EzCatDB: D00844
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DB codeD00844
RLCP classification1.30.35885.972 : Hydrolysis
CATH domainDomain 12.60.40.1500 : Immunoglobulin-like
Domain 23.20.20.80 : TIM BarrelCatalytic domain
E.C.3.2.1.37

CATH domainRelated DB codes (homologues)
3.20.20.80 : TIM BarrelS00202,S00210,S00748,S00906,S00907,S00911,S00912,S00915,M00134,M00160,D00479,S00204,S00205,S00206,S00207,S00203,S00208,S00209,S00211,S00213,S00214,M00113,T00307,D00165,D00166,D00169,D00176,D00501,D00502,D00503,D00861,D00864,M00026,M00112,M00193,M00346,T00057,T00062,T00063,T00066,T00067

Enzyme Name
UniProtKBKEGG

P36906Q9ZFM2
Protein nameBeta-xylosidaseBeta-xylosidaseXylan 1,4-beta-xylosidase
Xylobiase
Beta-xylosidase
Exo-1,4-beta-xylosidase
Beta-D-xylopyranosidase
Beta-xylosidase
Beta-xylosidase
Exo-1,4-xylosidase
Exo-1,4-beta-D-xylosidase
1,4-beta-D-xylan xylohydrolase
SynonymsEC 3.2.1.37
1,4-beta-D-xylan xylohydrolase
Xylan 1,4-beta-xylosidase
EC 3.2.1.37
1,4-beta-D-xylan xylohydrolase
Xylan 1,4-beta-xylosidase
PfamPF01229 (Glyco_hydro_39)
[Graphical view]
PF01229 (Glyco_hydro_39)
[Graphical view]
CAZyGH39 (Glycoside Hydrolase Family)
GH39 (Glycoside Hydrolase Family)

KEGG pathways
MAP codePathways
MAP00500Starch and sucrose metabolism
MAP00520Nucleotide sugars metabolism

UniProtKB:Accession NumberP36906Q9ZFM2
Entry nameXYNB_THESAXYNB_BACST
ActivityHydrolysis of 1,4-beta-D-xylans, to remove successive D-xylose residues from the non-reducing termini.Hydrolysis of 1,4-beta-D-xylans, to remove successive D-xylose residues from the non-reducing termini.
Subunit

Subcellular location

Cofactor


Compound table: links to PDB-related databases & PoSSuM

SubstratesProductsintermediates
KEGG-idL00052C02352C02337C00001L00052C02352C02337C02096I00061
CompoundXylan1,4-beta-D-Xylanbeta-D-XylosideH2OXylan1,4-beta-D-Xylanbeta-D-Xylosidebeta-D-XylosePeptidyl-Glu-D-xylose
Typearomatic ring (only carbon atom),carboxyl group,polysaccharidepolysaccharidepolysaccharideH2Oaromatic ring (only carbon atom),carboxyl group,polysaccharidepolysaccharidepolysaccharidecarbohydrate
ChEBI


