spacer
spacer

PDBsum entry 1xms

Go to PDB code: 
protein ligands metals links
DNA binding protein PDB id
1xms
Jmol
Contents
Protein chain
300 a.a. *
Ligands
ANP
Metals
_MN
Waters ×125
* Residue conservation analysis
PDB id:
1xms
Name: DNA binding protein
Title: "E. Coli reca in complex with mnamp-pnp"
Structure: Reca protein. Chain: a. Fragment: e. Coli reca with gly-ser-his-met at n-terminus. Synonym: recombinase a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: reca. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.10Å     R-factor:   0.223     R-free:   0.261
Authors: C.E.Bell,X.Xing
Key ref:
X.Xing and C.E.Bell (2004). Crystal structures of Escherichia coli RecA in complex with MgADP and MnAMP-PNP. Biochemistry, 43, 16142-16152. PubMed id: 15610008 DOI: 10.1021/bi048165y
Date:
04-Oct-04     Release date:   04-Jan-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A7G6  (RECA_ECOLI) -  Protein RecA
Seq:
Struc:
353 a.a.
300 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 stress   9 terms 
  Biochemical function     nucleotide binding     8 terms  

 

 
DOI no: 10.1021/bi048165y Biochemistry 43:16142-16152 (2004)
PubMed id: 15610008  
 
 
Crystal structures of Escherichia coli RecA in complex with MgADP and MnAMP-PNP.
X.Xing, C.E.Bell.
 
  ABSTRACT  
 
RecA catalyzes the DNA pairing and strand-exchange steps of homologous recombination, an important mechanism for repair of double-stranded DNA breaks. The binding of RecA to DNA is modulated by adenosine nucleotides. ATP increases the affinity of RecA for DNA, while ADP decreases the affinity. Previously, the crystal structures of E. coli RecA and its complex with ADP have been determined to resolutions of 2.3 and 3.0 A, respectively, but the model for the RecA-ADP complex did not include magnesium ion or side chains. Here, we have determined the crystal structures of RecA in complex with MgADP and MnAMP-PNP, a nonhydrolyzable analogue of ATP, at resolutions of 1.9 and 2.1 A, respectively. Both crystals grow in the same conditions and have RecA in a right-handed helical form with a pitch of approximately 82 A. The crystal structures show the detailed interactions of RecA with the nucleotide cofactors, including the metal ion and the gamma phosphate of AMP-PNP. There are very few conformational differences between the structures of RecA bound to ADP and AMP-PNP, which differ from uncomplexed RecA only in a slight opening of the P-loop residues 66-73 upon nucleotide binding. To interpret the functional significance of the structure of the MnAMP-PNP complex, a coprotease assay was used to compare the ability of different nucleotides to promote the active, extended conformation of RecA. Whereas ATPgammaS and ADP-AlF(4) facilitate a robust coprotease activity, ADP and AMP-PNP do not activate RecA at all. We conclude that the crystal structure of the RecA-MnAMP-PNP complex represents a preisomerization state of the RecA protein that exists after ATP has bound but before the conformational transition to the active state.
 

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.  
20308162 L.T.Chen, and A.H.Wang (2010).
A rationally designed peptide enhances homologous recombination in vitro and resistance to DNA damaging agents in vivo.
  Nucleic Acids Res, 38, 4361-4371.  
20056148 M.Rusu, and S.Birmanns (2010).
Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions.
  J Struct Biol, 170, 164-171.  
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.  
19876400 G.Walia, P.Kumar, and A.Surolia (2009).
The role of UPF0157 in the folding of M. tuberculosis dephosphocoenzyme A kinase and the regulation of the latter by CTP.
  PLoS One, 4, e7645.  
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
18386081 J.Petersen, C.J.Mitchell, K.Fisher, and D.J.Lowe (2008).
Structural basis for VO(2+)-inhibition of nitrogenase activity: (B) pH-sensitive inner-sphere rearrangements in the 1H-environment of the metal coordination site of the nitrogenase Fe-protein identified by ENDOR spectroscopy.
  J Biol Inorg Chem, 13, 637-650.  
17602667 H.Qiu, and Y.Wang (2007).
Probing adenosine nucleotide-binding proteins with an affinity-labeled nucleotide probe and mass spectrometry.
  Anal Chem, 79, 5547-5556.  
17228330 M.M.Cox (2007).
Motoring along with the bacterial RecA protein.
  Nat Rev Mol Cell Biol, 8, 127-138.  
16783375 D.Keramisanou, N.Biris, I.Gelis, G.Sianidis, S.Karamanou, A.Economou, and C.G.Kalodimos (2006).
Disorder-order folding transitions underlie catalysis in the helicase motor of SecA.
  Nat Struct Mol Biol, 13, 594-602.  
16648362 R.Krishna, G.P.Manjunath, P.Kumar, A.Surolia, N.R.Chandra, K.Muniyappa, and M.Vijayan (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.
PDB code: 2g88
16765891 V.E.Galkin, Y.Wu, X.P.Zhang, X.Qian, Y.He, X.Yu, W.D.Heyer, Y.Luo, and E.H.Egelman (2006).
The Rad51/RadA N-terminal domain activates nucleoprotein filament ATPase activity.
  Structure, 14, 983-992.
PDB code: 2gdj
16194225 C.E.Bell (2005).
Structure and mechanism of Escherichia coli RecA ATPase.
  Mol Microbiol, 58, 358-366.  
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.