Structure of alanine dehydrogenase from Archaeoglobus: Active site analysis and relation to bacterial cyclodeaminases and mammalian mu crystallin

Journal of Molecular Biology

Volumn 342, Issue 1, 2004, Pages 119-130

  Gallagher, D T ^a   Monbouquette, H G ^b   Schroder I ^b   Robinson, H ^c   Holden, M J ^a   Smith, N N ^a  

^a NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c BROOKHAVEN NATIONAL LABORATORY   (United States)

Author keywords

hyperthermophile; nicotinamide adenine dinucleotide; Rossmann fold

Indexed keywords

ALANINE DEHYDROGENASE; ARGININE; BACTERIAL ENZYME; CRYSTALLIN; DEAMINASE; DIMER; LYSINE; MU CRYSTALLIN; NICOTINAMIDE ADENINE DINUCLEOTIDE; PORPHOBILINOGEN SYNTHASE; UNCLASSIFIED DRUG; WATER;

ARCHAEOGLOBUS; ARTICLE; CARBOXY TERMINAL SEQUENCE; CATALYSIS; CONTROLLED STUDY; ENZYME STRUCTURE; GENE STRUCTURE; MAMMAL; MOLECULAR INTERACTION; MOLECULE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY;

ARCHAEA; ARCHAEOGLOBUS; ARCHAEOGLOBUS FULGIDUS; BACTERIA (MICROORGANISMS); MAMMALIA; METATHERIA; PHORMIDIUM; PHORMIDIUM LAPIDEUM;

EID: 4143094873     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.06.090     Document Type: Article

References (40)

