Comparative modelling and immunochemical reactivity of Escherichia coli UMP kinase☆
Section snippets
Materials and methods
Chemicals. Nucleotides, restriction enzymes, T4DNA ligase, and coupling enzymes were from Roche-Diagnostics, Mannheim, Germany. T7DNA polymerase and the four deoxynucleoside triphosphates used in sequencing reactions were from Pharmacia. Oligonucleotides were synthesized by the phosphoamidinate method. NDP kinase from Dictyostelium discoideum (2000 U/mg prot) was provided by M. Véron. Mab 44-2 was obtained by immunizing mice with a C-terminal truncated form of E. coli UMP kinase (amino acids
Sequence analysis of bacterial UMP kinases
Database screening using the program PSI-BLAST with UMP kinase from E. coli as a query first showed sequence similarities with UMP kinases from other bacteria (probability scores: e-66 to e-53). Various other bacterial kinases followed immediately after, in the PSI-BLAST output (pyrroline-5 carboxylate synthase with probability scores: e-49 to e-44; glutamate-5-kinase, e-43 to e-41; aspartokinases, e-41 to e-31 and carbamate kinases, e-30 to e-23). No similarity with eukaryotic UMP kinases was
Acknowledgements
This work was supported by grants from the Institut Pasteur, the Institut National de la Santé et de la Recherche Médicale (U554, the Centre National de la Recherche Scientifique (URA 2185 and UMR 5048), the Genopole Languedoc-Roussillon, and AstraZeneca R&D Boston Inc. We thank Pedro Alzari and Vicente Rubio for many fruitful discussion, Susan Michelson for critical comments, and Régine Lambrecht for excellent secretarial help.
References (33)
- et al.
Refined structure of porcine cytosolic adenylate kinase at 2.1 Å resolution
J. Mol. Biol.
(1988) - et al.
The structure of uridylate kinase with its substrates, showing the transition state geometry
J. Mol. Biol.
(1994) - et al.
CMP kinase from Escherichia coli is structurally related to other nucleoside monophosphate kinases
J. Biol. Chem.
(1996) - et al.
Structures of Escherichia coli CMP kinase alone and in complex with CDP: a new fold of the nucleoside monophosphate binding domain and insights into cytosine nucleotide specificity
Structure
(1998) - et al.
Comparative protein modelling by satisfaction of spatial restraints
J. Mol. Biol.
(1993) - et al.
VERIFY3D: assessment of protein models with three-dimensional profiles
Methods Enzymol.
(1997) XmMol: an X11 and motif program for macromolecular visualization and modeling
J. Mol. Graph.
(1995)- et al.
NPS: network protein sequence analysis
TIBS
(2000) - et al.
The 1.5 Å resolution crystal structure of the carbamate kinase-like carbamoyl phosphate synthetase from the hyperthermophilic archaeon Pyrococcus furiosus, bound to ADP, confirms that this thermostable enzyme is a carbamate kinase, and provides insight into substrate binding and stabiliin in carbamate kinases
J. Mol. Biol.
(2000) - et al.
Nucleotide sequence of a mutation in the proB gene of Escherichia coli that confers proline overproduction and enhanced tolerance to osmotic stress
Gene
(1988)
Escherichia coli UMP-kinase, a member of the aspartokinase family, is a hexamer regulated by guanine nucleotides and UTP
Biochemistry
Structural properties of UMP-kinase from Escherichia coli: modulation of protein solubility by pH and UTP
Biochemistry
Immunochemical analysis of UMP kinase from Escherichia coli
J. Bacteriol.
Mutational analysis of UMP kinase from Escherichia coli
J. Bacteriol.
Enhanced threading efficiency through Web-based comparisons and cross-validations
Bioinformatics
Thymidylate kinase of Mycobacterium tuberculosis: a chimera sharing properties common to eukaryotic and bacterial enzymes
Protein Sci.
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Abbreviations: CKef, Carbamate Kinase from Enterococcus faecalis; CPSpf, Carbamoyl Phosphate Synthase from Pyrococcus furiosus. The one-letter code is used for amino acids.