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PDBsum entry 1mo4
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Hydrolase PDB id
1mo4

 

 

 

 

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Contents
Protein chain
324 a.a. *
Ligands
AGS
Waters ×70
* Residue conservation analysis
PDB id:
1mo4
Name: Hydrolase
Title: Reca-atp-gamma-s complex
Structure: Reca. Chain: a. Synonym: recombinase a. Engineered: yes
Source: Mycobacterium tuberculosis. Organism_taxid: 1773. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
3.20Å     R-factor:   0.201     R-free:   0.254
Authors: S.Datta,N.Ganesh,N.R.Chandra,Tb Structural Genomics Consortium (Tbsgc)
Key ref:
S.Datta et al. (2003). Structural studies on MtRecA-nucleotide complexes: insights into DNA and nucleotide binding and the structural signature of NTP recognition. Proteins, 50, 474-485. PubMed id: 12557189 DOI: 10.1002/prot.10315
Date:
07-Sep-02     Release date:   18-Feb-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P9WHJ3  (RECA_MYCTU) -  Protein RecA from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Seq:
Struc: 		 
Seq:
Struc: 		790 a.a.
324 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 68 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.1.-.-
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1002/prot.10315 Proteins 50:474-485 (2003)
PubMed id: 12557189  
 
 
Structural studies on MtRecA-nucleotide complexes: insights into DNA and nucleotide binding and the structural signature of NTP recognition.
S.Datta, N.Ganesh, N.R.Chandra, K.Muniyappa, M.Vijayan.
 
