title: Paenibacillus sp. strain E18 bifunctional xylanase-glucanase with a single catalytic domain.
abstract: Xylanases are utilized in a variety of industries for the breakdown of plant materials. Most native and engineered bifunctional/multifunctional xylanases have separate catalytic domains within the same polypeptide chain. Here we report a new bifunctional xylanase (XynBE18) produced by Paenibacillus sp. E18 with xylanase and beta-1,3-1,4-glucanase activities derived from the same active center by substrate competition assays and site-directed mutagenesis of xylanase catalytic Glu residues (E129A and E236A). The gene consists of 981 bp, encodes 327 amino acids, and comprises only one catalytic domain that is highly homologous to the glycoside hydrolase family 10 xylanase catalytic domain. Recombinant XynBE18 purified from Escherichia coli BL21(DE3) showed specificity toward oat spelt xylan and birchwood xylan and beta-1,3-1,4-glucan (barley beta-glucan and lichenin). Homology modeling and molecular dynamic simulation were used to explore structure differences between XynBE18 and the monofunctional xylanase XynE2, which has enzymatic properties similar to those of XynBE18 but does not hydrolyze beta-1,3-1,4-glucan. The cleft containing the active site of XynBE18 is larger than that of XynE2, suggesting that XynBE18 is able to bind larger substrates such as barley beta-glucan and lichenin. Further molecular docking studies revealed that XynBE18 can accommodate xylan and beta-1,3-1,4-glucan, but XynE2 is only accessible to xylan. These results indicate a previously unidentified structure-function relationship for substrate specificities among family 10 xylanases.
authors.affiliation: Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, People's Republic of China.
authors.forename: Pengjun
authors.initials: P
authors.lastname: Shi
authors.forename: Jian
authors.initials: J
authors.lastname: Tian
authors.forename: Tiezheng
authors.initials: T
authors.lastname: Yuan
authors.forename: Xin
authors.initials: X
authors.lastname: Liu
authors.forename: Huoqing
authors.initials: H
authors.lastname: Huang
authors.forename: Yingguo
authors.initials: Y
authors.lastname: Bai
authors.forename: Peilong
authors.initials: P
authors.lastname: Yang
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Chen
authors.forename: Ningfeng
authors.initials: N
authors.lastname: Wu
authors.forename: Bin
authors.initials: B
authors.lastname: Yao
mesh_terms: D019943:Amino Acid Substitution / Q000235:genetics; D020134:Catalytic Domain; D044644:Endo-1,3(4)-beta-Glucanase / Q000235:genetics* / Q000378:metabolism*; D043364:Endo-1,4-beta Xylanases / Q000235:genetics* / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D056507:Paenibacillus / Q000201:enzymology*; D011994:Recombinant Proteins / Q000096:biosynthesis / Q000302:isolation & purification; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity; D014990:Xylans / Q000378:metabolism; D047071:beta-Glucans / Q000378:metabolism
chemical_list: D011994:Recombinant Proteins; D014990:Xylans; D047071:beta-Glucans; D044644:Endo-1,3(4)-beta-Glucanase; D043364:Endo-1,4-beta Xylanases
references.citation: J Comput Chem. 2005 Dec;26(16):1701-18
references.pmid: 16211538
references.citation: J Ind Microbiol Biotechnol. 2008 Jul;35(7):635-44
references.pmid: 18365260
references.citation: Anal Biochem. 1976 May 7;72:248-54
references.pmid: 942051
references.citation: Biosci Biotechnol Biochem. 2009 Apr 23;73(4):833-9
references.pmid: 19352037
references.citation: J Biol Chem. 2000 Jul 28;275(30):23020-6
references.pmid: 10930426
references.citation: FEMS Microbiol Rev. 1999 Jul;23(4):411-56
references.pmid: 10422261
references.citation: J Comput Aided Mol Des. 2008 Dec;22(12):915-23
references.pmid: 18663584
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D233-8
references.pmid: 18838391
references.citation: Acta Crystallogr D Biol Crystallogr. 2007 Aug;63(Pt 8):845-59
references.pmid: 17642511
references.citation: Proteins. 2008 May 1;71(2):938-49
references.pmid: 18004755
references.citation: Plant Physiol. 2001 Jan;125(1):54-7
references.pmid: 11154295
references.citation: FEBS Lett. 1995 Apr 10;362(3):281-5
references.pmid: 7729513
references.citation: Appl Microbiol Biotechnol. 2008 Jun;79(4):579-87
references.pmid: 18415095
references.citation: Genomics. 1995 Feb 10;25(3):674-81
references.pmid: 7759102
references.citation: Can J Biochem. 1979 Feb;57(2):125-34
references.pmid: 455113
references.citation: Proc Natl Acad Sci U S A. 1995 Jul 18;92(15):7090-4
references.pmid: 7624375
references.citation: Eur Biophys J. 2005 Jun;34(4):273-84
references.pmid: 15803330
references.citation: Microbiol Rev. 1988 Sep;52(3):305-17
references.pmid: 3141761
references.citation: Biotechnol Genet Eng Rev. 1996;13:101-31
references.pmid: 8948110
references.citation: J Bacteriol. 1993 May;175(10):2943-51
references.pmid: 8491715
references.citation: J Biol Chem. 2000 Jul 28;275(30):23027-33
references.pmid: 10767281
references.citation: J Mol Biol. 2000 Jul 14;300(3):575-85
references.pmid: 10884353
references.citation: Bioresour Technol. 2001 Jul;78(3):277-80
references.pmid: 11341688
references.citation: J Comput Chem. 2004 Oct;25(13):1656-76
references.pmid: 15264259
references.citation: J Agric Food Chem. 2002 Aug 28;50(18):5121-7
references.pmid: 12188617
references.citation: J Biochem Mol Biol. 2006 Jan 31;39(1):105-10
references.pmid: 16475280
references.citation: FEMS Microbiol Rev. 2005 Jan;29(1):3-23
references.pmid: 15652973
references.citation: Adv Biochem Eng Biotechnol. 1997;57:45-125
references.pmid: 9204751
references.citation: Crit Rev Biotechnol. 1997;17(1):39-67
references.pmid: 9118232