Reviewed, UniProtKB/Swiss-Prot Q7SQ98 (POL_ALV)

Names and origin

Protein names

Recommended name:
    Pol polyprotein
Cleaved into the following 2 chains:
    1- Recommended name:
            Reverse transcriptase/ribonuclease H
                Short name=RT
              EC=2.7.7.49
              EC=2.7.7.7
              EC=3.1.26.4
    2- Recommended name:
            Integrase
                Short name=IN
        Alternative name(s):
            pp32

Gene names

Name:

pol

Organism

Avian leukosis virus (ALV)

Taxonomic identifier

11864 [NCBI]

Taxonomic lineage

Viruses › Retro-transcribing viruses › Retroviridae › Orthoretrovirinae › Alpharetrovirus

Virus host

Gallus gallus (Chicken) [TaxID: 9031]

Protein attributes

Sequence length	895 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	Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Endonucleolytic cleavage to 5'-phosphomonoester.
Cofactor	Binds 8 manganese or magnesium ions per integrase homotetramer By similarity.
Subunit structure	The integrase forms a homotetramer. The reverse transcriptase forms a heterodimer of alpha and beta subunits By similarity.
Domain	The integrase is composed of three domains. The N-terminal domain is a zinc binding domain. The central domain is the catalytic domain. The C-terminal domain is a non-specific DNA binding domain By similarity.
Post-translational modification	Specific enzymatic cleavages in vivo yield mature proteins. The pol-derived portion of gag-pol precursor is processed to yield the reverse transcriptase beta subunit, which in turn is processed to yield the reverse transcriptase alpha subunit and the integrase By similarity.
Miscellaneous	This protein is synthesized as a Gag-Pol polyprotein.
Sequence similarities	Contains 1 integrase catalytic domain. Contains 1 integrase-type DNA-binding domain. Contains 1 integrase-type zinc finger. Contains 1 reverse transcriptase domain. Contains 1 RNase H domain.

Ontologies

Keywords
Biological process	DNA integration DNA recombination
Domain	Zinc-finger
Ligand	DNA-binding Magnesium Manganese Metal-binding Zinc
Molecular function	Endonuclease Hydrolase Nuclease Nucleotidyltransferase RNA-directed DNA polymerase Transferase
Technical term	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 transposition Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW DNA-directed DNA polymerase activity Inferred from electronic annotation. Source: EC RNA binding Inferred from electronic annotation. Source: InterPro RNA-directed DNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW integrase activity Inferred from electronic annotation. Source: InterPro magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW manganese ion binding Inferred from electronic annotation. Source: UniProtKB-KW ribonuclease H activity Inferred from electronic annotation. Source: EC zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 572	572	Reverse transcriptase/ribonuclease H Potential		PRO_0000040978
	Chain	573 – 895	323	Integrase Potential		PRO_0000040979
Regions
	Domain	42 – 230	189	Reverse transcriptase
	Domain	441 – 572	132	RNase H
	Domain	625 – 788	164	Integrase catalytic
	Zinc finger	573 – 613	41	Integrase-type
	DNA binding	794 – 842	49	Integrase-type
Sites
	Metal binding	636	1	Magnesium; catalytic; for integrase activity By similarity
	Metal binding	693	1	Magnesium; catalytic; for integrase activity By similarity
	Metal binding	729	1	Magnesium; catalytic; for integrase activity By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q7SQ98-1 [UniParc]. Last modified October 1, 2003. Version 1. Checksum: 768028C3E5830073	FASTA	895	98,588
	10 20 30 40 50 60 TVALHLAIPL KWKPDHTPVW IDQWPLPEGK LVALTQLVEK ELQLGHIEPS LSCWNTPVFV 70 80 90 100 110 120 IRKASGSYRL LHDLRAVNAK LVPFGAVQQG APVLSALPRG WPLMVLDLKD CFFSIPLAEQ 130 140 150 160 170 180 DREAFAFTLP SVNNQAPARR FQWKVLPQGM TCSPTICQLV VGQVLEPLRL KHPSLRMLHY 190 200 210 220 230 240 MDDLLLAASS HDGLEAAGEE VISTLERAGF TISPDKIQRE PGVQYLGYKL GSTYVAPVGL 250 260 270 280 290 300 VAEPRIATLW DVQKLVGSLQ WLRPALGIPP RLMGPFYEQL RGSDPNEARE WNLDMKMAWR 310 320 330 340 350 360 EIVQLSTTAA LERWDPALPL EGAVARCEQG AIGVLGQGLS THPRPCLWLF STQPTKAFTA 370 380 390 400 410 420 WLEVLTLLIT KLRASAVRTF GKEVDILLLP ACFREDLPLP EGILLALKGF AGKIRSSDTP 430 440 450 460 470 480 SIFDIARPLH VSLKVRVTDH PVPGPTVFTD ASSSTHKGVV VWREGPRWEI KEIADSGASV 490 500 510 520 530 540 QQLEARAVAM ALLLWPTTPT NVVTDSAFVA KMLLKMGQEG VPSTAAAFIL EDALSQRSAM 550 560 570 580 590 600 AAVLHVRSHS EVPGFFTEGN DVADSQATFQ AYPLREAKDL HTALHIGPRA LSKACNISMQ 610 620 630 640 650 660 QAREVVQTCP HCNSAPALEA GVNPRGLGPL QIWQTDFTLE PRMAPRSWLA VTVDTASSAI 670 680 690 700 710 720 VVTQHGRVTS VAAQHHWATA IAVLGRPKAI KTDNGSCFTS KSTREWLARW GIAHTTGIPG 730 740 750 760 770 780 NSQGQAMVER ANRLLKDKIR VLAEGDGFMK RIPTSKQGEL LAKAMYALNH FERGENTKTP 790 800 810 820 830 840 IQKHWRPTVL TEGPPVKIRI ETGEWEKGWN VLVWGRGYAA VKNRDTDKVI WVPSRKVKPD 850 860 870 880 890 ITQKDEVTKK DEASPLFAGI SDWAPWKGEQ EGLQEEVASN KQERPGEDTL AANES

References

[1]

"Genome sequence analysis of the avian retrovirus causing so-called fowl glioma and the promoter activity of the long terminal repeat." Tomioka Y., Ochiai K., Ohashi K., Ono E., Toyoda T., Kimura T., Umemura T. J. Gen. Virol. 85:647-652(2004) [PubMed: 14993650] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	AB112960 Genomic RNA. Translation: BAC78443.1.
3D structure databases
SMR	Q7SQ98. Positions 621-842.
ModBase	Search...
Enzyme and pathway databases
BRENDA	2.7.7.49. 282326. 3.1.26.4. 282326.
Family and domain databases
InterPro	IPR000477. DNA_pol_RVTase. IPR001037. Integrase_C_retrovir. IPR001584. Integrase_cat-core. IPR003308. Integrase_Zn-bd_dom_N. IPR002156. RNase_H. IPR010661. RVT_thumb. [Graphical view]
Gene3D	G3DSA:2.30.30.10. Integrase_C. 1 hit.
Pfam	PF00552. Integrase. 1 hit. PF02022. Integrase_Zn. 1 hit. PF00075. RnaseH. 1 hit. PF00665. rve. 1 hit. PF00078. RVT_1. 1 hit. PF06817. RVT_thumb. 1 hit. [Graphical view]
PROSITE	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_ALV

Accession

Primary (citable) accession number: Q7SQ98

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 27, 2004
Last sequence update:	October 1, 2003
Last modified:	June 16, 2009
This is version 49 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Virus (Virus annotation project)