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PDBsum entry 2g88

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protein ligands metals links
Recombination PDB id
2g88
Jmol
Contents
Protein chain
331 a.a. *
Ligands
DTP ×2
CIT
Metals
_MG
Waters ×108
* Residue conservation analysis
PDB id:
2g88
Name: Recombination
Title: Msreca-datp complex
Structure: Protein reca. Chain: a. Synonym: recombinase a. Engineered: yes
Source: Mycobacterium smegmatis. Organism_taxid: 1772. Gene: reca. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
3.20Å     R-factor:   0.237     R-free:   0.309
Authors: R.Krishna,G.P.Manjunath,P.Kumar,A.Surolia,N.R.Chandra, K.Muniyappa,M.Vijayan
Key ref: R.Krishna et al. (2006). Crystallographic identification of an ordered C-terminal domain and a second nucleotide-binding site in RecA: new insights into allostery. Nucleic Acids Res, 34, 2186-2195. PubMed id: 16648362
Date:
02-Mar-06     Release date:   16-May-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q7X416  (Q7X416_MYCSM) -  Protein RecA (Fragment)
Seq:
Struc:
308 a.a.
331 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     6 terms  

 

 
Nucleic Acids Res 34:2186-2195 (2006)
PubMed id: 16648362  
 
 
Crystallographic identification of an ordered C-terminal domain and a second nucleotide-binding site in RecA: new insights into allostery.
R.Krishna, G.P.Manjunath, P.Kumar, A.Surolia, N.R.Chandra, K.Muniyappa, M.Vijayan.
 
  ABSTRACT  
 
RecA protein is a crucial and central component of the homologous recombination and DNA repair machinery. Despite numerous studies on the protein, several issues concerning its action, including the allosteric regulation mechanism have remained unclear. Here we report, for the first time, a crystal structure of a complex of Mycobacterium smegmatis RecA (MsRecA) with dATP, which exhibits a fully ordered C-terminal domain, with a second dATP molecule bound to it. ATP binding is an essential step for all activities of RecA, since it triggers the formation of active nucleoprotein filaments. In the crystal filament, dATP at the first site communicates with a dATP of the second site of an adjacent subunit, through conserved residues, suggesting a new route for allosteric regulation. In addition, subtle but definite changes observed in the orientation of the nucleotide at the first site and in the positions of the segment preceding loop L2 as well as in the segment 102-105 situated between the 2 nt, all appear to be concerted and suggestive of a biological role for the second bound nucleotide.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21458462 V.E.Galkin, R.L.Britt, L.B.Bane, X.Yu, M.M.Cox, and E.H.Egelman (2011).
Two modes of binding of DinI to RecA filament provide a new insight into the regulation of SOS response by DinI protein.
  J Mol Biol, 408, 815-824.  
20944238 P.S.Kaushal, P.Singh, A.Sharma, K.Muniyappa, and M.Vijayan (2010).
X-ray and molecular-dynamics studies on Mycobacterium leprae single-stranded DNA-binding protein and comparison with other eubacterial SSB structures.
  Acta Crystallogr D Biol Crystallogr, 66, 1048-1058.
PDB codes: 3afp 3afq
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.  
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.  
18421138 C.Lecomte, C.Jelsch, B.Guillot, B.Fournier, and A.Lagoutte (2008).
Ultrahigh-resolution crystallography and related electron density and electrostatic properties in proteins.
  J Synchrotron Radiat, 15, 202-203.  
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
18216451 K.Ejsmont, J.P.Joly, E.Wenger, and C.Jelsch (2008).
(2S,3S)-2-(N,N-dibenzylamino)butane-1,3-diol refined using a multipolar atom model.
  Acta Crystallogr C, 64, o18-o20.  
18200608 O.Okhrimenko, and I.Jelesarov (2008).
A survey of the year 2006 literature on applications of isothermal titration calorimetry.
  J Mol Recognit, 21, 1.  
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
18461484 S.H.Leuba, S.P.Anand, J.M.Harp, and S.A.Khan (2008).
Expedient placement of two fluorescent dyes for investigating dynamic DNA protein interactions in real time.
  Chromosome Res, 16, 451-467.  
17228330 M.M.Cox (2007).
Motoring along with the bacterial RecA protein.
  Nat Rev Mol Cell Biol, 8, 127-138.  
  16880543 J.R.Prabu, S.Thamotharan, J.S.Khanduja, E.Z.Alipio, C.Y.Kim, G.S.Waldo, T.C.Terwilliger, B.Segelke, T.Lekin, D.Toppani, L.W.Hung, M.Yu, E.Bursey, K.Muniyappa, N.R.Chandra, and M.Vijayan (2006).
Structure of Mycobacterium tuberculosis RuvA, a protein involved in recombination.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 731-734.
PDB code: 2h5x
  16946478 M.Selvaraj, N.S.Singh, S.Roy, R.Sangeetha, U.Varshney, and M.Vijayan (2006).
Cloning, expression, purification, crystallization and preliminary X-ray analysis of peptidyl-tRNA hydrolase from Mycobacterium tuberculosis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 913-915.  
  17142904 P.Singh, R.K.Talawar, P.D.Krishna, U.Varshney, and M.Vijayan (2006).
Overexpression, purification, crystallization and preliminary X-ray analysis of uracil N-glycosylase from Mycobacterium tuberculosis in complex with a proteinaceous inhibitor.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1231-1234.  
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.