EzCatDB: S00748
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DB codeS00748
RLCP classification1.30.35880.983 : Hydrolysis
CATH domainDomain 13.20.20.80 : TIM BarrelCatalytic domain
E.C.3.2.1.89
CSA1fhl,1fob

CATH domainRelated DB codes (homologues)
3.20.20.80 : TIM BarrelS00202,S00210,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,D00844,D00861,D00864,M00026,M00112,M00193,M00346,T00057,T00062,T00063,T00066,T00067

Enzyme Name
UniProtKBKEGG

P48842P83691P83692
Protein nameArabinogalactan endo-1,4-beta-galactosidaseArabinogalactan endo-1,4-beta-galactosidaseArabinogalactan endo-1,4-beta-galactosidaseArabinogalactan endo-1,4-beta-galactosidase
Endo-1,4-beta-galactanase
Galactanase
Arabinogalactanase
SynonymsEC 3.2.1.89
Endo-1,4-beta-galactanase
Galactanase
EC 3.2.1.89
Endo-1,4-beta-galactanase
Galactanase
EC 3.2.1.89
Endo-1,4-beta-galactanase
Galactanase
PfamPF07745 (Glyco_hydro_53)
[Graphical view]
PF07745 (Glyco_hydro_53)
[Graphical view]
PF07745 (Glyco_hydro_53)
[Graphical view]
CAZyGH53 (Glycoside Hydrolase Family)
GH53 (Glycoside Hydrolase Family)
GH53 (Glycoside Hydrolase Family)


UniProtKB:Accession NumberP48842P83691P83692
Entry nameGANA_ASPACGANA_HUMINGANA_THIHE
ActivityEndohydrolysis of 1,4-beta-D-galactosidic linkages in arabinogalactans.Endohydrolysis of 1,4-beta-D-galactosidic linkages in arabinogalactans.Endohydrolysis of 1,4-beta-D-galactosidic linkages in arabinogalactans.
Subunit


Subcellular location


Cofactor



Compound table: links to PDB-related databases & PoSSuM

SubstratesProductsintermediates
KEGG-idL00048L00049C05796C00001L00048L00049C05796C03611I00121
CompoundRhamnogalacturonan IArabinogalactan type IGalactanH2ORhamnogalacturonan IArabinogalactanGalactanGalactose oligosaccharidePeptidyl-Glu-galactan
Typecarboxyl group,polysaccharidepolysaccharidepolysaccharideH2Ocarboxyl group,polysaccharidepolysaccharidepolysaccharidepolysaccharide
ChEBI


15377





PubChem


962
22247451





                 
1fhlA00UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1fobA00UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1hjqA00UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1hjsA00UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1hjsB00UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1hjsC00UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1hjsD00UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1hjuA00UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1hjuB00UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1hjuC00UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound
1hjuD00UnboundUnboundUnbound UnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
Literature [6], [8], [9], [11], Swiss-prot;Q65CX5, P48842, P83691 & P83692
pdbCatalytic residues
         
1fhlA00ARG 45;ASN 135;GLU 136;TYR 215;GLU 246
1fobA00ARG 45;ASN 135;GLU 136;TYR 215;GLU 246
1hjqA00ARG 45;ASN 134;GLU 135;TYR 214;GLU 245
1hjsA00ARG 45;ASN 134;GLU 135;TYR 214;GLU 245
1hjsB00ARG 45;ASN 134;GLU 135;TYR 214;GLU 245
1hjsC00ARG 45;ASN 134;GLU 135;TYR 214;GLU 245
1hjsD00ARG 45;ASN 134;GLU 135;TYR 214;GLU 245
1hjuA00ARG 45;ASN 134;GLU 135;TYR 214;GLU 245
1hjuB00ARG 45;ASN 134;GLU 135;TYR 214;GLU 245
1hjuC00ARG 45;ASN 134;GLU 135;TYR 214;GLU 245
1hjuD00ARG 45;ASN 134;GLU 135;TYR 214;GLU 245

