Q9PHK2 (TOP1P_XYLFA) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA topoisomerase I, plasmid
EC=5.99.1.2

Alternative name(s):
Omega-protein
Relaxing enzyme
Swivelase
Untwisting enzyme

Gene names

Ordered Locus Names:

XF_a0003

Encoded on

Plasmid pXF51

Organism

Xylella fastidiosa [Complete proteome] [HAMAP]

Taxonomic identifier

2371 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Xanthomonadales › Xanthomonadaceae › Xylella

Protein attributes

Sequence length	660 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone By similarity.
Catalytic activity	ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.
Subunit structure	Monomer By similarity.
Sequence similarities	Belongs to the type IA topoisomerase family. Contains 1 Toprim domain.

Ontologies

Keywords
Domain	Repeat Zinc-finger
Ligand	ATP-binding DNA-binding Metal-binding Nucleotide-binding Zinc
Molecular function	Isomerase Topoisomerase
Technical term	Complete proteome Plasmid
Gene Ontology (GO)
Biological process	DNA topological change Inferred from electronic annotation. Source: InterPro
Cellular component	chromosome Inferred from electronic annotation. Source: InterPro
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA topoisomerase type I activity Inferred from electronic annotation. Source: EC metal 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 – 660	660	DNA topoisomerase I, plasmid		PRO_0000145174
Regions
	Domain	1 – 106	106	Toprim
	Zinc finger	563 – 589	27	C4-type 1
	Zinc finger	613 – 643	31	C4-type 2
Sites
	Active site	287	1	O-(5'-phospho-DNA)-tyrosine intermediate By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q9PHK2 [UniParc]. Last modified October 1, 2000. Version 1. Checksum: AC4A5F000A503A1F	FASTA	660	72,556
	10 20 30 40 50 60 MKLMIIESPG KIEKLSTILG DGWKIAASVG HVRDLPQKEM GVAAPDFKPS YELTERGEGV 70 80 90 100 110 120 VAKLKNLLKQ ADSVYLATDP DREGEAISWH LQQCLKLSNP LRVTFNEITA NAVKASLVAP 130 140 150 160 170 180 RTIDVKRVAA QEARRVLDRL VGYMVSPELS RLTGKRLSAG RVQSPAVRLV VEREREIKAF 190 200 210 220 230 240 KVTNHFGAML FFADAKTSGE WSAEWLTKPK FVAEDNPYFM DRDFAAAVAQ VKAVVVKSFD 250 260 270 280 290 300 ESEAKRSPPP PFTTSTMQQA ASVTLGVDPK AAMDAAQKLY EQGHITYHRT DNPNVSDESL 310 320 330 340 350 360 GDIYAVSVKL GLDIAEKPRK FKAPAGAQVG HPAVTPTHWE VEEAGETSDQ KALYKLIRLR 370 380 390 400 410 420 AIACQLADAR YAVRTVRLEA AQPVGGKNVE FEARGRTLIY QGWLKLIAGD QTEEEDGNEK 430 440 450 460 470 480 ESSNPIPVCA PGECLDVARG KLLEKKTKPP SHYTQATLVK KLESEGIGRP ATYAAIMDNI 490 500 510 520 530 540 VSRGYVKTEK KYLFPTETGE LIVDSLVGKF EFLDLGFTRE IEESLDRIAQ GESGYKAVIA 550 560 570 580 590 600 KVHDQLNMEL STLQVSATPK HPCQECGKPL RRIPGKNGHF WGCSGYPDCS VTFPDEGGKP 610 620 630 640 650 660 GQKKPVEVSN FACVKCGNPL KHLVKKGKGG YDFWGCSGFK EGCKATYEDK KGKPNFEKAK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The genome sequence of the plant pathogen Xylella fastidiosa." Simpson A.J.G., Reinach F.C., Arruda P., Abreu F.A., Acencio M., Alvarenga R., Alves L.M.C., Araya J.E., Baia G.S., Baptista C.S., Barros M.H., Bonaccorsi E.D., Bordin S., Bove J.M., Briones M.R.S., Bueno M.R.P., Camargo A.A., Camargo L.E.A. , Carraro D.M., Carrer H., Colauto N.B., Colombo C., Costa F.F., Costa M.C.R., Costa-Neto C.M., Coutinho L.L., Cristofani M., Dias-Neto E., Docena C., El-Dorry H., Facincani