PDBsum entry 2fpm

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Recombination PDB id
Protein chain
311 a.a. *
_MG ×2
__K ×3
Waters ×100
* Residue conservation analysis
PDB id:
Name: Recombination
Title: Rada recombinase in complex with amp-pnp and high concentration of k+
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.
2.00Å     R-factor:   0.213     R-free:   0.239
Authors: Y.Wu,X.Qian,Y.He,I.A.Moya,Y.Luo
Key ref:
X.Qian et al. (2005). Crystal structure of Methanococcus voltae RadA in complex with ADP: hydrolysis-induced conformational change. Biochemistry, 44, 13753-13761. PubMed id: 16229465 DOI: 10.1021/bi051222i
16-Jan-06     Release date:   31-Jan-06    
Supersedes: 1z4d
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
O73948  (RADA_METVO) -  DNA repair and recombination protein RadA
322 a.a.
311 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  


DOI no: 10.1021/bi051222i Biochemistry 44:13753-13761 (2005)
PubMed id: 16229465  
Crystal structure of Methanococcus voltae RadA in complex with ADP: hydrolysis-induced conformational change.
X.Qian, Y.Wu, Y.He, Y.Luo.
Members of a superfamily of RecA-like recombinases facilitate a central strand exchange reaction in the DNA repair process. Archaeal RadA and Rad51 and eukaryal Rad51 and meiosis-specific DMC1 form a closely related group of recombinases distinct from bacterial RecA. Nevertheless, all such recombinases share a conserved core domain which carries the ATPase site and putative DNA-binding sites. Here we present the crystal structure of an archaeal RadA from Methanococcus voltae (MvRadA) in complex with ADP and Mg2+ at 2.1 A resolution. The crystallized RadA-ADP filament has an extended helical pitch similar to those of previously determined structures in the presence of nonhydrolyzable ATP analogue AMP-PNP. Structural comparison reveals two recurrent conformations with an extensive allosteric effect spanning the ATPase site and the putative DNA-binding L2 region. Varied conformations of the L2 region also imply a dynamic nature of recombinase-bound DNA.

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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.  
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
19295907 Y.W.Chang, T.P.Ko, C.D.Lee, Y.C.Chang, K.A.Lin, C.S.Chang, A.H.Wang, and T.F.Wang (2009).
Three new structures of left-handed RADA helical filaments: structural flexibility of N-terminal domain is critical for recombinase activity.
  PLoS ONE, 4, e4890.
PDB codes: 2zub 2zuc 2zud
17329376 L.T.Chen, T.P.Ko, Y.C.Chang, K.A.Lin, C.S.Chang, A.H.Wang, and T.F.Wang (2007).
Crystal structure of the left-handed archaeal RadA helical filament: identification of a functional motif for controlling quaternary structures and enzymatic functions of RecA family proteins.
  Nucleic Acids Res, 35, 1787-1801.
PDB code: 2dfl
17848989 L.T.Chen, T.P.Ko, Y.W.Chang, K.A.Lin, A.H.Wang, and T.F.Wang (2007).
Structural and functional analyses of five conserved positively charged residues in the L1 and N-terminal DNA binding motifs of archaeal RADA protein.
  PLoS ONE, 2, e858.
PDB code: 2z43
17228330 M.M.Cox (2007).
Motoring along with the bacterial RecA protein.
  Nat Rev Mol Cell Biol, 8, 127-138.  
16717288 C.Wiese, J.M.Hinz, R.S.Tebbs, P.B.Nham, S.S.Urbin, D.W.Collins, L.H.Thompson, and D.Schild (2006).
Disparate requirements for the Walker A and B ATPase motifs of human RAD51D in homologous recombination.
  Nucleic Acids Res, 34, 2833-2843.  
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
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 codes are shown on the right.