The X-ray crystallographic structure and activity analysis of a Pseudomonas-specific subfamily of the HAD enzyme superfamily evidences a novel biochemical function

Proteins: Structure, Function and Genetics

Volumn 70, Issue 1, 2008, Pages 197-207

  Peisach, Ezra ^a   Wang, Liangbing ^b   Burroughs, A Maxwell ^c,d   Aravind, L ^c   Dunaway Mariano, Debra ^b   Allen, Karen N ^a,e  

^a BOSTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF NEW MEXICO   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

^d BOSTON UNIVERSITY   (United States)

^e Department of Physiology and Biophysics R702 ^*  (United States)

Author keywords

Functional genomics; Haloacid dehalogenase; HNOB domain; Phosphonatase; Protein; Protein interactions; Pseudomonas; Substrate screening

Indexed keywords

BACTERIAL ENZYME; HALOACID DEHALOGENASE; HOMODIMER; MAGNESIUM ION; PHOSPHOACETALDEHYDE HYDROLASE; PROTEIN PSPTO 2114; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CATALYSIS; CATALYST; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME BINDING; ENZYME STRUCTURE; FUNCTIONAL GENOMICS; KINETICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PSEUDOMONAS SYRINGAE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

BACTERIAL PROTEINS; BASE SEQUENCE; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; DNA PRIMERS; ELECTROPHORESIS, POLYACRYLAMIDE GEL; POLYMERASE CHAIN REACTION; PROTEIN CONFORMATION; PSEUDOMONAS; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION;

PSEUDOMONAS; PSEUDOMONAS SYRINGAE;

EID: 37349085405     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21583     Document Type: Article

References (37)