A.P., Ferreira A.J.S., Ferreira V.C.A., Ferro J.A., Fraga J.S., Franca S.C., Franco M.C., Frohme M., Furlan L.R., Garnier M., Goldman G.H., Goldman M.H.S., Gomes S.L., Gruber A., Ho P.L., Hoheisel J.D., Junqueira M.L., Kemper E.L., Kitajima J.P., Krieger J.E., Kuramae E.E., Laigret F., Lambais M.R., Leite L.C.C., Lemos E.G.M., Lemos M.V.F., Lopes S.A., Lopes C.R., Machado J.A., Machado M.A., Madeira A.M.B.N., Madeira H.M.F., Marino C.L., Marques M.V., Martins E.A.L., Martins E.M.F., Matsukuma A.Y., Menck C.F.M., Miracca E.C., Miyaki C.Y., Monteiro-Vitorello C.B., Moon D.H., Nagai M.A., Nascimento A.L.T.O., Netto L.E.S., Nhani A. Jr., Nobrega F.G., Nunes L.R., Oliveira M.A., de Oliveira M.C., de Oliveira R.C., Palmieri D.A., Paris A., Peixoto B.R., Pereira G.A.G., Pereira H.A. Jr., Pesquero J.B., Quaggio R.B., Roberto P.G., Rodrigues V., de Rosa A.J.M., de Rosa V.E. Jr., de Sa R.G., Santelli R.V., Sawasaki H.E., da Silva A.C.R., da Silva A.M., da Silva F.R., Silva W.A. Jr., da Silveira J.F., Silvestri M.L.Z., Siqueira W.J., de Souza A.A., de Souza A.P., Terenzi M.F., Truffi D., Tsai S.M., Tsuhako M.H., Vallada H., Van Sluys M.A., Verjovski-Almeida S., Vettore A.L., Zago M.A., Zatz M., Meidanis J., Setubal J.C. Nature 406:151-159(2000) [PubMed: 10910347] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: 9a5c.
[2]	"Genetic organization of Plasmid pXF51 from the plant pathogen Xylella fastidiosa." Marques M.V., da Silva A.M., Gomes S.L. Plasmid 45:184-199(2001) [PubMed: 11407914] [Abstract] Cited for: DISCUSSION OF SEQUENCE.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE003851 Genomic DNA. Translation: AAF85572.1.
PIR	C82861.
RefSeq	NP_061659.1. NC_002490.1.
3D structure databases
ProteinModelPortal	Q9PHK2.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	1125448.
GenomeReviews	Gene locus XF_a0003 in contig AE003851_GR.
KEGG	xfa:XFa0003.
NMPDR	fig|160492.1.peg.2771.
PATRIC	24135901. VBIXylFas578_2957.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	HBG512935.
OMA	YYVNACD.
ProtClustDB	CLSK540625.
Enzyme and pathway databases
BioCyc	XFAS160492:XFA0003-MONOMER.
Family and domain databases
InterPro	IPR000380. Topo_IA. IPR003601. Topo_IA_2. IPR023406. Topo_IA_AS. IPR013497. Topo_IA_cen. IPR013824. Topo_IA_cen_sub1. IPR013825. Topo_IA_cen_sub2. IPR023405. Topo_IA_core_domain. IPR003602. Topo_IA_DNA-bd. IPR013498. Topo_IA_Znf. IPR005733. TopoI_bac-type. IPR006171. Toprim_domain. [Graphical view]
Gene3D	G3DSA:1.10.460.10. Topo_IA_cen_sub1. 2 hits. G3DSA:2.70.20.10. Topo_IA_cen_sub2. 2 hits.
KO	K03168.
PANTHER	PTHR11390. Topo_IA. 1 hit.
Pfam	PF01131. Topoisom_bac. 1 hit. PF01751. Toprim. 1 hit. PF01396. zf-C4_Topoisom. 1 hit. [Graphical view]
PRINTS	PR00417. PRTPISMRASEI.
SMART	SM00437. TOP1Ac. 1 hit. SM00436. TOP1Bc. 1 hit. SM00493. TOPRIM. 1 hit. [Graphical view]
SUPFAM	SSF56712. Topo_IA_core. 1 hit.
TIGRFAMs	TIGR01051. TopA_bact. 1 hit.
PROSITE	PS00396. TOPOISOMERASE_I_PROK. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

TOP1P_XYLFA

Accession

Primary (citable) accession number: Q9PHK2

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 20, 2001
Last sequence update:	October 1, 2000
Last modified:	January 25, 2012
This is version 83 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program