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D3V265 (D3V265_XENBS) Unreviewed, UniProtKB/TrEMBL

Last modified April 16, 2014. Version 31. Feed History...

Clusters with 100%, 90%, 50% identity | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
DNA topoisomerase 1 HAMAP-Rule MF_00952

EC=5.99.1.2 HAMAP-Rule MF_00952
Alternative name(s):
DNA topoisomerase I HAMAP-Rule MF_00952
Gene names
Name:topA HAMAP-Rule MF_00952 EMBL CBJ81415.1
Ordered Locus Names:XBJ1_2289 EMBL CBJ81415.1
OrganismXenorhabdus bovienii (strain SS-2004) [Complete proteome] [HAMAP] EMBL CBJ81415.1
Taxonomic identifier406818 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeXenorhabdus

Protein attributes

Sequence length863 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

Releases the supercoiling and torsional tension of DNA, which is 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 then 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. HAMAP-Rule MF_00952 SAAS SAAS005733

Catalytic activity

ATP-independent breakage of single-stranded DNA, followed by passage and rejoining. HAMAP-Rule MF_00952 RuleBase RU000518 SAAS SAAS005733

Cofactor

Magnesium. Binds two Mg2+ per subunit By similarity. HAMAP-Rule MF_00952

Subunit structure

Monomer By similarity. HAMAP-Rule MF_00952

Sequence similarities

Belongs to the type IA topoisomerase family. HAMAP-Rule MF_00952

Contains 1 Toprim domain. HAMAP-Rule MF_00952

Contains Toprim domain. SAAS SAAS005733

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Regions

Domain3 – 140138Toprim By similarity HAMAP-Rule MF_00952
Region190 – 1956Interaction with DNA By similarity HAMAP-Rule MF_00952

Sites

Active site3171O-(5'-phospho-DNA)-tyrosine intermediate By similarity HAMAP-Rule MF_00952
Metal binding91Magnesium 1; catalytic By similarity HAMAP-Rule MF_00952
Metal binding1091Magnesium 1; catalytic By similarity HAMAP-Rule MF_00952
Metal binding1091Magnesium 2 By similarity HAMAP-Rule MF_00952
Metal binding1111Magnesium 2 By similarity HAMAP-Rule MF_00952
Site331Interaction with DNA By similarity HAMAP-Rule MF_00952
Site1661Interaction with DNA By similarity HAMAP-Rule MF_00952
Site1671Interaction with DNA By similarity HAMAP-Rule MF_00952
Site1701Interaction with DNA By similarity HAMAP-Rule MF_00952
Site1751Interaction with DNA By similarity HAMAP-Rule MF_00952
Site1821Interaction with DNA By similarity HAMAP-Rule MF_00952
Site3191Interaction with DNA By similarity HAMAP-Rule MF_00952
Site5051Interaction with DNA By similarity HAMAP-Rule MF_00952

Sequences

Sequence LengthMass (Da)Tools
D3V265 [UniParc].

Last modified April 20, 2010. Version 1.
Checksum: BEBAEDE670B084B5

FASTA86396,862
        10         20         30         40         50         60 
MGKALVIVES PAKAKTINKY LGNDYVVKSS VGHIRDLPTS GAASQKSSNS STDKNKKKKD 

        70         80         90        100        110        120 
EKTALVNRMG VDPYHGWEAD YQILPGKEKV VAELKMLAEK ADHIYLATDL DREGEAIAWH 

       130        140        150        160        170        180 
LREVIGGGEA RFSRVVFNEI TKNAITQAFD NPGELNIDRV NAQQARRFMD RVVGYMVSPL 

       190        200        210        220        230        240 
LWKKVARGLS AGRVQSVAVR LIVEREREIK AFVPEEYWQL HADLMAKGDI DLHMEVTHEG 

       250        260        270        280        290        300 
GKPFKPINAQ QTQAAVSLLE KARYKVLDRE DRPTSSKPGA PFITSTLQQA ASTRLGFGVK 

