. Source: InterPro dUTP diphosphatase activity Inferred from electronic annotation. Source: EC integrase activity Inferred from electronic annotation. Source: InterPro ribonuclease H activity Inferred from electronic annotation. Source: InterPro zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

39 – 154

116

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

Peptidase A2

Domain

200 – 389

190

Reverse transcriptase

Domain

592 – 712

121

RNase H

Domain

899 – 1049

151

Integrase catalytic

Zinc finger

848 – 889

Integrase-type

DNA binding

1067 – 1115

Integrase-type

Sites

Active site

For protease activity

Secondary structure

1124

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P16088-1 [UniParc].

Last modified April 1, 1990. Version 1.
Checksum: EE8214169BE39CF9
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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

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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: 2762293] [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: 2813380] [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: 8383214] [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: 7664111] [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: 9271500] [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: 8976551] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 711-827.
+	Additional computationally mapped references.

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Cross-references

Sequence databases

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

PIR

GNLJFP. B33543.

3D structure databases

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	[»]
3FIV	X-ray	1.85	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	[»]

ModBase

Search...

Family and domain databases

InterPro

IPR008180. DeoxyUTPase.
IPR000477. DNA_pol_RVTase.
IPR001037. Integrase_C_retrovir.
IPR001584. Integrase_cat-core.
IPR003308. Integrase_Zn-bd_dom_N.
IPR001969. Pept_Asp_AS.
IPR009007. Pept_Aspartc_cat.
IPR001995. Peptidase_A2_cat.
IPR002156. RNase_H.
IPR010659. RVT_connect.
IPR010661. RVT_thumb.
[Graphical view]

Gene3D

G3DSA:2.30.30.10. Integrase_C. 1 hit.
G3DSA:2.40.70.10. Pept_Aspartc_cat. 1 hit.

Pfam

PF00692. dUTPase. 1 hit.
PF00552. Integrase. 1 hit.
PF02022. Integrase_Zn. 1 hit.
PF00075. RnaseH. 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]

ProDom

PD004900. dCTP_deaminase. 1 hit.
[Graphical view] [Entries sharing at least one domain]

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 Resources

LinkHub

P16088.

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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:	November 25, 2008
This is version 96 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Virus (Virus annotation project)

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Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Peptidase families

Classification of peptidase families and list of entries

SIMILARITY comments

Index of protein domains and families

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Keywords

Gene Ontology (GO)

Sequence annotation (Features)

Molecule processing

Regions

Sites

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Family and domain databases

Other Resources

Entry information

Relevant documents