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1vjn

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

    Title Crystal structure of Zn-dependent hydrolase of metallo-beta-lactamase superfamily (TM0207) from Thermotoga maritima at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 1vjn Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1190,TM0207, 89342
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 2
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.16 Rfactor 0.1784
    Waters
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    Solvent Content 49.90

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 1vjn
    1. The Buccaneer software for automated model building. 1. Tracing protein chains
    K Cowtan - Acta Crystallographica Section D: Biological , 2006 - scripts.iucr.org
     
    2. Structural characterization of proteins using residue environments
    SD Mooney, MHP Liang, R DeConde - PROTEINS: Structure, , 2005 - Wiley Online Library
     
    3. Shotgun crystallization strategy for structural genomics II: crystallization conditions that produce high resolution structures for T. maritima proteins
    R Page, AM Deacon, SA Lesley - Journal of structural and , 2005 - Springer
     
    4. Substrate recognition ability differs among various prokaryotic tRNase Zs
    A Minagawa, H Takaku, HS Shibata, R Ishii - Biochemical and , 2006 - Elsevier
     

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    Protein Summary


    The TM0207 gene from Thermotoga maritima  encodes the NP_228022 protein, a  putative Zn-dependent hydrolase of the metallo-beta-lactamase super-family ( PF00753; EC classification EC 3.5.2.6; ortholog gene cluster COG2220).

    1vjn structure belongs to the SCOP alpha+beta class, metallo-hydrolase superfamily. DALI top hits are with putative metal dependent hydrolases

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    (Z=18),
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    (Z=15), and the BA1088 protein
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    (Z=15).

    The structure of a protein with a similar function was reported for Bacillus cereus [Ref]Apart from the beta-lactamases, a number of other proteins contain this domain.  These proteins include thioesterases, members of the glyoxalase II family that catalyse the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid; and a competence protein that is essential for natural transformation in Neisseria gonorrhoeae and could be a transporter involved in DNA uptake. Except for the competence protein, these proteins bind two zinc ions per molecule as cofactor.  

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    Based on structure and sequence similarity, TM0207 was annotated as a metallo-b-lactamase, which converts a b-lactam ring to a substituted b-amino acid. TM0207 contains conserved active site residues present in IMP-1, a metallo-b-lactamase from Pseudomonas aeruginosa (PDB ID: 1DDK). As is common amongst metallo-b-lactamase enzymes, TM0207 is proposed to use Zn2+ as its divalent metal cofactor; this observation is corroborated by the conservation of chelating residues identified in IMP. The putative function was demonstrated experimentally using the b-lactam nitrocefin as a substrate. The Km value for TM02071, 15 µM, is similar to that observed for IMP-1, 63 µM1. However, the determined TM0207 kcat value of 0.12 s-1 was ≈225 fold lower than that reported for IMP-1 (27 s-1)2,3. The difference may be due to the temperature at which the proteins were assayed (20°C for TM0207 and 30°C for IMP-1). In addition, TM0207 is a thermophilic protein from the hyperthermophile Thermotoga maritima and may have a higher kcat at higher physiological temperatures (80°C). In the presence of 0.1 μM tazobactam (a proposed inhibitor of metallo-β-lactamases), the Km value increased to 35.5 µM (yielding a Ki of 6.7 x 10-3 M) while the Vmax remained relatively unchanged; this suggests that tazobactam is a weak competitive inhibitor of TM0207.

    1As isolated with no additional zinc; 50 mM HEPES pH 7.5, 150 mM NaCl, 1 μg/mL BSA

    2Laraki N, Franceschini N, Rossolini GM, Santucci P, Meunier C, de Pauw E, Amicosante G, Frere JM, Galleni M. Biochemical characterization of the Psuedomonas aeruginosa 101/1477 Metallo-β-Lactamase IMP-1 Produced by Escherichia coli. Antimicrobial Agents and Chemotherapy. 43:902-906 (1999).

    350 mM HEPES pH 7.5, 20 μg/mL BSA Laraki et al did not observe a difference in kinetic parameters with the addition of zinc.

    BioLEd Contributors: Joseph Breheny, Kanishk Jain, Amanda Lucht, Monica Moon, Joseph Salamoun, Mana Sassanpour, Elizabeth Rose, Timothy T. Wills, Cameron Mura, Carol Price, Linda Columbus. Funded by NSF DUE 1044858.

    Ligand Summary



    References

    Reviews

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