Structure and activity of exo-1,3/1,4-β-glucanase from marine bacterium Pseudoalteromonas sp. BB1 showing a novel C-terminal domain

FEBS Journal

Volumn 279, Issue 3, 2012, Pages 464-478

  Nakatani, Yoshio ^a   Cutfield, Susan M ^a   Cowieson, Nathan P ^b   Cutfield, John F ^a  

^a UNIVERSITY OF OTAGO   (New Zealand)

^b AUSTRALIAN SYNCHROTRON   (Australia)

Author keywords

CD spectroscopy; domain structure; glycoside hydrolase 3; Pseudoalteromonas sp.; small angle X ray scattering

Indexed keywords

ALANINE; GLUCAN 1,3 BETA GLUCOSIDASE; GLUCAN 1,4 BETA GLUCOSIDASE; GLYCOSIDASE; GLYCOSIDE HYDROLASE 3; TRYPTOPHAN; UNCLASSIFIED DRUG;

ARTICLE; BETA CHAIN; BINDING KINETICS; CARBOXY TERMINAL SEQUENCE; CIRCULAR DICHROISM; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME MECHANISM; ENZYME STABILITY; ENZYME SUBSTRATE; HYDROGEN BOND; MARINE BACTERIUM; MUTATION RATE; NONHUMAN; PRIORITY JOURNAL; PROTEIN CROSS LINKING; PROTEIN EXPRESSION; PSEUDOALTEROMONAS; SITE DIRECTED MUTAGENESIS; STRUCTURE ACTIVITY RELATION; THERMOSTABILITY; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; CRYSTALLOGRAPHY, X-RAY; ENZYME STABILITY; GLUCAN 1,3-BETA-GLUCOSIDASE; GLUCAN 1,4-BETA-GLUCOSIDASE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, TERTIARY; PSEUDOALTEROMONAS;

BACTERIA (MICROORGANISMS); HORDEUM; PSEUDOALTEROMONAS SP.;

EID: 84856110191     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2011.08439.x     Document Type: Article

References (44)