15377



28161

PubChem


962
22247451



125409

                 
1px8A01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1px8B01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1uhvA01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1uhvB01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1uhvC01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1uhvD01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1w91A01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1w91B01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1w91C01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1w91D01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1w91E01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1w91F01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1w91G01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1w91H01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
2bfgA01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
2bfgB01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
2bfgC01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
2bfgD01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
2bfgE01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
2bfgF01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
2bfgG01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
2bfgH01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
2bs9A01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
2bs9B01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
2bs9C01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
2bs9D01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
2bs9E01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
2bs9F01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
2bs9G01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
2bs9H01UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1px8A02UnboundUnboundUnbound UnboundUnboundUnboundBound:XYPUnbound
1px8B02UnboundUnboundUnbound UnboundUnboundUnboundBound:XYPUnbound
1uhvA02UnboundUnboundUnbound UnboundUnboundUnboundUnboundIntermediate-analogue:DFX
1uhvB02UnboundUnboundUnbound UnboundUnboundUnboundUnboundIntermediate-analogue:DFX
1uhvC02UnboundUnboundUnbound UnboundUnboundUnboundUnboundIntermediate-analogue:DFX
1uhvD02UnboundUnboundUnbound UnboundUnboundUnboundUnboundIntermediate-analogue:DFX
1w91A02UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1w91B02UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1w91C02UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1w91D02UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1w91E02UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1w91F02UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1w91G02UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1w91H02UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
2bfgA02UnboundUnboundAnalogue:ANX-XYP UnboundUnboundUnboundUnboundIntermediate-bound:XYS
2bfgB02UnboundUnboundUnbound UnboundUnboundUnboundUnboundIntermediate-bound:XYS
2bfgC02UnboundUnboundUnbound UnboundUnboundUnboundUnboundIntermediate-bound:XYS
2bfgD02UnboundUnboundAnalogue:ANX-XYP UnboundUnboundUnboundUnboundIntermediate-bound:XYS
2bfgE02UnboundUnboundUnbound UnboundUnboundUnboundUnboundIntermediate-bound:XYS
2bfgF02UnboundUnboundUnbound UnboundUnboundUnboundUnboundIntermediate-bound:XYS
2bfgG02UnboundUnboundUnbound UnboundUnboundUnboundUnboundIntermediate-bound:XYS
2bfgH02UnboundUnboundUnbound UnboundUnboundUnboundUnboundIntermediate-bound:XYS
2bs9A02UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
2bs9B02UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
2bs9C02UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
2bs9D02UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
2bs9E02UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
2bs9F02UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
2bs9G02UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
2bs9H02UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
Literature [5], [6], [7] & Swiss-prot;P36906, Q9ZFM2
pdbCatalytic residuescomment
          
1px8A01 
 
1px8B01 
 
1uhvA01 
 
1uhvB01 
 
1uhvC01 
 
1uhvD01 
 
1w91A01 
 
1w91B01 
 
1w91C01 
 
1w91D01 
 
1w91E01 
 
1w91F01 
 
1w91G01 
 
1w91H01 
 
2bfgA01 
 
2bfgB01 
 
2bfgC01 
 
2bfgD01 
 
2bfgE01 
 
2bfgF01 
 
2bfgG01 
 
2bfgH01 
 
2bs9A01 
 
2bs9B01 
 
2bs9C01 
 
2bs9D01 
 
2bs9E01 
 
2bs9F01 
 
2bs9G01 
 
2bs9H01 
 
1px8A02ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 277
 
1px8B02ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 277
 
1uhvA02ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 277
 
1uhvB02ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 277
 
1uhvC02ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 277
 
1uhvD02ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 277
 
1w91A02ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278
 
1w91B02ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278
 
1w91C02ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278
 
1w91D02ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278
 
1w91E02ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278
 
1w91F02ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278
 
1w91G02ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278
 
1w91H02ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278
 
2bfgA02ARG 52;ASN 159;       ;HIS 228;TYR 230;GLU 278
mutant E160A
2bfgB02ARG 52;ASN 159;       ;HIS 228;TYR 230;GLU 278
mutant E160A
2bfgC02ARG 52;ASN 159;       ;HIS 228;TYR 230;GLU 278
mutant E160A
2bfgD02ARG 52;ASN 159;       ;HIS 228;TYR 230;GLU 278
mutant E160A
2bfgE02ARG 52;ASN 159;       ;HIS 228;TYR 230;GLU 278
mutant E160A
2bfgF02ARG 52;ASN 159;       ;HIS 228;TYR 230;GLU 278
mutant E160A
2bfgG02ARG 52;ASN 159;       ;HIS 228;TYR 230;GLU 278
mutant E160A
2bfgH02ARG 52;ASN 159;       ;HIS 228;TYR 230;GLU 278
mutant E160A
2bs9A02ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278
 
