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PDBsum entry 2oe2

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protein ligands links
Recombination PDB id
2oe2
Jmol
Contents
Protein chain
326 a.a. *
Ligands
PO4
Waters ×45
* Residue conservation analysis
PDB id:
2oe2
Name: Recombination
Title: Msreca-native-low humidity 95%
Structure: Protein reca. Chain: a. Synonym: recombinase a. Engineered: yes
Source: Mycobacterium smegmatis. Organism_taxid: 1772. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
3.45Å     R-factor:   0.210     R-free:   0.278
Authors: R.Krishna,J.Rajan Prabu,G.P.Manjunath,S.Datta,N.R.Chandra, K.Muniyappa,M.Vijayan
Key ref:
R.Krishna et al. (2007). Snapshots of RecA protein involving movement of the C-domain and different conformations of the DNA-binding loops: crystallographic and comparative analysis of 11 structures of Mycobacterium smegmatis RecA. J Mol Biol, 367, 1130-1144. PubMed id: 17306300 DOI: 10.1016/j.jmb.2007.01.058
Date:
28-Dec-06     Release date:   19-Jun-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q5QJ16  (Q5QJ16_MYCSM) -  Protein RecA
Seq:
Struc:
349 a.a.
326 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     response to DNA damage stimulus   6 terms 
  Biochemical function     nucleotide binding     7 terms  

 

 
DOI no: 10.1016/j.jmb.2007.01.058 J Mol Biol 367:1130-1144 (2007)
PubMed id: 17306300  
 
 
Snapshots of RecA protein involving movement of the C-domain and different conformations of the DNA-binding loops: crystallographic and comparative analysis of 11 structures of Mycobacterium smegmatis RecA.
R.Krishna, J.R.Prabu, G.P.Manjunath, S.Datta, N.R.Chandra, K.Muniyappa, M.Vijayan.
 
  ABSTRACT  
 
Mycobacterium smegmatis RecA and its nucleotide complexes crystallize in three different, but closely related, forms characterized by specific ranges of unit cell dimensions. The six crystals reported here and five reported earlier, all grown under the same or very similar conditions, belong to these three forms, all in space group P6(1). They include one obtained by reducing relative humidity around the crystal. In all crystals, RecA monomers form filaments around a 6(1) screw axis. Thus, the c-dimension of the crystal corresponds to the pitch of the RecA filament. As reported for Escherichia coli RecA, the variation in the pitch among the three forms correlates well with the motion of the C-terminal domain of the RecA monomers with respect to the main domain. The domain motion is compatible with formation of inactive as well as active RecA filaments involving monomers with a fully ordered C domain. It does not appear to influence the movement upon nucleotide-binding of the switch residue, which is believed to provide the trigger for transmitting the effect of nucleotide binding to the DNA-binding region. Interestingly, partial dehydration of the crystal results in the movement of the residue similar to that caused by nucleotide binding. The ordering of the DNA-binding loops, which present ensembles of conformations, is also unaffected by domain motion. The conformation of loop L2 appears to depend upon nucleotide binding, presumably on account of the movement of the switch residue that forms part of the loop. The conformations of loops L1 and L2 are correlated and have implications for intermolecular communications within the RecA filament. The structures resulting from different orientations of the C domain and different conformations of the DNA-binding loops appear to represent snapshots of the RecA at different phases of activity, and provide insights into the mechanism of action of RecA.
 
  Selected figure(s)  
 
Figure 3.
Figure 7.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 367, 1130-1144) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19307712 B.Chetnani, S.Das, P.Kumar, A.Surolia, and M.Vijayan (2009).
Mycobacterium tuberculosis pantothenate kinase: possible changes in location of ligands during enzyme action.
  Acta Crystallogr D Biol Crystallogr, 65, 312-325.
PDB codes: 2zs7 2zs8 2zs9 2zsa 2zsb 2zsd 2zse 2zsf
19540850 D.Lucarelli, Y.A.Wang, V.E.Galkin, X.Yu, D.B.Wigley, and E.H.Egelman (2009).
The RecB nuclease domain binds to RecA-DNA filaments: implications for filament loading.
  J Mol Biol, 391, 269-274.  
19013467 V.E.Galkin, X.Yu, J.Bielnicki, D.Ndjonka, C.E.Bell, and E.H.Egelman (2009).
Cleavage of bacteriophage lambda cI repressor involves the RecA C-terminal domain.
  J Mol Biol, 385, 779-787.  
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
19020353 J.R.Prabu, G.P.Manjunath, N.R.Chandra, K.Muniyappa, and M.Vijayan (2008).
Functionally important movements in RecA molecules and filaments: studies involving mutation and environmental changes.
  Acta Crystallogr D Biol Crystallogr, 64, 1146-1157.
PDB codes: 2zr0 2zr7 2zr9 2zra 2zrb 2zrc 2zrd 2zre 2zrf 2zrg 2zrh 2zri 2zrj 2zrk 2zrl 2zrm 2zrn 2zro 2zrp
18647240 N.D.Thomsen, and J.M.Berger (2008).
Structural frameworks for considering microbial protein- and nucleic acid-dependent motor ATPases.
  Mol Microbiol, 69, 1071-1090.  
18453691 P.S.Kaushal, R.K.Talawar, P.D.Krishna, U.Varshney, and M.Vijayan (2008).
Unique features of the structure and interactions of mycobacterial uracil-DNA glycosylase: structure of a complex of the Mycobacterium tuberculosis enzyme in comparison with those from other sources.
  Acta Crystallogr D Biol Crystallogr, 64, 551-560.
PDB code: 2zhx
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