Structure of NADP+-dependent glutamate dehydrogenase from Escherichia coli - Reflections on the basis of coenzyme specificity in the family of glutamate dehydrogenases

FEBS Journal

Volumn 280, Issue 18, 2013, Pages 4681-4692

  Sharkey, Michael A ^a   Oliveira, Tânia F ^b,c   Engel, Paul C ^a   Khan, Amir R ^b  

^a UNIVERSITY COLLEGE DUBLIN   (Ireland)

^b TRINITY COLLEGE DUBLIN   (Ireland)

^c INSTITUTO DE TECNOLOGIA QUÍMICA E BIOLÓGICA   (Portugal)

Author keywords

enzyme catalysis; glutamate dehydrogenase; NADP+ specificity; protein structure; X ray crystallography

Indexed keywords

ADENOSINE 2' PHOSPHATE; ARGININE; ASPARTIC ACID; GLUTAMATE DEHYDROGENASE; GLUTAMATE DEHYDROGENASE (NADP); LYSINE; PHOSPHATE; RIBOSE PHOSPHATE; SERINE;

ALPHA HELIX; ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME KINETICS; ENZYME SPECIFICITY; ENZYME STRUCTURE; ESCHERICHIA COLI; HYDROGEN BOND; MEMBRANE POTENTIAL; MOLECULAR RECOGNITION; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN INTERACTION; STRUCTURE ANALYSIS;

ENZYME CATALYSIS; GLUTAMATE DEHYDROGENASE; NADP+ SPECIFICITY; PROTEIN STRUCTURE; X-RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; ASPARTIC ACID; BINDING SITES; COENZYMES; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GLUTAMATE DEHYDROGENASE (NADP+); HYDROGEN BONDING; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; KINETICS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; NADP; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT PROTEINS; SERINE; STATIC ELECTRICITY;

ANIMALIA; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 84883462342     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/febs.12439     Document Type: Article

References (34)

