title: Crystal structure of a novel two domain GH78 family α-rhamnosidase from Klebsiella oxytoca with rhamnose bound.
abstract: The crystal structure of the GH78 family α-rhamnosidase from Klebsiella oxytoca (KoRha) has been determined at 2.7 Å resolution with rhamnose bound in the active site of the catalytic domain. Curiously, the putative catalytic acid, Asp 222, is preceded by an unusual non-proline cis-peptide bond which helps to project the carboxyl group into the active centre. This KoRha homodimeric structure is significantly smaller than those of the other previously determined GH78 structures. Nevertheless, the enzyme displays α-rhamnosidase activity when assayed in vitro, suggesting that the additional structural domains found in the related enzymes are dispensible for function.
authors.affiliation: Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, Nr4 7UH, United Kingdom.
authors.forename: Ellis C
authors.initials: EC
authors.lastname: O'Neill
authors.affiliation: Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, Nr4 7UH, United Kingdom.
authors.forename: Clare E M
authors.initials: CE
authors.lastname: Stevenson
authors.affiliation: Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, Nr4 7UH, United Kingdom.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Paterson
authors.affiliation: Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, Nr4 7UH, United Kingdom.
authors.forename: Martin
authors.initials: M
authors.lastname: Rejzek
authors.affiliation: Laboratorio Nacional De Genómica Para La Biodiversidad (Langebio), CINVESTAV-IPN, Irapuato, Cp36821, México.
authors.forename: Anne-Laure
authors.initials: AL
authors.lastname: Chauvin
authors.affiliation: Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, Nr4 7UH, United Kingdom.
authors.forename: David M
authors.initials: DM
authors.lastname: Lawson
authors.affiliation: Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, Nr4 7UH, United Kingdom.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Field
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites / Q000235:genetics; D055162:Biocatalysis; D002236:Carbohydrate Conformation; D018360:Crystallography, X-Ray; D006026:Glycoside Hydrolases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D041121:Klebsiella oxytoca / Q000201:enzymology* / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D012210:Rhamnose / Q000737:chemistry* / Q000378:metabolism; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D006026:Glycoside Hydrolases; C022525:alpha-L-rhamnosidase; D012210:Rhamnose
keywords: E.C. 3.2.1.40; enzyme structure; flavonoid; glycosyl hydrolase family 78; rutin; α-l-rhamnosidase
references.citation: Mol Microbiol. 2000 Jan;35(1):173-9
references.pmid: 10632887
references.citation: Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1955-7
references.pmid: 12393928
references.citation: Anal Biochem. 1985 Sep;149(2):566-71
references.pmid: 3935009
references.citation: Biochemistry. 1987 Jan 27;26(2):476-86
references.pmid: 3548820
references.citation: Biochem Biophys Res Commun. 1998 Jan 26;242(3):552-9
references.pmid: 9464254
references.citation: Appl Microbiol Biotechnol. 1999 Jan;51(1):22-32
references.pmid: 10077819
references.citation: Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32
references.pmid: 15572765
references.citation: Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2256-68
references.pmid: 15572779
references.citation: Curr Microbiol. 2005 Aug;51(2):105-9
references.pmid: 15991055
references.citation: Acta Crystallogr D Biol Crystallogr. 2006 Sep;62(Pt 9):1002-11
references.pmid: 16929101
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W375-83
references.pmid: 17452350
references.citation: J Mol Biol. 2007 Nov 23;374(2):384-98
references.pmid: 17936784
references.citation: Curr Opin Plant Biol. 2008 Jun;11(3):266-77
references.pmid: 18486536
references.citation: Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):470-8
references.pmid: 20383000
references.citation: Org Biomol Chem. 2011 Mar 7;9(5):1653-60
references.pmid: 21253654
references.citation: Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):355-67
references.pmid: 21460454
references.citation: Appl Environ Microbiol. 2011 Sep;77(18):6524-30
references.pmid: 21784921
references.citation: J Bacteriol. 2012 May;194(9):2371-2
references.pmid: 22493189
references.citation: Bioresour Technol. 2012 Jul;115:222-7
references.pmid: 21890350
references.citation: Carbohydr Res. 2012 Sep 1;358:12-8
references.pmid: 22795862
references.citation: J Biol Chem. 2013 Apr 26;288(17):12376-85
references.pmid: 23486481
references.citation: Acta Crystallogr D Biol Crystallogr. 2013 Jul;69(Pt 7):1260-73
references.pmid: 23793152
references.citation: Bioorg Med Chem. 2013 Aug 15;21(16):4762-7
references.pmid: 23806835
references.citation: Bioresour Technol. 2013 Nov;147:640-4
references.pmid: 24012095
references.citation: Nucleic Acids Res. 2014 Jan;42(Database issue):D490-5
references.pmid: 24270786