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[6]FIGURE 3, p.15138-15141
[8]Figure 5
[9]p.109
[11]p.978

references
[1]
PubMed ID823153
JournalJ Biol Chem
Year1976
Volume251
Pages5904-10
AuthorsLabavitch JM, Freeman LE, Albersheim P
TitleStructure of plant cell walls. Purification and characterization of a beta-1,4-galactanase which degrades a structural component of the primary cell walls of dicots.
[2]
JournalCarbohydr Polym
Year1991
Volume16
Pages167-87
Authorsvan de Visa JW, Searle-van Leeuwena MJF, Silihaa HA, Kormelinka FJM, Voragena AGJ
TitlePurification and characterization of Endo-1,4-ƒÀ-D-galactanases from Aspergillus niger and Aspergillus aculeatus: Use in combination with arabinanases from Aspergillus niger in enzymic conversion of potato arabinogalactan
[3]
PubMed ID7712292
JournalCurr Opin Struct Biol
Year1994
Volume4
Pages885-92
AuthorsMcCarter JD, Withers SG
TitleMechanisms of enzymatic glycoside hydrolysis.
[4]
PubMed ID8535779
JournalStructure
Year1995
Volume3
Pages853-9
AuthorsDavies G, Henrissat B
TitleStructures and mechanisms of glycosyl hydrolases.
[5]
PubMed ID9398278
JournalBiochemistry
Year1997
Volume36
Pages15489-500
AuthorsBraithwaite KL, Barna T, Spurway TD, Charnock SJ, Black GW, Hughes N, Lakey JH, Virden R, Hazlewood GP, Henrissat B, Gilbert HJ
TitleEvidence that galactanase A from Pseudomonas fluorescens subspecies cellulosa is a retaining family 53 glycosyl hydrolase in which E161 and E270 are the catalytic residues.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
PubMed ID12484750
JournalBiochemistry
Year2002
Volume41
Pages15135-43
AuthorsRyttersgaard C, Lo Leggio L, Coutinho PM, Henrissat B, Larsen S
TitleAspergillus aculeatus beta-1,4-galactanase: substrate recognition and relations to other glycoside hydrolases in clan GH-A.
Related PDB1fhl,1fob
Related UniProtKBP48842
[7]
JournalCarbohydr Polym
Year2003
Volume53
Pages155-68
AuthorsLuonteria E, Laineb C, Uusitaloa S, Telemanc A, Siika-ahoa M, Tenkanen M
TitlePurification and characterization of Aspergillus ƒÀ-Image -galactanases acting on ƒÀ-1,4- and ƒÀ-1,3/6-linked arabinogalactans
[8]
CommentsX-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS), CATALYTIC ACTIVITY, GLYCOSYLATION AT ASN-111.
PubMed ID12761390
JournalProtein Sci
Year2003
Volume12
Pages1195-204
AuthorsLe Nours J, Ryttersgaard C, Lo Leggio L, Ostergaard PR, Borchert TV, Christensen LL, Larsen S
TitleStructure of two fungal beta-1,4-galactanases: searching for the basis for temperature and pH optimum.
Related PDB1hjq,1hjs,1hju
Related UniProtKBP83691,P83692
[9]
CommentsX-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 28-424 IN COMPLEX WITH CALCIUM IONS AND SUBSTRATE ANALOGS, COFACTOR.
PubMed ID15312766
JournalJ Mol Biol
Year2004
Volume341
Pages107-17
AuthorsRyttersgaard C, Le Nours J, Lo Leggio L, Jorgensen CT, Christensen LL, Bjornvad M, Larsen S
TitleThe structure of endo-beta-1,4-galactanase from Bacillus licheniformis in complex with two oligosaccharide products.
Related PDB1r8l,1ur0,1ur4
Related UniProtKBQ65CX5
[10]
PubMed ID16151143
JournalAppl Environ Microbiol
Year2005
Volume71
Pages5501-10
AuthorsHinz SW, Pastink MI, van den Broek LA, Vincken JP, Voragen AG
TitleBifidobacterium longum endogalactanase liberates galactotriose from type I galactans.
[11]
PubMed ID19089956
JournalProteins
Year2009
Volume75
Pages977-89
AuthorsLe Nours J, De Maria L, Welner D, Jorgensen CT, Christensen LL, Borchert TV, Larsen S, Lo Leggio L
TitleInvestigating the binding of beta-1,4-galactan to Bacillus licheniformis beta-1,4-galactanase by crystallography and computational modeling.
Related PDB2ccr,2j74
Related UniProtKBQ65CX5

comments
This enzyme belongs to glycosidase family-58, with a retaining mechanism.
This enzyme is homologous to a counterpart enzyme from Bacillus licheniformis (S00912 in EzCatDB). Although the homologous enzyme binds calcium ion, this enzyme does not bind any ion.
According to the literature [6], the reaction proceeds as follows:
(0) Arg45 and Tyr215 modulate the pKa of catalytic nucleophile, Glu246.
(1) Glu136 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 Asn135 and Tyr215 through hydrogen bonding to the oxygen atoms at subsite -1. (SN1-like reaction)
(2) Glu246 makes a nucleophilic attack on C1 atom of substrate, galactan, to form a covalent intermediate.
(3) Glu136 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
2010-04-082012-01-26


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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