       310        320        330        340        350        360 
KTMMMAQRLY EAGHITYMRT DSTNLSQDAL DMVRGYINDQ FGDKYLPKTA NIYSNKENSQ 

       370        380        390        400        410        420 
EAHEAIRPSS VDVMAEELKD MEADAQKLYQ LIWRQFIACQ MMPAKYDSTT LTIQAGNFEL 

       430        440        450        460        470        480 
RAKGRTLRFD GWTKVMPALR KGDEDHTLPV VEVGTELDLK QLSPSQHFTK PSARFSEASL 

       490        500        510        520        530        540 
VRELEKRGIG RPSTYASIIS TIQDRGYVRG ENRRFYAEKM GEIVNDRLEE NFNELMSYDF 

       550        560        570        580        590        600 
TARMEDQLDH VANNEANWKG VLDEFFTNFS EQLDVASKDP DEGGMRPNPM VSTSIDCPTC 

       610        620        630        640        650        660 
SRPMGIRTAT TGVFLGCSGY TLSPKERCKQ TINLIPENEI LNILEGDEAE TNALRARHRC 

       670        680        690        700        710        720 
KECGTAMDSY LIDNQRKLHV CGNNPACDGY EVEEGEFRIK GYDGPIVECD KCGSEMHLKM 

       730        740        750        760        770        780 
GRFGKYMGCT SEECKNTRKI LRSGEVAPPK EDPVPLPELP CEKSDAYFVL RDGAAGVFLA 

       790        800        810        820        830        840 
ASTFPKSRET RAPLVEELVK FKDRLPEKLC YLAKAPVADP EGHKTVVRFS RKTKQQYVSS 

       850        860 
EKNGKATGWA AFFVDGAWVV KEK 

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References

[1]"Complete genome sequence of Xenorhabdus nematophila (strain ATCC 19061 / DSM 3370 / LMG 1036 / NCIB 9965 / AN6)."
Goodrich-Blair H., Barbazuk B., Bode H.B., Darby C., Du Z., Forst S., Gaudriault S., Goldman B.S., Goodner B., Henkhaus J., Latreille P., Medigue C., Miller N., Norton S., Ogier J.C., Rouy Z., Slater S., Suen G.
Submitted (FEB-2010) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: SS-2004.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
FN667741 Genomic DNA. Translation: CBJ81415.1.
RefSeqYP_003468188.1. NC_013892.1.

3D structure databases

ProteinModelPortalD3V265.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaCBJ81415; CBJ81415; XBJ1_2289.
GeneID8831902.
KEGGxbo:XBJ1_2289.
PATRIC35299411. VBIXenBov95754_2063.

Organism-specific databases

CMRSearch...

Phylogenomic databases

HOGENOMHOG000004018.
KOK03168.

Enzyme and pathway databases

BioCycXBOV406818:GHLH-2275-MONOMER.

Family and domain databases

Gene3D1.10.460.10. 2 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPMF_00952. Topoisom_1_prok.
InterProIPR000380. 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.
IPR013263. TopoI_Znr_bac.
IPR028612. Topoisom_1_IA.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERPTHR11390. PTHR11390. 1 hit.
PfamPF08272. Topo_Zn_Ribbon. 2 hits.
PF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
PF01396. zf-C4_Topoisom. 1 hit.
[Graphical view]
PRINTSPR00417. PRTPISMRASEI.
SMARTSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMSSF56712. SSF56712. 1 hit.
TIGRFAMsTIGR01051. topA_bact. 1 hit.
PROSITEPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameD3V265_XENBS
AccessionPrimary (citable) accession number: D3V265
Entry history
Integrated into UniProtKB/TrEMBL: April 20, 2010
Last sequence update: April 20, 2010
Last modified: April 16, 2014
This is version 31 of the entry and version 1 of the sequence. [Complete history]
Entry statusUnreviewed (UniProtKB/TrEMBL)