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    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 282087
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1190,TM0207, 89342 Molecular Weight 23360.80 Da.
    Residues 208 Isoelectric Point 5.87
    Sequence mkitwfghacfalemegktivtdpfdesvgypipnvtadvvteshqhfdhnahhlvkgnfrvidrpgay tvngvkikgvetfhdpshgrergknivfvfegegikvchlgdlghvltpaqveeigeidvllvpvggty tigpkeakevadllnakviipmhyktkylkfnllpvddflklfdsyervgnilelfekpkerkvvvmevq
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.00 Rfree 0.21993
    Matthews' coefficent 2.16 Rfactor 0.1784
    Waters 154 Solvent Content 49.90

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    Ligand Information


    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

    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; 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 PDB:3kl7 (Z=18), PDB:3bv6 (Z=15), and the BA1088 protein PDB:1zkp (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.  


    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





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