PDBsum entry 2cvh

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protein Protein-protein interface(s) links
DNA binding protein PDB id
Protein chains
220 a.a. *
Waters ×297
* Residue conservation analysis
PDB id:
Name: DNA binding protein
Title: Crystal structure of the radb recombinase
Structure: DNA repair and recombination protein radb. Chain: a, b. Engineered: yes
Source: Thermococcus kodakarensis. Organism_taxid: 311400. Gene: pk-rec. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.20Å     R-factor:   0.193     R-free:   0.253
Authors: T.Akiba,N.Ishii,N.Rashid,M.Morikawa,T.Imanaka,K.Harata
Key ref: T.Akiba et al. (2005). Structure of RadB recombinase from a hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1: an implication for the formation of a near-7-fold helical assembly. Nucleic Acids Res, 33, 3412-3423. PubMed id: 15956102
03-Jun-05     Release date:   09-Aug-05    
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Protein chains
Pfam   ArchSchema ?
P95547  (RADB_PYRKO) -  DNA repair and recombination protein RadB
220 a.a.
220 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     response to DNA damage stimulus   5 terms 
  Biochemical function     nucleotide binding     5 terms  


Nucleic Acids Res 33:3412-3423 (2005)
PubMed id: 15956102  
Structure of RadB recombinase from a hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1: an implication for the formation of a near-7-fold helical assembly.
T.Akiba, N.Ishii, N.Rashid, M.Morikawa, T.Imanaka, K.Harata.
The X-ray crystal structure of RadB from Thermococcus kodakaraensis KOD1, an archaeal homologue of the RecA/Rad51 family proteins, have been determined in two crystal forms. The structure represents the core ATPase domain of the RecA/Rad51 proteins. Two independent molecules in the type 1 crystal were roughly related by 7-fold screw symmetry whereas non-crystallographic 2-fold symmetry was observed in the type 2 crystal. The dimer structure in the type 1 crystal is extended to construct a helical assembly, which resembles the filamentous structures reported for other RecA/Rad51 proteins. The molecular interface in the type 1 dimer is formed by facing a basic surface patch of one monomer to an acidic one of the other. The empty ATP binding pocket is located at the interface and barely concealed from the outside similarly to that in the active form of the RecA filament. The model assembly has a positively charged belt on one surface bordering the helical groove suitable for facile binding of DNA. Electron microscopy has revealed that, in the absence of ATP and DNA, RadB forms a filament with a similar diameter to that of the hypothetical assembly, although its helical properties were not confirmed.
  Selected figure(s)  
Figure 1.
Ribbon representation of TkRadB. denoted by H1-H7 and S1-S9, respectively, and the N- and C-terminals by N and C, respectively. The L1 and L2 loops are also labelled. Side-chains of Lys-33, Thr-34 and Asp-112 are presented as ball-and-stick models to show the location of the ATP binding site; the first two of the Walker A motif are in green and the last one of the Walker B motif in cyan.
Figure 3.
Structures of the asymmetric unit of the type 1 crystal (a) and the type 2 crystal (b). Side-chains of Lys-33, Thr-34 and Asp-112 in each monomer are presented as ball-and-stick models as in Figure 1. In (b), the non-crystallographic 2-fold rotation axis is perpendicular to the figure plane.
  The above figures are reprinted from an Open Access publication published by Oxford University Press: Nucleic Acids Res (2005, 33, 3412-3423) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20194117 A.Lopes, J.Amarir-Bouhram, G.Faure, M.A.Petit, and R.Guerois (2010).
Detection of novel recombinases in bacteriophage genomes unveils Rad52, Rad51 and Gp2.5 remote homologs.
  Nucleic Acids Res, 38, 3952-3962.  
19027026 J.N.Farb, and S.W.Morrical (2009).
Role of allosteric switch residue histidine 195 in maintaining active-site asymmetry in presynaptic filaments of bacteriophage T4 UvsX recombinase.
  J Mol Biol, 385, 393-404.  
17938853 D.Sheng, S.Zhu, T.Wei, J.Ni, and Y.Shen (2008).
The in vitro activity of a Rad55 homologue from Sulfolobus tokodaii, a candidate mediator in RadA-catalyzed homologous recombination.
  Extremophiles, 12, 147-157.  
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