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

    Title Crystal structure of D-serine deaminase from Burkholderia xenovorans LB400 (YP_556991.1) from BURKHOLDERIA XENOVORANS LB400 at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 3gwq Target Id 381087
    Molecular Characteristics
    Source Burkholderia xenovorans lb400
    Alias Ids TPS14555,YP_556991.1, BIG_836, 86760 Molecular Weight 47105.53 Da.
    Residues 425 Isoelectric Point 5.44
    Sequence mkvtnyqgatidpyskglgmvpgtsiqltdaarlewnllnedvslpaavlyadrvehnlkwmqafvaey gvklaphgkttmapqlfrrqletgawgitlatahqvraayhggvsrvlmanqlvgrrnmmmvaellsdp efeffclvdsvegveqlgeffksvnkqlqvllelgvpggrtgvrdaaqrnavleaitrypdtlklagve lyegvlkeehevreflqsavavtrelveqerfarapavlsgagsawydvvaeefvkasetgkvevvlrp gcylthdvgiyrkaqtdifarnpvakkmgegllpalqlwayvqsipepdraiiglgkrdsafdagmpep arhyrpgneaprdiaasegweifglmdqhaylripagadlkvgdmiafdishpcltfdkwrqvlvvdpa yrvtevietff
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.00 Rfree 0.205
    Matthews' coefficent 2.46 Rfactor 0.163
    Waters 472 Solvent Content 50.10

    Ligand Information


    Google Scholar output for 3gwq
    1. Crystal structure of a zinc-dependent D-serine dehydratase from chicken kidney
    H Tanaka, M Senda, N Venugopalan - Journal of Biological , 2011 - ASBMB
    2. Turning pyridoxal-5-phosphate-dependent enzymes into thermostable binding proteins: D-serine dehydratase from baker's yeast as a case study
    M Baldassarre, A Scir, F Tanfani - Biochimie, 2011 - Elsevier

    Protein Summary

    Gene Bxe_A4060 from Burkholderia xenovorans lb400 translates into the YP_556991 protein, a member of the alanine racemase N-term domain group (PF01168). YP_556991 protein is likely a bacterial homolog of the yeast D-serine dehydratase YGL196W.

    3gwq crystallizes as a dimer. It contains a TIM fold at the middle part (53-287) from the PLP-binding barrel superfamily, Ala racemase-like N-terminal domain fmaily. The N-terminal region is involved in dimerization, and the C-terminal sequence folds into a separate domain, located near the dimer interface. A search by DALI using 3gwq as query returns as top hits the BTRK protein 2j66 (Z=23), the diaminopimelate decarboxylase 3c5q (Z=23), and the Ala racemase 1vfs (Z=22). The active site in the TIM domain (near H76) bears similarity to 1njj (Z=22), but is not highly conserved. The closest structural matches to 3gwq found by SSM include: 1njj, 3c5q, 2qgh.

    It is likely that 3gwq is an enzyme that functions in D-amino acid metabolism, and binds PLP, based on gene neighborhood and the structure similarity of the middle section with 1xfc (Z=21). However, the active site differs significantly, except for Lys78 and Arg275. As a result, further analysis is needed to understand the function of this protein.


    Figure 1: 3gwq monomer

    pu9913a-monomer (1).png

    Figure 2: 3gwq dimer

    pu9913a-dimer (1).png


    To do: try co-xtallization with PLP.

    Ligand Summary




    No references found.

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