Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.

Science 19 May 1995:
Vol. 268. no. 5213, pp. 998 - 1004
DOI: 10.1126/science.7754395
Prev | Table of Contents | Next

Articles

Science, Vol 268, Issue 5213, 998-1004
Copyright © 1995 by American Association for the Advancement of Science

articles

The crystal structure of urease from Klebsiella aerogenes

E Jabri, MB Carr, RP Hausinger, and PA Karplus

Section of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA.

The crystal structure of urease from Klebsiella aerogenes has been determined at 2.2 A resolution and refined to an R factor of 18.2 percent. The enzyme contains four structural domains: three with novel folds playing structural roles, and an (alpha beta)8 barrel domain, which contains the bi-nickel center. The two active site nickels are 3.5 A apart. One nickel ion is coordinated by three ligands (with low occupancy of a fourth ligand) and the second is coordinated by five ligands. A carbamylated lysine provides an oxygen ligand to each nickel, explaining why carbon dioxide is required for the activation of urease apoenzyme. The structure is compatible with a catalytic mechanism whereby urea ligates Ni-1 to complete its tetrahedral coordination and a hydroxide ligand of Ni-2 attacks the carbonyl carbon. A surprisingly high structural similarity between the urease catalytic domain and that of the zinc-dependent adenosine deaminase reveals a remarkable example of active site divergence.


