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PDBsum entry 2vyf

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protein metals Protein-protein interface(s) links
Hydrolase PDB id
2vyf
Jmol
Contents
Protein chains
398 a.a. *
377 a.a. *
Metals
_AU ×4
* Residue conservation analysis
PDB id:
2vyf
Name: Hydrolase
Title: Crystal structure of the dnac
Structure: Replicative DNA helicase. Chain: a, b. Synonym: dnac. Engineered: yes
Source: Geobacillus kaustophilus hta426. Organism_taxid: 235909. Expressed in: escherichia coli. Expression_system_taxid: 511693.
Resolution:
3.60Å     R-factor:   0.293     R-free:   0.324
Authors: Y.H.Lo,K.L.Tsai,Y.J.Sun,C.D.Hsiao
Key ref: Y.H.Lo et al. (2009). The crystal structure of a replicative hexameric helicase DnaC and its complex with single-stranded DNA. Nucleic Acids Res, 37, 804-814. PubMed id: 19074952
Date:
23-Jul-08     Release date:   30-Dec-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q5KU75  (Q5KU75_GEOKA) -  Replicative DNA helicase
Seq:
Struc:
454 a.a.
398 a.a.
Protein chain
Pfam   ArchSchema ?
Q5KU75  (Q5KU75_GEOKA) -  Replicative DNA helicase
Seq:
Struc:
454 a.a.
377 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA replication   2 terms 
  Biochemical function     DNA binding     4 terms  

 

 
Nucleic Acids Res 37:804-814 (2009)
PubMed id: 19074952  
 
 
The crystal structure of a replicative hexameric helicase DnaC and its complex with single-stranded DNA.
Y.H.Lo, K.L.Tsai, Y.J.Sun, W.T.Chen, C.Y.Huang, C.D.Hsiao.
 
  ABSTRACT  
 
DNA helicases are motor proteins that play essential roles in DNA replication, repair and recombination. In the replicative hexameric helicase, the fundamental reaction is the unwinding of duplex DNA; however, our understanding of this function remains vague due to insufficient structural information. Here, we report two crystal structures of the DnaB-family replicative helicase from Geobacillus kaustophilus HTA426 (GkDnaC) in the apo-form and bound to single-stranded DNA (ssDNA). The GkDnaC-ssDNA complex structure reveals that three symmetrical basic grooves on the interior surface of the hexamer individually encircle ssDNA. The ssDNA-binding pockets in this structure are directed toward the N-terminal domain collar of the hexameric ring, thus orienting the ssDNA toward the DnaG primase to facilitate the synthesis of short RNA primers. These findings provide insight into the mechanism of ssDNA binding and provide a working model to establish a novel mechanism for DNA translocation at the replication fork.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21210194 C.C.Chen, and C.Y.Huang (2011).
Inhibition of Klebsiella pneumoniae DnaB helicase by the flavonol galangin.
  Protein J, 30, 59-65.  
20129058 M.Makowska-Grzyska, and J.M.Kaguni (2010).
Primase directs the release of DnaC from DnaB.
  Mol Cell, 37, 90.  
19255093 K.V.Loscha, K.Jaudzems, C.Ioannou, X.C.Su, F.R.Hill, G.Otting, N.E.Dixon, and E.Liepinsh (2009).
A novel zinc-binding fold in the helicase interaction domain of the Bacillus subtilis DnaI helicase loader.
  Nucleic Acids Res, 37, 2395-2404.
PDB code: 2k7r
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.