PDBsum entry 2f1i

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Recombination PDB id
Protein chain
299 a.a. *
_MG ×2
Waters ×7
* Residue conservation analysis
PDB id:
Name: Recombination
Title: Recombinase in complex with amp-pnp
Structure: DNA repair and recombination protein rada. Chain: a. Engineered: yes. Mutation: yes
Source: Methanococcus voltae. Organism_taxid: 2188. Gene: rada. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.90Å     R-factor:   0.209     R-free:   0.256
Authors: X.Qian,Y.He,Y.Wu,Y.Luo
Key ref:
X.Qian et al. (2006). Asp302 determines potassium dependence of a RadA recombinase from Methanococcus voltae. J Mol Biol, 360, 537-547. PubMed id: 16782126 DOI: 10.1016/j.jmb.2006.05.058
14-Nov-05     Release date:   30-May-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
O73948  (RADA_METVO) -  DNA repair and recombination protein RadA
322 a.a.
299 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

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


DOI no: 10.1016/j.jmb.2006.05.058 J Mol Biol 360:537-547 (2006)
PubMed id: 16782126  
Asp302 determines potassium dependence of a RadA recombinase from Methanococcus voltae.
X.Qian, Y.He, Y.Wu, Y.Luo.
Archaeal RadA/Rad51 are close homologues of eukaryal Rad51/DMC1. Such recombinases, as well as their bacterial RecA orthologues, form helical nucleoprotein filaments in which a hallmark strand exchange reaction occurs between homologous DNA substrates. Our recent ATPase and structure studies on RadA recombinase from Methanococcus voltae have suggested that not only magnesium but also potassium ions are absorbed at the ATPase center. Potassium, but not sodium, stimulates the ATP hydrolysis reaction with an apparent dissociation constant of approximately 40 mM. The minimal inhibitory effect by 40 mM NaCl further suggests that the protein does not have adequate affinity for sodium. The wild-type protein's strand exchange activity is also stimulated by potassium with an apparent dissociation constant of approximately 35 mM. We made site-directed mutations at the potassium-contacting residues Glu151 and Asp302. The mutant proteins are expectedly defective in promoting ATP hydrolysis. Similar potassium preference in strand exchange is observed for the E151D and E151K proteins. The D302K protein, however, shows comparable strand exchange efficiencies in the presence of either potassium or sodium. Crystallized E151D filaments reveal a potassium-dependent conformational change similar to what has previously been observed with the wild-type protein. We interpret these data as suggesting that both ATP hydrolysis and DNA strand exchange requires accessibility to an "active" conformation similar to the crystallized ATPase-active form in the presence of ATP, Mg2+ and K+.
  Selected figure(s)  
Figure 5.
Figure 5. The ATPase site of the E151D mutant RadA in stereo. Two MvRadA subunits are colored yellow and gray, respectively. K^+, Mg^2+ and water molecules are colored purple, red and green, respectively. (a) E151D RadA/AMP–PNP in a 0.5 M KCl. (b) E151D RadA/AMP–PNP complex in 0.5 M NaCl. (c) E151D RadA/ADP complex in 0.5 M KCl. Most residues in the L2 region are ordered in (a), but similarly disordered in (b) and (c). In addition to a nucleoside triphosphate and Mg^2+, K^+ appears to be required for stabilizing the more ordered “active” L2 conformation.
Figure 6.
Figure 6. Two conformations of the E151D monomer in stereo. The E151D monomer has an N-terminal dsDNA-binding domain (top) and a larger ATPase core domain (bottom). The ATPase domain has two half-sites for binding ATP (gold). Two putative DNA-binding regions L1 (green) and L2 (magenta and blue for the two observed conformations, respectively) are located near the filament axis (dotted vertical line). Both ends of the L2 region contact the ATP-binding site. Two K^+ (in yellow) were observed to form bridges between the γ–phosphate of AMP–PNP and the short helix in the L2 region (in magenta). When KCl was substituted for NaCl, the L2 region (in blue) became largely disordered.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 360, 537-547) copyright 2006.  
  Figures were selected by the author.  
    Author's comment    
  Rad51-like strand exchange proteins (or recombinases) are known to be stimulated by cations. Such stimulation is correlated with a disorder-order transition in the DNA-interacting L2 region triggered by incorporation of cation(s) such as potassium in the ATPase center.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20096651 V.Marini, and L.Krejci (2010).
Srs2: the "Odd-Job Man" in DNA repair.
  DNA Repair (Amst), 9, 268-275.  
20015079 W.Kagawa, and H.Kurumizaka (2010).
From meiosis to postmeiotic events: uncovering the molecular roles of the meiosis-specific recombinase Dmc1.
  FEBS J, 277, 590-598.  
19066203 A.A.Grigorescu, J.H.Vissers, D.Ristic, Y.Z.Pigli, T.W.Lynch, C.Wyman, and P.A.Rice (2009).
Inter-subunit interactions that coordinate Rad51's activities.
  Nucleic Acids Res, 37, 557-567.  
19465774 Y.Li, Y.He, and Y.Luo (2009).
Conservation of a conformational switch in RadA recombinase from Methanococcus maripaludis.
  Acta Crystallogr D Biol Crystallogr, 65, 602-610.
PDB codes: 3etl 3ew9 3ewa
17050545 X.Qian, Y.He, X.Ma, M.N.Fodje, P.Grochulski, and Y.Luo (2006).
Calcium stiffens archaeal Rad51 recombinase from Methanococcus voltae for homologous recombination.
  J Biol Chem, 281, 39380-39387.
PDB code: 2i1q
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