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D2RAK7 (D2RAK7_GARV4) Unreviewed, UniProtKB/TrEMBL

Last modified May 1, 2013. Version 28. 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:
UvrABC system protein B HAMAP-Rule MF_00204
Short name=Protein UvrB HAMAP-Rule MF_00204
Alternative name(s):
Excinuclease ABC subunit B HAMAP-Rule MF_00204
Gene names
Name:uvrB HAMAP-Rule MF_00204 EMBL ADB14078.1
Ordered Locus Names:HMPREF0424_0606
OrganismGardnerella vaginalis (strain 409-05) [Complete proteome] [HAMAP]
Taxonomic identifier553190 [NCBI]
Taxonomic lineageBacteria › Actinobacteria › Actinobacteridae › Bifidobacteriales › Bifidobacteriaceae › Gardnerella ›

Protein attributes

Sequence length704 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA2B2 complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage By similarity. HAMAP-Rule MF_00204 SAAS SAAS024759

Subunit structure

Forms a heterotetramer with UvrA during the search for lesions. Interacts with UvrC in an incision complex By similarity. HAMAP-Rule MF_00204 RuleBase RU003587 SAAS SAAS024759

Subcellular location

Cytoplasm By similarity HAMAP-Rule MF_00204 RuleBase RU003587 SAAS SAAS024759.

Domain

The beta-hairpin motif is involved in DNA binding By similarity. HAMAP-Rule MF_00204

Sequence similarities

Belongs to the UvrB family. HAMAP-Rule MF_00204 RuleBase RU003587

Contains 1 UVR domain. HAMAP-Rule MF_00204 RuleBase RU003587 SAAS SAAS024759

Contains 1 helicase ATP-binding domain. HAMAP-Rule MF_00204 SAAS SAAS024759

Contains 1 helicase C-terminal domain. HAMAP-Rule MF_00204 SAAS SAAS024759

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Regions

Domain33 – 190158Helicase ATP-binding By similarity HAMAP-Rule MF_00204
Domain436 – 602167Helicase C-terminal By similarity HAMAP-Rule MF_00204
Domain660 – 69536UVR By similarity HAMAP-Rule MF_00204
Nucleotide binding46 – 538ATP By similarity HAMAP-Rule MF_00204
Motif99 – 12224Beta-hairpin By similarity HAMAP-Rule MF_00204

Sequences

Sequence LengthMass (Da)Tools
D2RAK7 [UniParc].

Last modified March 2, 2010. Version 1.
Checksum: FE32726AC13343BB

FASTA70479,959
        10         20         30         40         50         60 
MSNKIQRTNK PFVVKAPYKP SGDQPQAIDE LANRIENGEN DVVLMGATGT GKTATTAWLI 

        70         80         90        100        110        120 
ERLQRPTLII EPNKTLAAQL CAEFRELMPD NAVSYFVSYY DYYQPEAYIP QTDTYIEKDS 

       130        140        150        160        170        180 
NINDDVERLR HAATANLLTR RDCVVVATVS CIYGLGTPEE YAERMLMLSV GEQLERDDLL 

       190        200        210        220        230        240 
RQFVSMQYKR NDIAFTRGTF RVRGDTVEII PVYEELAVRI EFFGDEIDRI TMLHPLTGEV 

       250        260        270        280        290        300 
IRQESSVHIF PASHYIAGPE RMERALEAIE KERDERVAQL KKQNKLLEAQ RLEMRTTYDL 

       310        320        330        340        350        360 
EMLRQVGVCP GVENYSRHFD GRDAGTPPHT LLDFFPDDFL LVLDESHVTV PQIGAMYEGD 

       370        380        390        400        410        420 
ASRKRTLVEH GFRLPSAMDN RPLKWKEFLE HVGQTVYLSA TPGDYELGLS DGVVEQIIRP 

       430        440        450        460        470        480 
TGLLDPKIEV RPVEGQVDDL LAEIKERVAK DERVLVTTLT KKMAEDLTDY FLELGIKVEY 

       490        500        510        520        530        540 
LHSDVDTLRR VELLRELREG KIDVIVGINL LREGLDLPEV SLVAILDADK EGFLRSYRSL 

       550        560        570        580        590        600 
IQTIGRAARN VSGTVLMYAD TVTDAMSKAI SETERRREKQ IAYNKAHGID PKPLRKKISD 

       610        620        630        640        650        660 
VNDMLAKEDV DTQTLLAGGY RNANKAGNSH YGVPKEPNLG QQSKEKRMAN VSELPQDDIM 

       670        680        690        700 
SLIKNLSEQM HVAAEQLQFE LAARLRDEIR DLKKELRQIS DAQS

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References

[1]"Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential."
Yeoman C.J., Yildirim S., Thomas S.M., Durkin A.S., Torralba M., Sutton G., Buhay C.J., Ding Y., Dugan-Rocha S.P., Muzny D.M., Qin X., Gibbs R.A., Leigh S.R., Stumpf R., White B.A., Highlander S.K., Nelson K.E., Wilson B.A.
PLoS ONE 5:E12411-E12411(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: 409-05.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		CP001849 Genomic DNA. Translation: ADB14078.1.
RefSeqYP_003373842.1. NC_013721.1.

3D structure databases

ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaADB14078; ADB14078; HMPREF0424_0606.
GeneID8709472.
KEGGgva:HMPREF0424_0606.
PATRIC32147120. VBIGarVag136958_0534.

Organism-specific databases

CMRSearch...

Phylogenomic databases

HOGENOMHOG000073580.
KOK03702.
OMAFTIAHVI.

Enzyme and pathway databases

BioCycGVAG553190:GJPT-607-MONOMER.

Family and domain databases

Gene3D4.10.860.10. 1 hit.
HAMAPMF_00204. UvrB.
InterProIPR006935. Helicase/UvrB_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR001943. UVR_dom.
IPR004807. UvrB.
IPR024759. UvrB_YAD/RRR_dom.
[Graphical view]
PANTHERPTHR24029. PTHR24029. 1 hit.
PfamPF00271. Helicase_C. 1 hit.
PF04851. ResIII. 1 hit.
PF02151. UVR. 1 hit.
PF12344. UvrB. 1 hit.
[Graphical view]
SMARTSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMSSF46600. UvrB_C. 1 hit.
TIGRFAMsTIGR00631. uvrb. 1 hit.
PROSITEPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS50151. UVR. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameD2RAK7_GARV4
AccessionPrimary (citable) accession number: D2RAK7
Entry history
Integrated into UniProtKB/TrEMBL: March 2, 2010
Last sequence update: March 2, 2010
Last modified: May 1, 2013
This is version 28 of the entry and version 1 of the sequence. [Complete history]
Entry statusUnreviewed (UniProtKB/TrEMBL)
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