1. H.P. Klenk, R.A. Clayton, J.F. Tomb, O. White, K.E. Nelson, and K.A. Ketchum The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus Nature 390 1997 364 370
2. Schröder, I., Vadas, A., Johnson, E., Lim, S. & Monbouquette, H. G. (2004). A novel archaeal alanine dehydrogenase homologous to ornithine cyclodeaminase and mu crystallin. J. Bacteriol. In the press.
3. T. Ohshima, and K. Soda Biochemistry and biotechnology of amino acid dehydrogenases Advan. Biochem. Eng. Biotechnol. 42 1990 187 209
4. A.B. Andersen, P. Andersen, and L. Ljungqvist Structure and function of a 40,000-molecular-weight protein antigen of Mycobacterium tuberculosis Infect. Immun. 60 1992 2317 2323
5. N. Itoh, and R. Morikawa Crystallization and properties of l-alanine dehydrogenase from Streptomyces phaeochromogenes Agric. Biol. Chem. 47 1983 2511 2519
6. A. Galkin, L. Kulakova, H. Ashida, Y. Sawa, and N. Esaki Cold-adapted alanine dehydrogenases from two antarctic bacterial strains: gene cloning, protein characterization, and comparison with mesophilic and thermophilic counterparts Appl. Environ. Microbiol. 65 1999 4014 4020
7. A. Vancura, I. Vancurova, J. Volc, S.K. Jones, M. Flieger, G. Basarova, and V. Behal Alanine dehydrogenase from Streptomyces fradiae: purification and properties Eur. J. Biochem. 179 1989 221 227
8. M.T. Smith, and D.W. Emerich Alanine dehydrogenase from soybean nodule bacteroids: purification and properties Arch. Biochem. Biophys. 304 1993 379 385
9. I. Vancurova, A. Vancura, and J. Volc Purification and partial characterization of alanine dehydrogenase from Streptomyces aureofaciens Arch. Microbiol. 150 1988 438 440
10. P.J. Baker, Y. Sawa, H. Shibata, S.E. Sedelnikova, and D.W. Rice Analysis of the structure and substrate binding of Phormidium lapideum alanine dehydrogenase Nature Struct. Biol. 5 1998 561 567
11. M.G. Rossmann, A. Liljas, C.-I. Branden, and L.J. Banaszak Evolutionary and structural relationships among dehydrogenases P.D. Boyer The Enzymes 1975 Academic Press New York 61 102
12. J.L. Vanhooke, J.B. Thoden, N.M.W. Brunhuber, J.S. Blanchard, and H.M. Holden Phenylalanine dehydrogenase from Rhodococcus sp. M4: high-resolution X-ray analyses of inhibitory ternary complexes reveal key features in the oxidative deamination mechanism Biochemistry 38 1999 2326 2339
13. P.J. Baker, A.P. Turnbull, S.E. Sedelnikova, T.J. Stillman, and D.W. Rice A role for quaternary structure in the substrate specificity of leucine dehydrogenase Structure 3 1995 693 705
14. T.J. Stillman, P.J. Baker, K.L. Britton, and D.W. Rice Conformational flexibility in glutamate dehydrogenase: role of water in substrate reconition and catalysis J. Mol. Biol. 234 1993 1131 1139
15. G. Scapin, S. Reddy, and J.S. Blanchard Three-dimensional structure of meso-diaminopimelic acid dehydrogenase from Corynebacterium glutamicum Biochemistry 35 1996 13540 13551
16. M. Nakasako, T. Fujisawa, S. Adachi, T. Kudo, and S. Higuchi Large-scale domain movements and hydration structure changes in the active-site cleft of unligated glutamate dehydrogenase from Thermococcus profundus studied by cryogenic X-ray crystal structure analysis and small-angle X-ray scattering Biochemistry 40 2001 3069 3079
17. K.S. Yip, T.J. Stillman, K.L. Britton, P.J. Artymiuk, P.J. Baker, and S.E. Sedelnikova The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures Structure 3 1995 1147 1158
18. A.J.H. Vadas, I. Schröder, and H.G. Monbouquette Room-temperature synthesis of l-alanine using the alanine dehydrogenase of the hyperthermophilic archaeon Archaeoglobus fulgidus Biotechnol. Prog. 18 2002 909 911
19. B. Lee, and F.M. Richards The interpretation of protein structures: estimation of static accessibility J. Mol. Biol. 55 1971 379 400
20. G. Deckert, P.V. Warren, T. Gaasterland, W.G. Young, A.L. Lennox, and D.E. Graham The complete genome of the hyperthermophilic bacterium Aquifex aeolicus Nature 392 1998 353
21. A.G. Murzin, S.E. Brenner, T. Hubbard, and C. Chothia SCOP: a structural classification of proteins database for the investigation of sequences and structures J. Mol. Biol. 247 1995 536 540
22. C.E. Grimshaw, P.F. Cook, and W.W. Cleland Use of isotope effects and pH studies to determine the chemical mechanism of Bacillus subtilis l-alanine dehydrogenase Biochemistry 20 1981 5655 5661
23. N. Sans, G. Schröder, and J. Schröder The Noc region of Ti plasmid C58 codes for arginase and ornithine cyclodeaminase Eur. J. Biochem. 167 1987 81 87
24. R.Y. Kim, R. Gasser, and G.J. Wistow Mu-crystallin is a mammalian homolog of Agrobacterium ornithine cyclodeaminase and is expressed in human retina Proc. Natl Acad. Sci. USA 89 1992 9292 9296
25. G. Chang, and H. Lee Endogenous enzymatic activities of taxon-specific lens crystallins Zool. Stud. 33 1994 177 185
26. R. Jaenicke, and C. Slingsby Lens crystallins and their microbial homologs: structure, stability, and function Crit. Rev. Biochem. Mol. Biol. 36 2001 435 499
27. L. Segovia, J. Horwitz, R. Gasser, and G. Wistow Two roles for mu-crystallin: a lens structural protein in diurnal marsupials and a possible enzyme in mammalian retinas Mol. Vision 3 1997 www.emory.edu/molvis/v3/segovia
28. M.P. Vie, C. Evrard, J. Osty, A. Breton-Gilet, P. Blanchet, and M. Pomerance Purification, molecular cloning, and functional expression of the human nicodinamide-adenine dinucleotide phosphate-regulated thyroid hormone-binding protein Mol. Endocrinol. 11 1997 1728 1736
29. A. Wojtczak, V. Cody, J. Luft, and W. Pangborn Structures of human transthyretin complexed with thyroxin at 2.0 resolution and 3′, 5′-dinitro-N-acetyl-l-thyronine at 2.2 resolution Acta Crystallog. sect. D 52 1996 758 765
30. S. Mousses, L. Bubendorf, U. Wagner, G. Hostetter, J. Kononen, and R. Cornelison Clinical validation of candidate genes associated with prostate cancer progression in the CWR22 model system using tissue microarrays Cancer Res. 62 2002 1256 1260
31. S. Abe, T. Katagiri, A. Saito-Hisaminato, S. Usami, Y. Inoue, T. Tsunoda, and Y. Nakamura Identification of CRYM as a candidate responsible for nonsyndromic deafness, through cDNA microarray analysis of human cochlear and vestibular tissues Am. J. Hum. Genet. 72 2003 73 82
32. N. Smith, M. Mayhew, H. Robinson, A. Heroux, D. Charlton, M. Holden, and D.T. Gallagher Crystallization and phasing of alanine dehydrogenase from Archaeoglobus fulgidus Acta Crystallog. sect. D 59 2003 2328 2331
33. T.C. Terwilliger, and J. Berendsen Automated MAD and MIR structure solution Acta Crystallog. sect. D 55 1999 849 861
34. A.T. Brunger, P.D. Adams, G.M. Clore, W.L. DeLano, P. Gros, and R.W. Grosse-Kunstleve Crystallography NMR system: a new software suite for macromolecular structure determination Acta Crystallog. sect. D 54 1998 905 921
35. D. McRee A versatile program for manipulating atomic coordinates and electron density J. Struct. Biol. 125 1999 156 165
36. R.A. Laskowski, M.W. Macarthur, D.S. Moss, and J.M. Thornton PROCHECK: a program to check the stereochemical quality of protein structures J. Appl. Crystallog. 26 1993 283 291
37. L. Holm, and C. Sander Mapping the protein universe Science 273 1996 595 602
38. I.N. Shindyalov, and P.E. Bourne Protein structure alignment by incremental combinatorial extension (CE) of the optimal path Protein Eng. 11 1998 739 747
39. P.J. Kraulis MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures J. Appl. Crystallog. 24 1991 946 950
40. L. Goodstadt, and C.P. Ponting CHROMA: consensus-based colouring of multiple alignments for publication Bioinformatics 17 2001 845 846