1. Britton KL, Baker PJ, Engel PC, Rice DW, &, Stillman TJ, (1993) Evolution of substrate diversity in the superfamily of amino acid dehydrogenases. Prospects for rational chiral synthesis. J Mol Biol 234, 938-945.
2. Paradisi F, Collins S, Maguire AR, &, Engel PC, (2007) Phenylalanine dehydrogenase mutants: efficient biocatalysts for synthesis of non-natural phenylalanine derivatives. J Biotechnol 128, 408-411.
3. Yamada A, Dairi T, Ohno Y, Huang XL, &, Asano Y, (1995) Nucleotide sequencing of phenylalanine dehydrogenase gene from Bacillus badius IAM 11059. Biosci Biotechnol Biochem 59, 1994-1995.
4. Nakamura K, Fujii T, Kato Y, Asano Y, &, Cooper AJ, (1996) Quantitation of L-amino acids by substrate recycling between an aminotransferase and a dehydrogenase: application to the determination of L-phenylalanine in human blood. Anal Biochem 234, 19-22.
5. Baker PJ, Britton KL, Engel PC, Farrants GW, Lilley KS, Rice DW, &, Stillman TJ, (1992) Subunit assembly and active site location in the structure of glutamate dehydrogenase. Proteins 12, 75-86.
6. Stillman TJ, Baker PJ, Britton KL, Rice DW, &, Rodgers HF, (1992) Effect of additives on the crystallization of glutamate dehydrogenase from Clostridium symbiosum. Evidence for a ligand-induced conformational change. J Mol Biol 224, 1181-1184.
7. Stillman TJ, Migueis AM, Wang XG, Baker PJ, Britton KL, Engel PC, &, Rice DW, (1999) Insights into the mechanism of domain closure and substrate specificity of glutamate dehydrogenase from Clostridium symbiosum. J Mol Biol 285, 875-885.
8. Peterson PE, &, Smith TJ, (1999) The structure of bovine glutamate dehydrogenase provides insights into the mechanism of allostery. Structure 7, 769-782.
9. Britton KL, Baker PJ, Rice DW, &, Stillman TJ, (1992) Structural relationship between the hexameric and tetrameric family of glutamate dehydrogenases. Eur J Biochem 209, 851-859.
10. Kort R, Liebl W, Labedan B, Forterre P, Eggen RI, &, de Vos WM, (1997) Glutamate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima: molecular characterization and phylogenetic implications. Extremophiles 1, 52-60.
11. Yarrison G, Young DW, &, Choules GL, (1972) Glutamate dehydrogenase from Mycoplasma laidlawii. J Bacteriol 110, 494-503.
12. Baker PJ, Britton KL, Rice DW, Rob A, &, Stillman TJ, (1992) Structural consequences of sequence patterns in the fingerprint region of the nucleotide binding fold. Implications for nucleotide specificity. J Mol Biol 228, 662-671.
13. Wierenga RK, &, Hol WG, (1983) Predicted nucleotide-binding properties of p21 protein and its cancer-associated variant. Nature 302, 842-844.
14. Wierenga R, De Maeyer M, &, Hol W, (1985) Interaction of pyrophosphate moieties with alpha-helices in dinucleotide-binding proteins. Biochemistry 24, 1346-1357.
15. Hanukoglu I, &, Gutfinger T, (1989) cDNA sequence of adrenodoxin reductase. Identification of NADP-binding sites in oxidoreductases. Eur J Biochem 180, 479-484.
16. Scrutton NS, Berry A, &, Perham RN, (1990) Redesign of the coenzyme specificity of a dehydrogenase by protein engineering. Nature 343, 38-43.
17. Lilley KS, Baker PJ, Britton KL, Stillman TJ, Brown PE, Moir AJ, Engel PC, Rice DW, Bell JE, &, Bell E, (1991) The partial amino acid sequence of the NAD(+)-dependent glutamate dehydrogenase of Clostridium symbiosum: implications for the evolution and structural basis of coenzyme specificity. Biochim Biophys Acta 1080, 191-197.
18. + in a glutamate dehydrogenase and a reappraisal of the specificity of the wild-type enzyme. FEBS J 278, 2460-2468.
19. Oliveira T, Panjikar S, Carrigan JB, Hamza M, Sharkey MA, Engel PC, &, Khan AR, (2012) Crystal structure of NAD+-dependent Peptoniphilus asaccharolyticus glutamate dehydrogenase reveals determinants of cofactor specificity. J Struct Biol 177, 543-552.
20. +-dependent glutamate dehydrogenase of Escherichia coli. J Mol Biol 234, 1270-1273.
21. Totir M, Echols N, Nanao M, Gee CL, Moskaleva A, Gradia S, Iavarone AT, Berger JM, May AP, Zubieta C, et al,. (2012) Macro-to-micro structural proteomics: native source proteins for high-throughput crystallization. PLoS ONE 7, e32498.
22. Sharkey MA, &, Engel PC, (2009) Modular coenzyme specificity: a domain-swopped chimera of glutamate dehydrogenase. Proteins 77, 268-278.
23. Stillman TJ, Baker PJ, Britton KL, &, Rice DW, (1993) Conformational flexibility in glutamate dehydrogenase. Role of water in substrate recognition and catalysis. J Mol Biol 234, 1131-1139.
24. Smith TJ, Peterson PE, Schmidt T, Fang J, &, Stanley CA, (2001) Structures of bovine glutamate dehydrogenase complexes elucidate the mechanism of purine regulation. J Mol Biol 307, 707-720.
25. Bhuiya MW, Sakuraba H, Ohshima T, Imagawa T, Katunuma N, &, Tsuge H, (2005) The first crystal structure of hyperthermostable NAD-dependent glutamate dehydrogenase from Pyrobaculum islandicum. J Mol Biol 345, 325-337.
26. Sharkey MA, &, Engel PC, (2008) Apparent negative co-operativity and substrate inhibition in overexpressed glutamate dehydrogenase from Escherichia coli. FEMS Microbiol Lett 281, 132-139.
27. Otwinowski Z, &, Minor W, (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276, 307-326.
28. Kabsch W, (1988) Automatic indexing of rotation diffraction patterns. J Appl Crystallogr 21, 67-71.
29. Collaborative Computational Project Number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50, 760-763.
30. McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, &, Read RJ, (2007) Phaser crystallographic software. J Appl Crystallogr 40, 658-674.
31. Emsley P, &, Cowtan K, (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60, 2126-2132.
32. Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, et al,. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66, 213-221.
33. Painter J, &, Merritt EA, (2006) Optimal description of a protein structure in terms of multiple groups undergoing TLS motion. Acta Crystallogr D Biol Crystallogr 62, 439-450.
34. Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB 3rd, Snoeyink J, Richardson JS, et al,. (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35, W375-W383.