At the periphery of the amidohydrolase superfamily: Bh0493 from Bacillus halodurans catalyzes the isomerization of D-galacturonate to D-tagaturonate

Biochemistry

Volumn 47, Issue 4, 2008, Pages 1194-1206

  Nguyen, Tinh T ^a   Brown, Shoshana ^b   Fedorov, Alexander A ^c   Fedorov, Elena V ^c   Babbitt, Patricia C ^b   Almo, Steven C ^c   Raushel, Frank M ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMIDOHYDROLASE; D-GALACTURONATE; D-TAGATURONATE;

BACTERIA; CATALYSIS; ESCHERICHIA COLI; ESTERS; HYDROLYSIS; NUCLEIC ACIDS; SUGARS;

ENZYMES;

AMIDASE; AMINO ACID; CARBOHYDRATE DERIVATIVE; FRUCTURONIC ACID; GALACTURONIC ACID; GLUCURONATE ISOMERASE; ISOMERASE; NUCLEIC ACID; ORGANOPHOSPHATE; SUGAR; TAGATURONIC ACID; UNCLASSIFIED DRUG; URONIC ACID;

ARTICLE; BACILLUS; BACILLUS HALODURANS; BACTERIAL GENE; BH0493 GENE; BH0705 GENE; CATALYSIS; ENZYME ACTIVITY; ENZYME KINETICS; ENZYME SPECIFICITY; ESCHERICHIA COLI; HYDROLYSIS; ISOMERIZATION; NONHUMAN; OPERON; PHYLOGENY; PRIORITY JOURNAL; PROTEIN FAMILY; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

AMIDOHYDROLASES; BACILLUS; BINDING SITES; CATALYSIS; CHROMOSOMES, BACTERIAL; COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; HEXURONIC ACIDS; ISOMERISM; KINETICS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; PHYLOGENY; PROTEIN SUBUNITS; SEQUENCE ALIGNMENT;

BACILLUS HALODURANS; ESCHERICHIA COLI;

EID: 38549133831     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi7017738     Document Type: Article

References (41)