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Edwardsiella ictaluri Encodes an Acid-Activated Urease That Is Required for Intracellular Replication in Channel Catfish (Ictalurus punctatus) Macrophages.
N. J. Booth, J. B. Beekman, and R. L. Thune (2009)
Appl. Envir. Microbiol. 75, 6712-6720
   Abstract »    Full Text »    PDF »
Effects of vaccination by a recombinant antigen ureB138 (a segment of the {beta}-subunit of urease) against Helicobacter pylori infection.
F. Morihara, R. Fujii, E. Hifumi, A. Nishizono, and T. Uda (2007)
J. Med. Microbiol. 56, 847-853
   Abstract »    Full Text »    PDF »
The UreEF Fusion Protein Provides a Soluble and Functional Form of the UreF Urease Accessory Protein.
J. K. Kim, S. B. Mulrooney, and R. P. Hausinger (2006)
J. Bacteriol. 188, 8413-8420
   Abstract »    Full Text »    PDF »
The Crystal Structures of Dihydropyrimidinases Reaffirm the Close Relationship between Cyclic Amidohydrolases and Explain Their Substrate Specificity.
B. Lohkamp, B. Andersen, J. Piskur, and D. Dobritzsch (2006)
J. Biol. Chem. 281, 13762-13776
   Abstract »    Full Text »    PDF »
Biosynthesis of Active Bacillus subtilis Urease in the Absence of Known Urease Accessory Proteins.
J. K. Kim, S. B. Mulrooney, and R. P. Hausinger (2005)
J. Bacteriol. 187, 7150-7154
   Abstract »    Full Text »    PDF »
UreG, a Chaperone in the Urease Assembly Process, Is an Intrinsically Unstructured GTPase That Specifically Binds Zn2+.
B. Zambelli, M. Stola, F. Musiani, K. De Vriendt, B. Samyn, B. Devreese, J. Van Beeumen, P. Turano, A. Dikiy, D. A. Bryant, et al. (2005)
J. Biol. Chem. 280, 4684-4695
   Abstract »    Full Text »    PDF »
Analysis of two alleles of the urease gene from potato: polymorphisms, expression, and extensive alternative splicing of the corresponding mRNA.
C.-P. Witte, S. Tiller, E. Isidore, H. V. Davies, and M. A. Taylor (2005)
J. Exp. Bot. 56, 91-99
   Abstract »    Full Text »    PDF »
Amine-synthesizing enzyme N-substituted formamide deformylase: Screening, purification, characterization, and gene cloning.
H. Fukatsu, Y. Hashimoto, M. Goda, H. Higashibata, and M. Kobayashi (2004)
PNAS 101, 13726-13731
   Abstract »    Full Text »    PDF »
Proteus mirabilis Genes That Contribute to Pathogenesis of Urinary Tract Infection: Identification of 25 Signature-Tagged Mutants Attenuated at Least 100-Fold.
L. S. Burall, J. M. Harro, X. Li, C.V. Lockatell, S. D. Himpsl, J. R. Hebel, D. E. Johnson, and H. L. T. Mobley (2004)
Infect. Immun. 72, 2922-2938
   Abstract »    Full Text »    PDF »
Metabolic Versatility of Prokaryotes for Urea Decomposition.
R. P. Hausinger (2004)
J. Bacteriol. 186, 2520-2522
   Full Text »    PDF »
Structural Characterization of the Nickel-binding Properties of Bacillus pasteurii Urease Accessory Protein (Ure)E in Solution.
H.-S. Won, Y.-H. Lee, J.-H. Kim, I. S. Shin, M. H. Lee, and B.-J. Lee (2004)
J. Biol. Chem. 279, 17466-17472
   Abstract »    Full Text »    PDF »
Chemical Cross-linking and Mass Spectrometric Identification of Sites of Interaction for UreD, UreF, and Urease.
Z. Chang, J. Kuchar, and R. P. Hausinger (2004)
J. Biol. Chem. 279, 15305-15313
   Abstract »    Full Text »    PDF »
The Functional Role of the Binuclear Metal Center in D-Aminoacylase: ONE-METAL ACTIVATION AND SECOND-METAL ATTENUATION.
W.-L. Lai, L.-Y. Chou, C.-Y. Ting, R. Kirby, Y.-C. Tsai, A. H.-J. Wang, and S.-H. Liaw (2004)
J. Biol. Chem. 279, 13962-13967
   Abstract »    Full Text »    PDF »
Soybean cultivars 'Williams 82' and 'Maple Arrow' produce both urea and ammonia during ureide degradation.
C. D. Todd and J. C. Polacco (2004)
J. Exp. Bot. 55, 867-877
   Abstract »    Full Text »    PDF »
A Possible Primordial Peptide Cycle.
C. Huber, W. Eisenreich, S. Hecht, and G. Wachtershauser (2003)
Science 301, 938-940
   Abstract »    Full Text »    PDF »
Interallelic Complementation at the Ubiquitous Urease Coding Locus of Soybean.
A. Goldraij, L. J. Beamer, and J. C. Polacco (2003)
Plant Physiology 132, 1801-1810
   Abstract »    Full Text »    PDF »
Crystal Structure of D-Hydantoinase from Burkholderia pickettii at a Resolution of 2.7 Angstroms: Insights into the Molecular Basis of Enzyme Thermostability.
Z. Xu, Y. Liu, Y. Yang, W. Jiang, E. Arnold, and J. Ding (2003)
J. Bacteriol. 185, 4038-4049
   Abstract »    Full Text »    PDF »
A New Type of Metal Recognition by Human T Cells: Contact Residues for Peptide-independent Bridging of T Cell Receptor and Major Histocompatibility Complex by Nickel.
K. Gamerdinger, C. Moulon, D. R. Karp, J. van Bergen, F. Koning, D. Wild, U. Pflugfelder, and H. U. Weltzien (2003)
J. Exp. Med. 197, 1345-1353
   Abstract »    Full Text »    PDF »
Dihydropyrimidine amidohydrolases and dihydroorotases share the same origin and several enzymatic properties.
Z. Gojkovic, L. Rislund, B. Andersen, M. P. B. Sandrini, P. F. Cook, K. D. Schnackerz, and J. Piskur (2003)
Nucleic Acids Res. 31, 1683-1692
   Abstract »    Full Text »    PDF »
Characterization and Expression of a Novel Member (JBURE-II) of the Urease Gene Family from Jackbean [Canavalia ensiformis (L.) DC].
M. Pires-Alves, M. F. Grossi-de-Sa, G. B. S. Barcellos, C. R. Carlini, and M. G. Moraes (2003)
