2Q8U

CRYSTAL STRUCTURE OF MRE11 FROM THERMOTOGA MARITIMA MSB8 (TM1635) AT 2.20 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Crystal structure of the first eubacterial Mre11 nuclease reveals novel features that may discriminate substrates during DNA repair.

Das, D.Moiani, D.Axelrod, H.L.Miller, M.D.McMullan, D.Jin, K.K.Abdubek, P.Astakhova, T.Burra, P.Carlton, D.Chiu, H.J.Clayton, T.Deller, M.C.Duan, L.Ernst, D.Feuerhelm, J.Grant, J.C.Grzechnik, A.Grzechnik, S.K.Han, G.W.Jaroszewski, L.Klock, H.E.Knuth, M.W.Kozbial, P.Krishna, S.S.Kumar, A.Marciano, D.Morse, A.T.Nigoghossian, E.Okach, L.Paulsen, J.Reyes, R.Rife, C.L.Sefcovic, N.Tien, H.J.Trame, C.B.van den Bedem, H.Weekes, D.Xu, Q.Hodgson, K.O.Wooley, J.Elsliger, M.A.Deacon, A.M.Godzik, A.Lesley, S.A.Tainer, J.A.Wilson, I.A.

(2010) J Mol Biol 397: 647-663

  • DOI: 10.1016/j.jmb.2010.01.049
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Mre11 nuclease plays a central role in the repair of cytotoxic and mutagenic DNA double-strand breaks. As X-ray structural information has been available only for the Pyrococcus furiosus enzyme (PfMre11), the conserved and variable features of this n ...

    Mre11 nuclease plays a central role in the repair of cytotoxic and mutagenic DNA double-strand breaks. As X-ray structural information has been available only for the Pyrococcus furiosus enzyme (PfMre11), the conserved and variable features of this nuclease across the domains of life have not been experimentally defined. Our crystal structure and biochemical studies demonstrate that TM1635 from Thermotoga maritima, originally annotated as a putative nuclease, is an Mre11 endo/exonuclease (TmMre11) and the first such structure from eubacteria. TmMre11 and PfMre11 display similar overall structures, despite sequence identity in the twilight zone of only approximately 20%. However, they differ substantially in their DNA-specificity domains and in their dimeric organization. Residues in the nuclease domain are highly conserved, but those in the DNA-specificity domain are not. The structural differences likely affect how Mre11 from different organisms recognize and interact with single-stranded DNA, double-stranded DNA and DNA hairpin structures during DNA repair. The TmMre11 nuclease active site has no bound metal ions, but is conserved in sequence and structure with the exception of a histidine that is important in PfMre11 nuclease activity. Nevertheless, biochemical characterization confirms that TmMre11 possesses both endonuclease and exonuclease activities on single-stranded and double-stranded DNA substrates, respectively.


    Organizational Affiliation

    Joint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Exonuclease, putativeA, B336Thermotoga maritima MSB8Mutation(s): 5 
Gene Names: TM_1635sbcD
Find proteins for Q9X1X0 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Explore Q9X1X0 
Go to UniProtKB:  Q9X1X0
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.598α = 90
b = 113.414β = 101.77
c = 80.951γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2017-10-25
    Changes: Author supporting evidence
  • Version 1.5: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description