1. Gerlt, J. A., and Babbitt, P. C. (2000) Can sequence determine function? Genome Biol. 5, 1-10.
2. Eisen, J. A. (1998) Phylogenomics: Improving functional predictions for uncharacterized genes by evolutionary analysis, Genome Res. 8, 163-167.
3. Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D., and Yeates, T. O. (1999) Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles, Proc. Natl. Acad. Sci. U.S.A. 96, 4285-4288.
4. Marcotte, E. M., Pelligrini, M., Ng, H. L., Rice, D. W., Yeates, T. O., and Eisenberg, D. (1999) Detecting protein function and protein-protein interactions from genome sequences, Science (Washington, DC, U.S.) 285, 751-753.
5. Chia, J., and Kolatkar, P. R. (2004) Implications for domain fusion protein-protein interactions based on structural information, BMC Bioinf. 5, 161.
6. Enright, A. J., Iliopoulos, I., Kyrpides, N. C., and Ouzounis, C. A. (1999) Protein interaction maps for complete genomes based on gene fusion events, Nature (London, U.K.) 402, 86-90.
7. Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G. D., and Maltsev, N. (1999) The use of gene clusters to infer functional coupling, Proc. Natl. Acad. Sci. U.S.A. 96, 2896-2901.
8. Marti-Arbona, R., Xu, C., Steele, S., Weeks, A., Kuty, G. F., Siebert, C. M., and Raushel, F. M. (2006) Annotating enzymes of unknown function: N-Formimino-L-glutamate deiminase is a member of the amidohydrolase superfamily, Biochemistry 45, 1997-2005.
9. Friedberg, I., Jambon, M., and Godzik, A. (2006) New avenues in protein function prediction, Protein Sci. 15, 1527-1529.
10. Roodveldt, C., and Tawfik, D. S. (2005) Shared promiscuous activities and evolutionary features in various members of the amidohydrolase superfamily, Biochemistry 44, 12728-12736.
11. Siebert, C. M., and Raushel, F. M. (2005) Structural and catalytic diversity within the amidohydrolase superfamily, Biochemistry 44, 6383-6391.
12. Holm, L., and Sander, C. (1997) An evolutionary treasure: Unification of a broad set of amidohydrolases related to urease, Proteins 28, 72-82.
13. Williams, L., Nguyen, T., Li, Y., Porter, T. N., and Raushel, F. M. (2006) Uronate isomerase: A nonhydrolytic member of the amidohydrolase superfamily with an ambivalent requirement for a divalent metal ion, Biochemistry 45, 7453-7462.
14. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs, Nucleic Acids Res. 25, 3389-3402.
15. Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., and Ideker, T. (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks, Genome Res. 13, 2498-2504.
16. Pegg, S. C., Brown, S. D., Ojha, S., Seffernick, J., Meng, E. C., Morris, J. H., Chang, P. J., Huang, C. C., Ferrin, T. E., and Babbitt, P. C. (2006) Biochemistry 45, 2545-2555.
17. Edgar, R. C. (2004) MUSCLE: A multiple sequence alignment method with reduced time and space complexity, BMC Bioinf. 5, 113.
18. Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., and Gerrin, T. E. (2004) UCSF Chimera: A visualization system for exploratory research and analysis, J. Comput. Chem. 25, 1605-1612.
19. Jewett, A. I., Huang, C. C., and Ferrin, T. E. (2003) MINRMS: An efficient algorithm for determining protein structure similarity using root-mean-squared distance, Bioinformatics 19, 625-634.
20. Li, W., Jaroszewski, L., and Godzik, A. (2002) Tolerating some redundancy significantly speeds up clustering of large protein databases, Bioinformatics 18, 77-82.
21. Altekar, G., Dwarkadas, S., Huelsenbeck, J. P., and Ronquist, F. (2004) Parallel metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference, Bioinformatics 20, 407-415.
22. Ronquist, F., and Huelsenbeck, J. P. (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models, Bioinformatics 19, 1572-1574.
23. Otwinowski, Z., and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode, in Methods in Enzymology (Carter, C. W. J., Sweet, R. M., Abelson, J. N., and Simon, M. I., Eds.) pp 307-326, Academic Press, New York.
24. Terwilliger, T. C., and Berendzen, J. (1999) Automated MAD and MIR structure solution, Acta Crystallogr., Sect. D: Biol. Crystallogr. 55, 849-861.
25. Terwilliger, T. C. (2000) Maximum-likelihood density modification, Acta Crystallogr., Sect. D: Biol. Crystallogr. 56, 965-972.
26. Perrakis, A., Morris, R, and Lamzin, V. S. (1999) Automated protein model building combined with iterative structure refinement, Nat. Struct. Biol. 6, 458-463.
27. Jones, A. T. (1985) Interactive computer graphics: FRODO, Methods Enzymol. 115, 157-171.
28. Brunger, A. T., Adams, P. D., Clore, G. M., DeLAno, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Crystallography and NMR system: A new software suite for macromolecular structure determination, Acta Crystallogr., Sect. D: Biol. Crystallogr. 54, 905-921.
29. McCoy, A. J., Grosse-Kunstleve, R. W., Storoni, L. C., and Read, R. J. (2005) Likelihood-enhanced fast translation functions, Acta Crystallogr., Sect. D: Biol. Crystallogr. 61, 458-464.
30. Cook, P. I., and Cleland, W. W. (2007) Initial velocity studies in the absence of added inhibitors, in Enzyme Kinetics and Mechanism, p 11, Garland Science Publishing, New York.
31. Liu, A., and Zhang, H. (2006) Transition metal-catalyzed non-oxidative decarboxylation reactions, Biochemistry 45, 10407-10411.
32. Seffernick, J. L., de Souza, M. L., Sadowsky, M. J., and Wackett, L. P. (2001) Melamine deaminase and atrazine chlorohydrolase: 98% identical but functionally different, J. Bacteriol. 183, 2405-2410.
33. Glasner, M. E., Fayazmanesh, N., Chiang, R. A., Sakai, A., Jacobson, M. P., Gerlt, J. A., and Babbitt, P. C. (2006) Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily, J. Mol. Biol. 360, 228-250.
34. Hermann, J., Marti-Arbona, R., Fedorov, E., Fedorov, A., Almo, S., Shoichet, B. K., and Raushel, F. M. (2007) Structure-based activity prediction for an enzyme of unknown function, Nature (London, U.K.) 448, 775-779.
35. Rivolta, C., Soldo, B., Lazarevic, V., Joris, B., Mauel, C., and Karamata, D. (1998) A 35.7 kb DNA fragment from the Bacillus subtilis chromosome containing a putative 12.3 kb operon involved in hexuronate catabolism and a perfectly symmetrical hypothetical catabolite-responsive element, Microbiology (Reading, U.K.) 144, 877-884.
36. Shulami, S., Gat, O., Sonenshein, A. L., and Shoham, Y. (1999) The glucuronic acid utilization gene cluster from Bacillus stearothermophilus T-6, J. Bacteriol. 181, 3695-3704.
37. Benning, M. M., Kuo, J. M., Raushel, F. M., and Holden, H. M. (1994) Three-dimensional structure of phosphotriesterase: An enzyme capable of detoxifying organophosphate nerve agents, Biochemistry 33, 15001-15007.
38. Thoden, J. B., Phillips, G. N., Neal, T. M., Raushel, F. M., and Holden, H. M. (2001) Molecular structure of dihydroorotase: A paradigm for catalysis through the use of a binuclear metal center, Biochemistry 40, 6989-6997.
39. Hall, R. S., Brown, S., Fedorov, A. A., Fedorov, E. V., Xu, C., Babbitt, P. C., Almo, S. C., and Raushel, F. M. (2007) Structural diversity within the mononuclear and binuclear active sites of N-acetyl-D- glucosamine-6-phosphate deacetylase, Biochemistry 46, 7953-7962.
40. Ireton, G. C., McDermott, G., Black, M. E., and Stoddard, B. L. (2002) The structure of Escherichia coli cytosine deaminase, J. Mol. Biol. 315, 687-697.
41. Thoden, J. B., Marti-Arbona, R., Raushel, F. M., and Holden, H. M. (2003) High-resolution X-ray structure of isoaspartyl dipeptidase from Escherichia coli, Biochemistry 42, 4874-4882.