1. Koonin EV, Tatusov RL. Computer analysis of bacterial haloacid dehalogenases defines a large superfamily of hydrolases with diverse specificity. Application of an iterative approach to database search. J Mol Biol 1994;244:125-132.
2. Collet JF, van Schaftingen E, Stroobant V. A new family of phosphotransferases related to P-type ATPases. Trends Biochem Sci 1998;23:284.
3. Baker AS, Ciocci MJ, Metcalf WW, Kim J, Babbitt PC, Wanner BL, Martin BM, Dunaway-Mariano D. Insights into the mechanism of catalysis by the P-C bond-cleaving enzyme phosphonoacetaldehyde hydrolase derived from gene sequence analysis and mutagenesis. Biochemistry 1998;37:9305-9315.
4. Burroughs AM, Allen KN, Dunaway-Mariano D, Aravind L. Evolutionary genomics of the HAD superfamily: understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes. J Mol Biol 2006;361:1003-1034.
5. Morais MC, Zhang W, Baker AS, Zhang G, Dunaway-Mariano D, Allen KN. The crystal structure of Bacillus cereus phosphonoacetaldehyde hydrolase: insight into catalysis of phosphorus bond cleavage and catalytic diversification within the HAD enzyme superfamily. Biochemistry 2000;39:10385-10396.
6. Li YF, Hata Y, Fujii T, Hisano T, Nishihara M, Kurihara T, Esaki N. Crystal structures of reaction intermediates of L-2-haloacid dehalogenase and implications for the reaction mechanism. J Biol Chem 1998;273:15035-15044.
7. Shin DH, Roberts A, Jancarik J, Yokota H, Kim R, Wemmer DE, Kim SH. Crystal structure of a phosphatase with a unique substrate binding domain from Thermotoga maritima. Protein Sci 2003;12:1464-1472.
8. Selengut JD. MDP-1 is a new and distinct member of the haloacid dehalogenase family of aspartate-dependent phosphohydrolases. Biochemistry 2001;40:12704-12711.
9. Lu Z, Dunaway-Mariano D, Allen KN. HAD superfamily phosphotransferase substrate diversification: structure and function analysis of HAD subclass IIB sugar phosphatase BT4131. Biochemistry 2005;44:8684-8696.
10. Tremblay LW, Dunaway-Mariano D, Allen KN. Structure and activity analyses of Escherichia coli K-12 NagD provide insight into the evolution of biochemical function in the haloalkanoic acid dehalogenase superfamily. Biochemistry 2006;45:1183-1193.
11. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-3402.
12. Notredame C, Higgins DG, Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000;302:205-217.
13. Cuff JA, Barton GJ. Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins 2000;40:502-511.
14. Bradford MM. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 1976;72:248-254.
15. Appel RD, Bairoch A, Hochstrasser DF. A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server. Trends Biochem Sci 1994;19:258-260.
16. Otwinowski Z, Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 1997;276:307-326.
17. Terwilliger TC, Berendzen J. Automated MAD and MIR structure solution. Acta Crystallogr D Biol Crystallogr 1999;55 (Part 4):849-861.
18. Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 1998;54 (Part 5):905-921.
19. Murshudov GN, Vagin AA, Dodson EJ. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 1997;53 (Part 3):240-255.
20. Emsley P, Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 2004;60 (Part 12, Part 1):2126-2132.
21. Zhang G, Dai J, Wang L, Dunaway-Mariano D, Tremblay LW, Allen KN. Catalytic cycling in β-phosphoglucomutase: a kinetic and structural analysis. Biochemistry 2005;44:9404-9416.
22. Aravind L, Iyer LM, Koonin EV. Comparative genomics and structural biology of the molecular innovations of eukaryotes. Curr Opin Struct Biol 2006;16:409-419.
23. Holm L, Sander C. Dali/FSSP classification of three-dimensional protein folds. Nucleic Acids Res 1997;25:231-234.
24. Zhang G, Morais MC, Dai J, Zhang W, Dunaway-Mariano D, Allen KN. Investigation of metal ion binding in phosphonoacetaldehyde hydrolase identifies sequence markers for metal-activated enzymes of the HAD enzyme superfamily. Biochemistry 2004;43:4990-4997.
25. Laskowski RA, Watson JD, Thornton JM. From protein structure to biochemical function? J Struct Funct Genomics 2003;4:167-177.
26. Laskowski RA, Watson JD, Thornton JM. ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res 2005;33 (Web Server issue):W89-W93.
27. Kumar S, Tamura K, Nei M. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 2004;5:150-163.
28. del Sol A, Fujihashi H, Amoros D, Nussinov R. Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families. Protein Sci 2006;15:2120-2128.
29. Chakrabarti P, Janin J. Dissecting protein-protein recognition sites. Proteins 2002;47:334-343.
30. Fortpied J, Maliekal P, Vertommen D, Van Schaftingen E. Magnesium-dependent phosphatase-1 is a protein-fructosamine-6-phosphatase potentially involved in glycation repair. J Biol Chem 2006;281:18378-18385.
31. Peisach E, Selengut JD, Dunaway-Mariano D, Allen KN. X-ray crystal structure of the hypothetical phosphotyrosine phosphatase MDP-1 of the haloacid dehalogenase superfamily. Biochemistry 2004;43:12770-12779.
32. Jones S, Shanahan HP, Berman HM, Thornton JM. Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins. Nucleic Acids Res 2003;31:7189-7198.
33. Aravind L. Guilt by association: contextual information in genome analysis. Genome Res 2000;10:1074-1077.
34. Galperin MY, Koonin EV. Who's your neighbor? New computational approaches for functional genomics. Nat Biotechnol 2000;18:609-613.
35. Huynen M, Snel B, Lathe W, Bork P. Exploitation of gene context. Curr Opin Struct Biol 2000;10:366-370.
36. Aravind L, Koonin EV. The HD domain defines a new superfamily of metal-dependent phosphohydrolases. Trends Biochem Sci 1998;23:469-472.
37. Iyer LM, Anantharaman V, Aravind L. Ancient conserved domains shared by animal soluble guanylyl cyclases and bacterial signaling proteins. BMC Genomics 2003;4:5.