  ABSTRACT  
 
RecA protein plays a crucial role in homologous recombination and repair of DNA. Central to all activities of RecA is its binding to Mg(+2)-ATP. The active form of the protein is a helical nucleoprotein filament containing the nucleotide cofactor and single-stranded DNA. The stability and structure of the helical nucleoprotein filament formed by RecA are modulated by nucleotide cofactors. Here we report crystal structures of a MtRecA-ADP complex, complexes with ATPgammaS in the presence and absence of magnesium as well as a complex with dATP and Mg+2. Comparison with the recently solved crystal structures of the apo form as well as a complex with ADP-AlF4 confirms an expansion of the P-loop region in MtRecA, compared to its homologue in Escherichia coli, correlating with the reduced affinity of MtRecA for ATP. The ligand bound structures reveal subtle variations in nucleotide conformations among different nucleotides that serve in maintaining the network of interactions crucial for nucleotide binding. The nucleotide binding site itself, however, remains relatively unchanged. The analysis also reveals that ATPgammaS rather than ADP-AlF4 is structurally a better mimic of ATP. From among the complexed structures, a definition for the two DNA-binding loops L1 and L2 has clearly emerged for the first time and provides a basis to understand DNA binding by RecA. The structural information obtained from these complexes correlates well with the extensive biochemical data on mutants available in the literature, contributing to an understanding of the role of individual residues in the nucleotide binding pocket, at the molecular level. Modeling studies on the mutants again point to the relative rigidity of the nucleotide binding site. Comparison with other NTP binding proteins reveals many commonalties in modes of binding by diverse members in the structural family, contributing to our understanding of the structural signature of NTP recognition.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. A: A view down the axis of the MtRecA filament highlighting the residues in the two loops, L1 and L2, that form part of the inner core of the filament. DNA is expected to bind at the groove in the centre. Superposition of the residues corresponding to the loop (and five residues preceeding and five residues succeding the loop) regions (B) L1 and (C) L2, L1 seen clearly in the ATP SMg^+2 complex and L2 seen in ATP S complex, are shown in black. The loops in the other structures were only partially decipherable from their electron density maps, and are shown in gray shades. 		Figure 5.
Figure 5. Superposition of the core of the M domain (residues 38 to 239) (dark line) and the corresponding regions in the 13 structural neighbours (thin lines). Several residues are numbered.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2003, 50, 474-485) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20507912 A.Saladin, C.Amourda, P.Poulain, N.Férey, M.Baaden, M.Zacharias, O.Delalande, and C.Prévost (2010).
Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments.
  Nucleic Acids Res, 38, 6313-6323.  
19910465 R.L.Britt, N.Haruta, S.L.Lusetti, S.Chitteni-Pattu, R.B.Inman, and M.M.Cox (2010).
Disassembly of Escherichia coli RecA E38K/DeltaC17 nucleoprotein filaments is required to complete DNA strand exchange.
  J Biol Chem, 285, 3211-3226.  
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.  
19033358 X.P.Zhang, V.E.Galkin, X.Yu, E.H.Egelman, and W.D.Heyer (2009).
Loop 2 in Saccharomyces cerevisiae Rad51 protein regulates filament formation and ATPase activity.
  Nucleic Acids Res, 37, 158-171.  
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
18057007 D.E.Kainov, E.J.Mancini, J.Telenius, J.Lísal, J.M.Grimes, D.H.Bamford, D.I.Stuart, and R.Tuma (2008).
Structural basis of mechanochemical coupling in a hexameric molecular motor.
  J Biol Chem, 283, 3607-3617.
PDB codes: 2vhc 2vhj 2vhq 2vht 2vhu
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
17228330 M.M.Cox (2007).
Motoring along with the bacterial RecA protein.
  Nat Rev Mol Cell Biol, 8, 127-138.  
17449621 S.P.Anand, H.Zheng, P.R.Bianco, S.H.Leuba, and S.A.Khan (2007).
DNA helicase activity of PcrA is not required for the displacement of RecA protein from DNA or inhibition of RecA-mediated strand exchange.
  J Bacteriol, 189, 4502-4509.  
17098184 E.H.Egelman (2006).
RecA assembly, one molecule at a time.
  Structure, 14, 1600-1602.  
  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
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.  
15889153 J.Zaitseva, S.Jenewein, T.Jumpertz, I.B.Holland, and L.Schmitt (2005).
H662 is the linchpin of ATP hydrolysis in the nucleotide-binding domain of the ABC transporter HlyB.
  EMBO J, 24, 1901-1910.
PDB code: 1xef
15777481 M.Rossbach, O.Daumke, C.Klinger, A.Wittinghofer, and M.Kaufmann (2005).
Crystal structure of THEP1 from the hyperthermophile Aquifex aeolicus: a variation of the RecA fold.
  BMC Struct Biol, 5, 7.
PDB code: 1ye8
15235592 A.B.Conway, T.W.Lynch, Y.Zhang, G.S.Fortin, C.W.Fung, L.S.Symington, and P.A.Rice (2004).
Crystal structure of a Rad51 filament.
  Nat Struct Mol Biol, 11, 791-796.
PDB code: 1szp
15310852 J.A.James, A.K.Aggarwal, R.M.Linden, and C.R.Escalante (2004).
Structure of adeno-associated virus type 2 Rep40-ADP complex: insight into nucleotide recognition and catalysis by superfamily 3 helicases.
  Proc Natl Acad Sci U S A, 101, 12455-12460.
PDB code: 1u0j
14747728 K.Saikrishnan, S.K.Kalapala, M.Bidya Sagar, A.R.Rao, U.Varshney, and M.Vijayan (2004).
Purification, crystallization and preliminary X-ray studies of Mycobacterium tuberculosis RRF.
  Acta Crystallogr D Biol Crystallogr, 60, 368-370.  
12915092 M.Bellinzoni, and G.Riccardi (2003).
Techniques and applications: The heterologous expression of Mycobacterium tuberculosis genes is an uphill road.
  Trends Microbiol, 11, 351-358.  
12837805 S.Datta, R.Krishna, N.Ganesh, N.R.Chandra, K.Muniyappa, and M.Vijayan (2003).
Crystal structures of Mycobacterium smegmatis RecA and its nucleotide complexes.
  J Bacteriol, 185, 4280-4284.
PDB codes: 1ubc 1ube 1ubf 1ubg
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.

 

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