Crystal Structure of a Cellulosomal Family 3 Carbohydrate Esterase from Clostridium thermocellum Provides Insights into the Mechanism of Substrate Recognition

Journal of Molecular Biology

Volumn 379, Issue 1, 2008, Pages 64-72

  Correia, Márcia A S ^a   Prates, José A M ^a   Brás, Joana ^a   Fontes, Carlos M G A ^a   Newman, Joseph A ^b   Lewis, Richard J ^b   Gilbert, Harry J ^b   Flint, James E ^b  

^a UNIVERSITY OF LISBON   (Portugal)

^b NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

acetyl xylan; catalytic triad; esterases; X ray crystallography

Indexed keywords

ACETIC ACID; ACETIC ACID DERIVATIVE; ASPARAGINE; ASPARTAME; CARBOHYDRATE; CARBOHYDRATE ESTERASE 3; CELLULOSOME; ESTERASE; GLYCINE; HISTIDINE; HYDROLASE; POLYSACCHARIDE; SERINE; XYLAN;

ALPHA HELIX; AMINO TERMINAL SEQUENCE; ARTICLE; BETA SHEET; BIOCATALYST; CARBOHYDRATE METABOLISM; CARBOXY TERMINAL SEQUENCE; CATALYSIS; CELL WALL; CLOSTRIDIUM THERMOCELLUM; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME SUBSTRATE; HYDROGEN BOND; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN FOLDING; PROTEIN FUNCTION; THERMOSTABILITY;

CLOSTRIDIUM THERMOCELLUM;

EID: 43049170350     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2008.03.037     Document Type: Article

References (34)