Plant Cell Physiol. 44, 139-145
   Abstract »    Full Text »    PDF »
Crystal Structure of D-Aminoacylase from Alcaligenes faecalis DA1. A NOVEL SUBSET OF AMIDOHYDROLASES AND INSIGHTS INTO THE ENZYME MECHANISM.
S.-H. Liaw, S.-J. Chen, T.-P. Ko, C.-S. Hsu, C.-J. Chen, A. H.-J. Wang, and Y.-C. Tsai (2003)
J. Biol. Chem. 278, 4957-4962
   Abstract »    Full Text »    PDF »
Evolution of an organophosphate-degrading enzyme: a comparison of natural and directed evolution.
H. Yang, P.D. Carr, S.Y. McLoughlin, J.W. Liu, I. Horne, X. Qiu, C.M.J. Jeffries, R.J. Russell, J.G. Oakeshott, and D.L. Ollis (2003)
Protein Eng. Des. Sel. 16, 135-145
   Abstract »    Full Text »    PDF »
Metal Ion Dependence of Recombinant Escherichia coli Allantoinase.
S. B. Mulrooney and R. P. Hausinger (2003)
J. Bacteriol. 185, 126-134
   Abstract »    Full Text »    PDF »
External Nickel Inhibits Epithelial Sodium Channel by Binding to Histidine Residues within the Extracellular Domains of alpha and gamma Subunits and Reducing Channel Open Probability.
S. Sheng, C. J. Perry, and T. R. Kleyman (2002)
J. Biol. Chem. 277, 50098-50111
   Abstract »    Full Text »    PDF »
Urea-dependent Signal Transduction by the Virulence Regulator UreR.
I. Gendlina, D. M. Gutman, V. Thomas, and C. M. Collins (2002)
J. Biol. Chem. 277, 37349-37358
   Abstract »    Full Text »    PDF »
Three-Dimensional Quantitative Structure-Activity Relationship and Comparative Molecular Field Analysis of Dipeptide Hydroxamic Acid Helicobacter pylori Urease Inhibitors.
H. Mishra, A. L. Parrill, and J. S. Williamson (2002)
Antimicrob. Agents Chemother. 46, 2613-2618
   Abstract »    Full Text »    PDF »
Identification of an Antigenic Epitope in Helicobacter pylori Urease That Induces Neutralizing Antibody Production.
K. Hirota, K. Nagata, Y. Norose, S. Futagami, Y. Nakagawa, H. Senpuku, M. Kobayashi, and H. Takahashi (2001)
Infect. Immun. 69, 6597-6603
   Abstract »    Full Text »    PDF »
Interaction of Proteus mirabilis Urease Apoenzyme and Accessory Proteins Identified with Yeast Two-Hybrid Technology.
S. R. Heimer and H. L. T. Mobley (2001)
J. Bacteriol. 183, 1423-1433
   Abstract »    Full Text »
Prochlorococcus marinus strain PCC 9511, a picoplanktonic cyanobacterium, synthesizes the smallest urease.
K. A. Palinska, T. Jahns, R. Rippka, and N. Tandeau de Marsac (2000)
Microbiology 146, 3099-3107
   Abstract »    Full Text »    PDF »
Calcineurin: Form and Function.
F. Rusnak and P. Mertz (2000)
Physiol Rev 80, 1483-1521
   Abstract »    Full Text »    PDF »
GTP-dependent activation of urease apoprotein in complex with the UreD, UreF, and UreG accessory proteins.
A. Soriano and R. P. Hausinger (1999)
PNAS 96, 11140-11144
   Abstract »    Full Text »    PDF »
Genetic and Physiologic Characterization of Urease of Actinomyces naeslundii.
E. Morou-Bermudez and R. A. Burne (1999)
Infect. Immun. 67, 504-512
   Abstract »    Full Text »    PDF »
The Identification, Purification, and Characterization of CooJ. A NICKEL-BINDING PROTEIN THAT IS CO-REGULATED WITH THE Ni-CONTAINING CO DEHYDROGENASE FROM RHODOSPIRILLUM RUBRUM.
R. K. Watt and P. W. Ludden (1998)
J. Biol. Chem. 273, 10019-10025
   Abstract »    Full Text »    PDF »
AtzC Is a New Member of the Amidohydrolase Protein Superfamily and Is Homologous to Other Atrazine-Metabolizing Enzymes.
M. J. Sadowsky, Z. Tong, M. d. Souza, and L. P. Wackett (1998)
J. Bacteriol. 180, 152-158
   Abstract »    Full Text »
Crystal structures of the copper and nickel complexes of RNase A: Metal-induced interprotein interactions and identification of a novel copper binding motif.
R. Balakrishnan, N. Ramasubbu, K. I. Varughese, and R. Parthasarathy (1997)
PNAS 94, 9620-9625
   Abstract »    Full Text »    PDF »
Characterization of the Mononickel Metallocenter in H134A Mutant Urease.
I.-S. Park, L. O. Michel, M. A. Pearson, E. Jabri, P. A. Karplus, S. Wang, J. Dong, R. A. Scott, B. P. Koehler, M. K. Johnson, et al. (1996)
J. Biol. Chem. 271, 18632-18637
   Abstract »    Full Text »    PDF »
Cloning, Expression, and Characterization of the TATA-binding Protein (TBP) Promoter Binding Factor, a Transcription Activator of the Acanthamoeba TBP Gene.
W. Huang and E. Bateman (1995)
J. Biol. Chem. 270, 28839-28847
   Abstract »    Full Text »    PDF »
The Binding of Substrate Analogs to Phosphotriesterase.
M. M. Benning, S.-B. Hong, F. M. Raushel, and H. M. Holden (2000)
J. Biol. Chem. 275, 30556-30560
   Abstract »    Full Text »    PDF »
Activase Region on Chloroplast Ribulose-1,5-bisphosphate Carboxylase/Oxygenase. NONCONSERVATIVE SUBSTITUTION IN THE LARGE SUBUNIT ALTERS SPECIES SPECIFICITY OF PROTEIN INTERACTION.
C. M. Ott, B. D. Smith, A. R. Portis Jr., and R. J. Spreitzer (2000)
J. Biol. Chem. 275, 26241-26244
   Abstract »    Full Text »    PDF »
Crystal Structure of Klebsiella aerogenes UreE, a Nickel-binding Metallochaperone for Urease Activation.
H. K. Song, S. B. Mulrooney, R. Huber, and R. P. Hausinger (2001)
J. Biol. Chem. 276, 49359-49364
   Abstract »    Full Text »    PDF »


To Advertise     Find Products

Science. ISSN 0036-8075 (print), 1095-9203 (online)