.
The Open Protein Structure Annotation Network
PDB Keyword
.

1ztc

  • We have highlighted your search term Columbus for you. If you'd like to remove the search term, click here.
Table of contents
  1. 1. Protein Summary
  2. 2. Ligand Summary
  3. 3. References

Title Crystal structure of hypothetical protein (tm0894) from Thermotoga maritima at 2.10 A resolution. To be published
Site JCSG
PDB Id 1ztc Target Id 359759
Molecular Characteristics
Source Thermotoga maritima msb8
Alias Ids TPS1431,TM0894, 429686 Molecular Weight 23944.27 Da.
Residues 209 Isoelectric Point 6.19
Sequence melkilvtggnvfvpgrlnahfstvvylehkdrriiidpgnlssmdeleekfselgispdditdvlfth vhldhifnsvlfenatfyvhevyktknylsfgtivgriyskvisswknvvllkgeeslfdekvkvfhtp wharehlsflldtenagrvlitgditpnrlsyydiikgygsvqvknfldrvgridllvfphdaplkpevkk
  BLAST   FFAS

Structure Determination
Method XRAY Chains 4
Resolution (Å) 2.10 Rfree 0.178
Matthews' coefficent 4.23 Rfactor 0.157
Waters 454 Solvent Content 70.67

Ligand Information
Ligands
Metals

Jmol

 
Google Scholar output for 1ztc
1. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
 

Protein Summary

The gene TM0894 from Thermotoga maritima encodes a putative metallo-beta-lactamase PFAM:PF00753 EC:3.5.2.6.  The Thermotoga maritima sequence is 98% identical to the beta-lactamase domain-containing protein from Thermotoga neapolitana (DSM 4359).  Metallo-beta-lactamases belong to the class B lactamases.  These proteins bind two zinc ions per molecule as cofactor.  Zinc atoms can be substituted with nickel or cobalt atoms 3I11.

According to FFAS and FATCAT, the closest structural homolog in the pdb is PDB:3dha, a monomeric N-acyl Homoserine Lactone Hydrolase (rigid FATCAT P-value 2.89E-8, FFAS score -57.3, 17% identity). Unlike this and other metallo-beta-lactamases TM0894 forms a tetramer with  near-tetrahedral architecture and extensive interactions that include intersubunit beta-sheets (between chains A-D and B-C). TM0894 lacks a loop and other variable structural elements that flank the active site and provide a binding cleft for the substrate (compare for example with 1m2x). This function could be provided by residues from a neighboring subunit, which form a cavity of similar size, possibly suggesting a different specificity. Note that the tetrameric L1 enzyme (pdb 2aio) similarly presents a tetrahedral arrangement of subunits but uses a very different surface for their interaction.

A structurally very identical protein is given by PDB:2r2d. Superposition of 1ztc and 2r2d with TopMatch give 169 equivalent residues with an rmsd of 2.5 and 22% sequence identity. Two zinc ions are present in 2r2d and they occupy equivalent positions as the nickel ions in 1ztc. Also, chelation is carried out by the conserved residues His-140/191, His-71/113, His-69/111, His-74/116, His-199/259, Asp-162/213,  and Asp-73/115 (1ztc/2r2d, respectively). This provides additional evidence that 1ztc is a metallo-beta-lactamase.

************************************************************************************************************************************************

Based on structure and sequence similarity, TM0894 is a putative metallo-b-lactamase, which converts a b-lactam ring to a substituted b-amino acid. Specifically, TM0894 is most similar to the metal-binding motif of the B3 subclass1 such as FEZ-12 and L13 (the only other known homo-tetramer metallo-b-lactamase), except that a conserved serine (which is a cysteine in subclasses B1 and B2) is replaced with an aspartate in TM0894. The overall fold of TM0894 is of the metallo-b-lactamase superfamily, but differs in helical packing from representative structures from all three subclasses. TM0894 demonstrated b-lactamase activity with the substrate nitrocefin (Figure 1). The exact temperature and solution conditions for the TM0894 assay were different from those used to characterize FEZ-1 and L1; nonetheless, Table 1 provides a comparison of the kinetic parameters. Although the KM and kcat values of TM0894 are comparable to those of FEZ-1 and L1, the catalytic efficiency is an order of magnitude lower. The catalytic efficiency of TM0894 was not found to increase at 80°C (9.0 x 104 M-1s-1)

 

 

KM (μM)

kcat (s-1)

kcat/KM (M-1s-1)

TM0894*

120

12

9.5 x 104

FEZ-1

100

90

9.0 x 105

L1#

7

20

2.9 x 106

*100 mM phosphate buffer, 100 mM NaCl, pH 7.2, 37°C (as isolated and no additional metal); 15 mM sodium cacodylate, pH 6.0, 30°C (as isolated with no additional metal)4;#50 mM sodium cacodylate, pH 7.0, and 0.1 mM ZnCl2, 35°C5

 

 

BioLEd Contributors: Joseph Breheny, Kanishk Jain, Li Lin, Ann Shefferly, Kimberly Showalter, Matthew Waugh, Nicholas Wu, Cameron Mura, Carol Price, Linda Columbus. Funded by NSF DUE 1044858.

References

1Garau G, García-Sáez I, Bebrone C, Anne C, Mercuri P, Galleni M, Frère JM,Dideberg O. Update of the standard numbering scheme for class B beta-lactamases.Antimicrob Agents Chemother. 2004 48:2347-9

2García-Sáez I, Mercuri PS, Papamicael C, Kahn R, Frère JM, Galleni M, Rossolini GM, Dideberg O. Three-dimensional structure of FEZ-1, a monomeric subclass B3 metallo-beta-lactamase from Fluoribacter gormanii, in native form and in complex with D-captopril. J Mol Biol. 2003 325:651-6

3Ullah JH, Walsh TR, Taylor IA, Emery DC, Verma CS, Gamblin SJ, et al. The crystal structure of the L1 metallobeta-lactamase from Stenotrophomonas maltophilia at 1.7A° resolution. J Mol Biol 1998;284:125–36. 

4Mercuri PS, Bouillenne F, Boschi L, Lamotte-Brasseur J, Amicosante G, Devreese B, et al. Biochemical characterization of the FEZ-1 metallo-beta-lactamase of Legionella gormanii ATCC 33297T produced in Escherichia coli. Antimicrob Agents Chemother 2001;45:1254–62.

5Felici A, Amicosante G, Oratore A, Strom R, Ledent P, Joris B, Fanuel L, Frère J M. An overview of the kinetic parameters of class B -lactamasesBiochem J. 1993 291: 151–155. 

Ligand Summary



References

Reviews

References

 

No references found.

Tag page

Files (1)

FileSizeDateAttached by 
 Figure1.png
Temperature Dependence
44.46 kB15:56, 24 Jan 2012kj3kvActions
You must login to post a comment.
All content on this site is licensed under a Creative Commons Attribution 3.0 License
Powered by MindTouch