1. C.T. Brett K. Waldren M. Black B. Charlewood Physiology and Biochemistry of Plant Cell Walls. Topics in Plant Functional Biology vol. 1 1996 Chapman and Hall London
2. A.J. Ragauskas C.K. Williams B.H. Davison G. Britovsek J. Cairney C.A. Eckert The path forward for biofuels and biomaterials Science 311 2006 484 489
3. M. Sticklen Plant genetic engineering to improve biomass characteristics for biofuels Curr. Opin. Biotechnol. 17 2006 315 319
4. L.M. Ferreira T.M. Wood G. Williamson C. Faulds G.P. Hazlewood G.W. Black H.J. Gilbert A modular esterase from Pseudomonas fluorescens subsp. cellulosa contains a non-catalytic cellulose-binding domain Biochem. J. 294 1993 349 355
5. B. Henrissat A classification of glycosyl hydrolases based on amino acid sequence similarities Biochem. J. 280 1991 309 316
6. E.J. Taylor T.M. Gloster J.P. Turkenburg F. Vincent A.M. Brzozowski C. Dupont Structure and activity of two metal ion-dependent acetylxylan esterases involved in plant cell wall degradation reveals a close similarity to peptidoglycan deacetylases J. Biol. Chem. 281 2006 10968 10975
7. E.A. Bayer J.P. Belaich Y. Shoham R. Lamed The cellulosomes: multienzyme machines for degradation of plant cell wall polysaccharides Annu. Rev. Microbiol. 58 2004 521 554
8. E.A. Bayer R. Kenig R. Lamed Adherence of Clostridium thermocellum to cellulose J. Bacteriol. 156 1983 818 827
9. V. Aurilia J.C. Martin S.I. McCrae K.P. Scott M.T. Rincon H.J. Flint Three multidomain esterases from the cellulolytic rumen anaerobe Ruminococcus flavefaciens 17 that carry divergent dockerin sequences Microbiology 146 2000 1391 1397
10. B.P. Dalrymple D.H. Cybinski I. Layton C.S. McSweeney G.P. Xue Y.J. Swadling J.B. Lowry Three Neocallimastix patriciarum esterases associated with the degradation of complex polysaccharides are members of a new family of hydrolases Microbiology 143 1997 2605 2614
11. F. Vincent S.J. Charnock K.H. Verschueren J.P. Turkenburg D.J. Scott W.A. Offen Multifunctional xylooligosaccharide/cephalosporin C deacetylase revealed by the hexameric structure of the Bacillus subtilis enzyme at 1.9 Å resolution J. Mol. Biol. 330 2003 593 606
12. D.E. Blair O. Hekmat A.W. Schuttelkopf B. Shrestha K. Tokuyasu S.G. Withers D.M. van Aalten Structure and mechanism of chitin deacetylase from the fungal pathogen Colletotrichum lindemuthianum Biochemistry 45 2006 9416 9426
13. L.M. Ferreira T.M. Wood G. Williamson C. Faulds G.P. Hazlewood G.W. Black H.J. Gilbert A modular esterase from Pseudomonas fluorescens subsp. cellulosa contains a non-catalytic cellulose-binding domain Biochem. J. 294 1993 349 355
14. R.A. Laskowski D.S. Moss J.M. Thornton Main-chain bond lengths and bond angles in protein structures J. Mol. Biol. 231 1993 1049 1067
15. S. Jones J.M. Thornton Protein-protein interactions: a review of protein dimer structures Prog. Biophys. Mol. Biol. 63 1995 31 65
16. I.K. McDonald J.M. Thornton Satisfying hydrogen bonding potential in proteins J. Mol. Biol. 238 1994 777 793
17. E. Krissinel K. Henrick Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions Acta Crystallogr. D 60 2004 2256 2268
18. Y.C. Lo S.C. Lin J.F. Shaw Y.C. Liaw Crystal structure of Escherichia coli thioesterase I/protease I/lysophospholipase L1: consensus sequence blocks constitute the catalytic center of SGNH-hydrolases through a conserved hydrogen bond network J. Mol. Biol. 330 2003 539 551
19. Y.C. Lo S.C. Lin J.F. Shaw Y.C. Liaw Substrate specificities of Escherichia coli thioesterase I/protease I/lysophospholipase L1 are governed by its switch loop movement Biochemistry 44 2005 1971 1979
20. A. Molgaard S. Kauppinen S. Larsen Rhamnogalacturonan acetylesterase elucidates the structure and function of a new family of hydrolases Structure 8 2000 373 383
21. Y.S. Ho L. Swenson U. Derewenda L. Serre Y. Wei Z. Dauter Brain acetylhydrolase that inactivates platelet-activating factor is a G-protein-like trimer Nature 385 1997 89 93
22. A.B. Boraston B.W. McLean G. Chen A. Li R.A. Warren D.G. Kilburn Co-operative binding of triplicate carbohydrate-binding modules from a thermophilic xylanase Mol. Microbiol. 43 2002 187 194
23. A.C. Freelove D.N. Bolam P. White G.P. Hazlewood H.J. Gilbert A novel carbohydrate-binding protein is a component of the plant cell wall-degrading complex of Piromyces equi J. Biol. Chem. 276 2001 43010 43017
24. V. Ramakrishnan J.T. Finch V. Graziano P.L. Lee R.M. Sweet Crystal structure of globular domain of histone H5 and its implications for nucleosome binding Nature 362 1993 219 223
25. K.G. Johnson J.D. Fontana C.R. MacKenzie Measurement of acetylxylan esterase in Streptomyces Method. Enzymol. 160 1988 551 560
26. P. Evans Data reduction CCP4 Daresbury Study Weekend: Data Collection and Processing, DL/SCI/R34 1993 Central Laboratory of the Research Councils Daresbury Laboratory, Warrington, UK 114 122
27. T. Pape T.R. Schneider HKL2MAP: a graphical user interface for phasing with SHELX programs J. Appl. Crystallogr. 37 2004 843 844
28. T.R. Schneider G.M. Sheldrick Substructure solution with SHELXD Acta Crystallogr. D 58 2002 1772 1779
29. Collaborative Computational Project Number 4′ The CCP4 suite: programs for protein crystallography Acta Crystallogr. D 50 1994 760 763
30. K. Cowtan ‘dm’: an automated procedure for phase improvement by density modification Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography 31 1994 34 38
31. G.N. Murshudov A.A. Vagin E.J. Dodson Refinement of macromolecular structures by the maximum-likelihood method Acta Crystallogr. Biol. D 53 1997 240 255
32. V.S. Lamzin K.S. Wilson Automated refinement for protein crystallography Methods Enzymol. 277 1997 269 305
33. P. Emsley K. Cowtan Coot: model-building tools for molecular graphics Acta Crystallogr. Biol. D 60 2004 2126 2132
34. A. Vagin A. Teplyakov MOLREP: an automated program for molecular replacement J. Appl. Crystallogr. 30 1997 1022 1025