1. Singh BK, (2010) Exploring microbial diversity for biotechnology: the way forward. Trends Biotechnol 28, 111-116.
2. Damian AL, &, Adria JL, (2008) Contribution of microorganisms to industrial biology. Mol Biotechnol 38, 41-53.
3. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66-74. (Pubitemid 38451457)
4. DeLong EF, (2005) Microbial community genomics in the ocean. Nat Rev Microbiol 3, 459-469.
5. Nakatani Y, Lamont IL, &, Cutfield JF, (2010) Discovery and characterization of a distinctive exo-β-1,3-glucanase from the marine bacterium Pseudoalteromonas sp. BB1. Appl Environ Microbiol 76, 6760-6768.
6. Henrissat B, &, Davies GJ, (1997) Structural and sequence-based classification of glycoside hydrolases. Curr Opin Struct Biol 18, 527-533.
7. Harvey A, Hrmova M, De Gori R, Varghese J, &, Fincher G, (2000) Comparative modeling of the three-dimensional structures of family 3 glycoside hydrolases. Proteins 41, 257-269.
8. Hrmova M, &, Fincher G, (2007) Dissecting the catalytic mechanism of a plant β-d-glucan glucohydrolase through structural biology using inhibitors and substrate analogues. Carbohydr Res 342, 1613-1623. (Pubitemid 47058064)
9. Rinaudo M, (2007) Seaweed polysaccharides. In Comprehensive Glycoscience. From Chemistry To Systems Biology (, Kamerling JP, ed) Vol. 2, pp. 691-735. Elsevier, New York.
10. Hrmova M, Harvey AJ, Wang J, Shirley NJ, Jones GP, Stone BA, Hoj PB, &, Fincher GB, (1996) Barley-β-d-glucan exohydrolases with β-glucosidase activity. J Biol Chem 271, 5277-5286.
11. Boraston AB, Bolam DN, Gilbert HJ, &, Davies GJ, (2004) Carbohydrate-binding modules: fine-tuning polysaccharide recognition. Biochem J 382, 769-781. (Pubitemid 39312891)
12. Berman H, (2008) The Protein Data Bank: a historical perspective. Acta Crystallogr A 64, 88-95.
13. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, &, Henrissat B, (2009) The Carbohydrate-Active enzymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res 37, D233-D238.
14. Varghese J, Hrmova M, &, Fincher G, (1999) Three-dimensional structure of a barley beta-d-glucan exohydrolase, a family 3 glycosyl hydrolase. Structure 15, 179-190. (Pubitemid 29159703)
15. Litzinger S, Fischer S, Polzer P, Diederichs K, Welte W, &, Mayer C, (2010) Structural and kinetic analysis of Bacillus subtilis N- acetylglucosaminidase reveals a unique Asp-His dyad mechanism. J Biol Chem 285, 35675-35684.
16. Stubbs KA, Balcewich M, Mark BL, &, Vocadlo DJ, (2007) Small molecule inhibitors of a glcoside hydrolase attenuate inducible AmpC-mediated β-lactam resistance. J Biol Chem 282, 21382-21391. (Pubitemid 47099917)
17. Pozzo T, Pasten JL, Karlsson EN, &, Logan DT, (2010) Structural and functional analyses of β-glucosidase 3B from Thermotoga neapolitana: a thermostable three-domain representative of glycoside hydrolase 3. J Mol Biol 397, 724-739.
18. Yoshida E, Hidaka M, Fushinobu S, Koyanagi T, Minami H, Tamaki H, Kitaoka M, Katayama T, &, Kumagai H, (2010) Role of a PA14 domain in determining substrate specificity of a glycoside hydrolase family 3 β-glucosidase from Kluyveromyces marxianus. Biochem J 431, 39-49.
19. Hrmova M, De Gori R, Smith BJ, Fairweather JK, Driguez H, Varghese JN, &, Fincher GB, (2002) Structural basis for broad substrate specificity in higher plant β-d-glucan glucohydrolases. Plant Cell 14, 1033-1052. (Pubitemid 34609215)
20. Harding M, (2001) Geometry of metal-ligand interactions in proteins. Acta Crystallogr D 57, 401-411. (Pubitemid 32203174)
21. Harding M, (2002) Metal-ligand geometry relevant to proteins and in proteins: sodium and potassium. Acta Crystallogr D 58, 872-874. (Pubitemid 34557307)
22. Holm L, &, Sander C, (1995) Dali: a network tool for protein structure comparison. Trends Biochem Sci 20, 478-480.
23. Krissinel E, &, Henrick K, (2004) Secondary structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D 60, 2256-2268. (Pubitemid 41742778)
24. Suhre K, &, Sanejouand Y-H, (2004) ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res 32, 610-614.
25. Matthews BW, (1968) Solvent content of protein crystals. J Mol Biol 33, 491-497.
26. Jacques DA, &, Trewhella J, (2010) Small-angle scattering for structural biology-expanding the frontier while avoiding the pitfalls. Protein Sci 19, 642-657.
27. Wierenga RK, (2001) The TIM-barrel fold: a versatile framework for efficient enzymes. FEBS Lett 492, 193-198. (Pubitemid 32217827)
28. Luang S, Hrmova M, &, Cairns JRK, (2010) High-level expression of barley β-d-glucan exohydrolase HvExoI from a codon-optimised cDNA in Pichia pastoris. Protein Expr Purif 73, 90-98.
29. Guezennec J, (2002) Deep-sea hydrothermal vents: a new source of innovative bacterial exopolysaccharides of biotechnological interest? J Ind Microbiol Biotechnol 29, 204-208. (Pubitemid 35229937)
30. Turkenburg JP, Brzozowski AM, Svendsen A, Borchert TV, Davies GJ, &, Wilson KS, (2009) Structure of a pullulanase from Bacillus acidopullulyticus. Proteins 76, 516-519.
31. Yang ZR, Thomson R, McMell P, &, Esnouf RM, (2005) RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins. Bioinformatics 21, 3369-3376. (Pubitemid 41222441)
32. Krissenel E, &, Henrick K, (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372, 774-797. (Pubitemid 47321791)
33. Kobe B, Guncar G, Buchholz R, Huber T, Maco B, Cowieson N, Martin J, Marfori M, &, Forwood JK, (2008) Crystallography and protein-protein interactions: biological interfaces and crystal contacts. Biochem Soc Trans 36, 1438-1441.
34. Liu H, &, Naismith JH, (2008) An efficient one-step site-directed deletion, insertion, single and multiple-site plasmid mutagenesis protocol. BMC Biotechnol 8, 91-100.
35. Bruss ML, &, Black AL, (1978) Enzymatic microdetermination of glycogen. Anal Biochem 84, 309-312. (Pubitemid 8275983)
36. Collaborative Computational Project Number 4 (1994) The CCP4 Suite: programs for protein crystallography. Acta Crystallogr D 50, 760-763.
37. Kabsch W, (1993) Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J Appl Crystallogr 26, 795-800.
38. McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, &, Read RJ, (2007) Phaser crystallographic software. J Appl Crystallogr 40, 658-674. (Pubitemid 47080256)
39. Murshudov GN, Vagin AA, &, Dodson EJ, (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D 53, 240-255. (Pubitemid 27235885)
40. Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, &, Terwilliger TC, (2002) PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr D 58, 1948-1954. (Pubitemid 35337293)
41. Emsley P, Lohkamp B, Scott WG, &, Cowtan K, (2010) Features and development of Coot. Acta Crystallogr D 66, 486-501.
42. DeLano WL, (2002) The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos ().
43. Svergun DI, (1992) Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J Appl Crystallogr 25, 495-503. (Pubitemid 23564996)
44. Bernado P, Mylonas E, Petoukhov MV, Blackledge M, &, Svergun DI, (2007) Structural characterization of flexible proteins using small-angle X-ray scattering. J Am Chem Soc 129, 5656-5664. (Pubitemid 46697655)