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3t0p

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

    Title Crystal structure of a Putative DNA polymerase III beta subunit (EUBREC_0002; ERE_29750) from Eubacterium rectale ATCC 33656 at 2.26 A resolution. To be published
    Site JCSG
    PDB Id 3t0p Target Id 394339
    Molecular Characteristics
    Source Eubacterium rectale atcc 33656
    Alias Ids TPS27849,YP_002935947.1, _0106.000668_, _0032.000316_, 325449 Molecular Weight 41901.05 Da.
    Residues 370 Isoelectric Point 4.80
    Sequence mklicskanllkgvnivskavptrttmailecilidasaneiklmandmelgietiidgtieergiial dakifseivrklpdndvtietdasfktviscekakfniigksgddfsyipyvernesivlsqftlkevi rqtifsiadndnnklmtgelfeieenklrvvsldghrisiryiemknhydskkvvvpgktlqeiskiip gsadedvviyitnnhivfefenttvvsrliegeyfkidqmlssdydtkvrinkrelldcidratllvke gdkkpiimnitdgnmelrinsfigsmnedididkdgkdimigfnpkffidalrvideeevnlymvnpka pcfikddegkfiylilpvnfntaan
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.26 Rfree 0.2092
    Matthews' coefficent 2.71 Rfactor 0.1733
    Waters 251 Solvent Content 54.58

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    This target protein comes from: 

     

     

    Eubacterium rectale, which represents a predominant group among human intestinal Firmicutes (51%) belonging to a group of anaerobic Gram-positive nonspore-forming rods. Their predominance is comparable to Gram-negative gut inhabitants such as B. thetaiotaomicron, B. vulgatus and B. distasonis. 

     

     

    There is no structural novelty [Fig.1A and 1B] in this DNA polymerase III from the gut bacteria Eubacterium rectale.

    Among all currently deposited DNA polymerases, JCSG determined to date 2 structures of the beta chains, sc. DNA clamps, one from Streptococcus Pneumoniae (2AWA), the other from Thermatoga Maritima(1VPK). Both share a sequence similarity of ~27-28%. FFAS predicts however the highest functional score for that target with the E.Coli DNA Polymerase III. The E.Coli 1JQJ PDB entry, representing the beta-delta complex[1], also called the pre-initiation complex, when overlapped over the MH15438A target, shows the most difficult to refine loop of the structure, exactly at the interface between the 2 binding partners, the beta and delta subunits. The delta subunit 'docks' between that loop, near residues 275-279 'KEGDK' and the C-terminus, which similarly to that loop, is equally disordered with missing 'NTAAN' portion of the monomer.

    Similar to clamps in E.Coli and S.pyogenes bacteria, also here the flexible loop starts with ALys275

    which builds an intermolecular ion pair with BGlu76 at the interface between the 2 monomers[2]. It has to be stated that the ring on the other symmetry related side with the pair BLys275 and AGlu76 is very disordered, implying that the monomer junctions are not identical, i.e. the ring 'opens' only between the latter pair of residues.

    Kuriyan group defined that interface as a 'spring-loaded' mechanism for clamp opening, claiming that the energetic strain gets released upon interaction with delta subunit of the clamp loader complex.

    The toroidal fold of the entire clamp [Fig.1 and 2.] shows the least sequence conservation across that binding delta-subunit surface. The internal ring interface and the opposite bottom side of the toroid, represents a surface with the most sequence conservation, implying that the DNA-protein interactions inside of the ring, and most probably the direction from which the DNA enters the ring, are the most common 'motifs' among species.

    Unlike many other determined structures of DNA clamp, this particular dimer crystalllized with many ligands, EDO and ACTs, predominantly located on the sides of the toroidal structure. This fact is probably related to the host of that protein(i.e. E. Rectale), which must have a very specific, environment dependent way of inhibiting the DNA replication.

     

    Literature:

    1. Jeruzalmi D. et al. Mechanism of processivity clamp opening by the delta subunit wrench of the clamp loader complex of E.Coli DNA polymerase III. 2001 Cell,  V.106:417-428.

    2. Georgescu R.E. et al. Structure of a sliding clamp on DNA.  2008 Cell, v. 132:43-54.

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (2)

    FileSizeDateAttached by 
     YAS-HbondsLIGHT-side.png
    Side view of the Yasara presentation with hydrogen bonds of the dimer.
    708.21 kB20:57, 11 Apr 2011cbtrameActions
     YAS-HbondsLIGHT-top.png
    Yasara presentation of the dimer along the central axis
    629.99 kB20:56, 11 Apr 2011cbtrameActions
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