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The Open Protein Structure Annotation Network
PDB Keyword
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2q8u

    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Crystal structure of the first eubacterial Mre11 nuclease reveals novel features that may discriminate substrates during DNA repair. J.Mol.Biol. 397 647-663 2010
    Site JCSG
    PDB Id 2q8u Target Id 372975
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1616,TM1635 Molecular Weight 37090.69 Da.
    Residues 324 Isoelectric Point 5.74
    Sequence minlkelkilhtsdwhlgvtswtssrpvdrreelkkaldkvveeaekrevdlilltgdllhsrnnpsvv alhdlldylkrmmrtapvvvlpgnhdwkglklfgnfvtsissditfvmsfepvdveakrgqkvrilpfp ypdesealrknegdfrfflesrlnklyeealkkedfaifmghftveglagyagieqgreiiinralips vvdyaalghihsfreiqkqpltiypgsliridfgeeadekgavfvelkrgeppryeridasplplktly ykkidtsalksirdfcrnfpgyvrvvyeedsgilpdlmgeidnlvkie
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.20 Rfree 0.241
    Matthews' coefficent 2.75 Rfactor 0.198
    Waters 159 Solvent Content 55.29

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2q8u
    1. Crystal structure of the first eubacterial Mre11 nuclease reveals novel features that may discriminate substrates during DNA repair
    D Das, D Moiani, HL Axelrod, MD Miller - Journal of molecular , 2010 - Elsevier
     
    2. Crystal Structure of Human Mre11: Understanding Tumorigenic Mutations
    YB Park, J Chae, YC Kim, Y Cho - Structure, 2011 - Elsevier
     
    3. Structure of Mre11Nbs1 complex yields insights into ataxia-telangiectasialike disease mutations and DNA damage signaling
    CB Schiller, K Lammens, I Guerini, B Coordes - Nature Structural & , 2012 - nature.com
     
    4. Functional Evaluation of Bacteriophage T4 Rad50 Signature Motif Residues
    TJ Herdendorf, SW Nelson - Biochemistry, 2011 - ACS Publications
     
    5. Nucleases of metallo-_-lactamase and protein phosphatase families in DNA repair; DNA Repair-On the Pathways to Fixing DNA Damage and Errors
    FJ Fernandez, M Lopez-Estepa, MC Vega - 2011 - digital.csic.es
     
    6. Structural Characterization of the DNA Repair Protein Complex SbcC-SbcD of Thermotoga maritima
    DJ Bemeleit - 2008 - edoc.ub.uni-muenchen.de
     

    Protein Summary

    Gene TM1635 from Thermotoga maritima encodes the NP_229435 protein with two domains: its N-terminus belongs to the calcineurin-like phosphoesterase group (PF00149); its C-terminus to the type 5 capsule protein repressor C-terminal group (PF12320). 

     

    NP_229435 entry has the annotation of a putative exonuclease  from Thermotoga Maritima.

     

    The structure seems to be that of a Mre11-like exonuclease possibly involved in a DNA damage repair pathway similar to the role of such proteins in other organisms.

    The protein forms a dimer based on the crystal structure. It may be a weak dimer since SEC indicates a monomer. Phenylalanine residues at the dimer interface may be responsible for holding the dimer together. The relative orientation of the 2 monomers forming the dimer is different from that seen in the published structure of the Mre11 dimer from P. furiosus (PDB id 1ii7). This dimer could be either due to lattice packing affects or is actually a different dimer than that seen for Mre11.

     

    There is a high sequence homology to exonucleases from many other organisms. However, there is no structural coverage of proteins that are close in sequence. There is structural coverage of a Mre11 exonuclease from P. furiosus (1II7.pdb) with less than 28% sequence identity.

     

    Despite the low sequence identity compared with 1ii7, the putative active site in this protein is almost identically conserved (Mre11 active site residues D8, H10, D49, N84, H173, H206 & H208 are conserved as D14, H16, D58, H180, H216 and H218).

     

    The figure below shows a representation of one molecule of TM1635 with the putative active site residues:

     

     

     

     

     

     

     

    The figure below shows a superimposition of this protein (green) with the Mre11 (cyan) showing the high level of overall structural similarity but also some structural differences which could affect the biochemical properties of this molecule.


    Ligand Summary



    References

    Reviews

    References

     

    No references found.

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