2bs9B02ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278
 
2bs9C02ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278
 
2bs9D02ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278
 
2bs9E02ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278
 
2bs9F02ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278
 
2bs9G02ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278
 
2bs9H02ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[5]Scheme 1
[6]Figure 5, p.159-162
[7]Figure 4, p.841-844

references
[1]
CommentsCHARACTERIZATION.
PubMed ID8612648
JournalEur J Biochem
Year1996
Volume236
Pages706-13
AuthorsArmand S, Vieille C, Gey C, Heyraud A, Zeikus JG, Henrissat B
TitleStereochemical course and reaction products of the action of beta-xylosidase from Thermoanaerobacterium saccharolyticum strain B6A-RI.
[2]
CommentsACTIVE SITE GLU-277, MASS SPECTROMETRY.
PubMed ID9761746
JournalBiochem J
Year1998
Volume335
Pages449-55
AuthorsVocadlo DJ, MacKenzie LF, He S, Zeikus GJ, Withers SG
TitleIdentification of glu-277 as the catalytic nucleophile of Thermoanaerobacterium saccharolyticum beta-xylosidase using electrospray MS.
[3]
PubMed ID11322958
JournalFEBS Lett
Year2001
Volume495
Pages115-9
AuthorsBravman T, Mechaly A, Shulami S, Belakhov V, Baasov T, Shoham G, Shoham Y
TitleGlutamic acid 160 is the acid-base catalyst of beta-xylosidase from Bacillus stearothermophilus T-6: a family 39 glycoside hydrolase.
[4]
PubMed ID12146939
JournalBiochemistry
Year2002
Volume41
Pages9736-46
AuthorsVocadlo DJ, Wicki J, Rupitz K, Withers SG
TitleA case for reverse protonation: identification of Glu160 as an acid/base catalyst in Thermoanaerobacterium saccharolyticum beta-xylosidase and detailed kinetic analysis of a site-directed mutant.
[5]
PubMed ID12146938
JournalBiochemistry
Year2002
Volume41
Pages9727-35
AuthorsVocadlo DJ, Wicki J, Rupitz K, Withers SG
TitleMechanism of Thermoanaerobacterium saccharolyticum beta-xylosidase: kinetic studies.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS)
PubMed ID14659747
JournalJ Mol Biol
Year2004
Volume335
Pages155-65
AuthorsYang JK, Yoon HJ, Ahn HJ, Lee BI, Pedelacq JD, Liong EC, Berendzen J, Laivenieks M, Vieille C, Zeikus GJ, Vocadlo DJ, Withers SG, Suh SW
TitleCrystal structure of beta-D-xylosidase from Thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase.
Related PDB1px8,1uhv
Related UniProtKBP36906
[7]
CommentsX-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS)
PubMed ID16212978
JournalJ Mol Biol
Year2005
Volume353
Pages838-46
AuthorsCzjzek M, Ben David A, Bravman T, Shoham G, Henrissat B, Shoham Y
TitleEnzyme-substrate complex structures of a GH39 beta-xylosidase from Geobacillus stearothermophilus.
Related PDB2bfg,2bs9
Related UniProtKBQ9ZFM2

comments
This enzyme belongs to glycosidase family-39, with a retaining mechanism.
According to the literature [6] and [7], the reaction proceeds as follows:
(0) Arg52 and Tyr230 modulate the activity of catalytic nucleophile, Glu277, whereas His228 modulates the activity of a general acid-base, Glu160.
(1) Glu160 acts as a general acid to protonate the leaving oxygen, O4 atom at subsite +1, forming an oxocarbenium-ion-like transition-state. The transition-state is stabilized by Asn159 and Tyr230 through hydrogen bonding to the oxygen atoms of xylose at subsite -1. (SN1-like reaction)
(2) Glu277 makes a nucleophilic attack on C1 atom of substrate, xylan, to form a covalent intermediate with a xylose unit at the non-reducing end (or subsite -1).
(3) Glu160 acts as a general base to deprotonate a water molecule, to activate it.
(4) The activated water makes a nucleophilic attack on the C1 atom of the covalent intermediate. Thus, the substitution reaction completes.

createdupdated
2010-04-192012-01-27


Copyright: Nozomi Nagano, JST & CBRC-AIST
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Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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