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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
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

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

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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