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    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.


    Kinetic assays establish 3GWQ as a D-serine deaminase

    The gene for protein YP_556991.1 from Burkholderia xenovorans was putatively annotated by the JCSG as a D-serine deaminase (BxDSD; PDB id 3GWQ; D-serine deaminases catalytically degrade D-serine to pyruvate and ammonia in a mechanism that involves a PLP-aminoacrylate intermediate1. The crystal structure for BxDSD was resolved to 2.00Å by the JCSG.

    Sequence analysis indicates that BxDSD is a member of the fold type-III pyridoxal 5-phosphate (PLP)-dependent enzyme bacterial cryptic D-serine dehydratase family 2,3. This family is characterized by an α/β(TIM) barrel at the N-terminus and a β-sandwich domain at the C-terminus. A catalytic lysine (Lys78 in BxDSD), essential in forming the Schiff base linkage with the C4’ atom in PLP, is conserved across these homologous proteins.

    Kinetics data substantiate the previously putative annotation of BxDSDas a D-serine deaminase. Kinetic parameters were determined using a lactate dehydrogenase (LDH) coupled assay. LDH catalyzes the conversion of pyruvate to lactate with the concomitant oxidation of NADH to NAD+; the concentration of NADH can be monitored spectrophotometrically at 340 nm. Assays were performed at room temperature (approximately 22°C, unless otherwise indicated) in reaction mixtures containing 50 mM potassium phosphate buffer (pH 7.6, unless otherwise indicated), 100 μM PLP, 0.3 mM β-NADH, 6 units/mL LDH from bovine heart, and 0.10 μM BxDSD. 

    A comparison of the kinetic parameters between BxDSD,E. coli DSD (EcDSD) and G. gallus DSD (GgDSD) indicated that BxDSD, fold type III, has similar Km and kcat to GgDSD, fold type III, but a catalytic efficiency much closer to EcDSD, fold type II (Table 1; Figure 1, panel A). A glycine inhibition assay indicated that glycine competitively inhibits BxDSD activity (Figure 1, panel B) (Ki 0.61 mM). 

    BioLEd Contributors: Katherine DeSilva, Zenad Jarrar, Austin McCalla, Elleansar Okwei, Madeline Sargent, Madeline, Jennifer Yi, Catrina Campbell, Ellen Schleckman, Cameron Mura, Carol Price, Linda Columbus. Funded by NSF DUE 1044858.



    1.    Yamada, T., Komoto, J., Takata, Y., Ogawa, H., Pitot, H. C., Takusagawa, F. 2003. Crystal Structure of Serine Dehydratase from Rat Liver. Biochemistry42 (44):12854–65.

    2.    Altshul, S. F., Gish, W., Miller, W., Myers, E. W., Lipman, D. J. 1990. Basic local alignment search tool. J. Mol. Biol . 215:403-410.

    3.    Madej T, Gibrat JF,Bryant SH. 1995. Threading a database of protein cores. Protein Struct. Funct. Genet. 23:356-369.

    4.    Ito, T., Koga, K., Hemmi, H., Yoshimura, T. 2011. Role of zinc ion for catalytic activity in Dserine dehydratase from Saccharomyces cerevisiae. The FEBS Journal. 279:612-624.

    5.    Suzuki, C.; Murakami, M.; Yokobori, H.; Tanaka, H.; Ishida, T.; Horiike, K.; Nagata, Y. 2011. Rapid determination of free D-serine with chicken D-serine dehydratase. J. of Chromatography B. 879:3326-3330.



    Table 1. Comparison of kinetic parameters of D-serine substrate.Comparison of kinetic parameters between BxDSD: EcDSD, and GgDSD.


    Km mM)


    kcat/Km (mM-1s-1)

























    Ligand Summary




    No references found.

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