S00748
type: Enzyme
rlcp: p983
cath: TIM Barrel
ec: https://purl.uniprot.org/enzyme/3.2.1.89
csa: 1fhl
csa: 1fob
uniprot: P48842
uniprot: P83691
uniprot: P83692
kegg enzyme: Arabinogalactan endo-1,4-beta-galactosidase
kegg enzyme: Endo-1,4-beta-galactanase
kegg enzyme: Galactanase
kegg enzyme: Arabinogalactanase
kegg substrate: Rhamnogalacturonan I
kegg substrate: Arabinogalactan type I
kegg substrate: Galactan
kegg substrate: H2O
kegg product: Rhamnogalacturonan I
kegg product: Arabinogalactan type I
kegg product: Galactan
kegg product: Galactose oligosaccharide
kegg intermediate: Peptidyl-Glu-galactan
pdb: 1fhlA00
pdb: 1fobA00
pdb: 1hjqA00
pdb: 1hjsA00
pdb: 1hjsB00
pdb: 1hjsC00
pdb: 1hjsD00
pdb: 1hjuA00
pdb: 1hjuB00
pdb: 1hjuC00
pdb: 1hjuD00
pdb bound state: Unbound
  compound: Rhamnogalacturonan I
  pdb: 1fhlA00
pdb bound state: Unbound
  compound: Rhamnogalacturonan I
  pdb: 1fobA00
pdb bound state: Unbound
  compound: Rhamnogalacturonan I
  pdb: 1hjqA00
pdb bound state: Unbound
  compound: Rhamnogalacturonan I
  pdb: 1hjsA00
pdb bound state: Unbound
  compound: Rhamnogalacturonan I
  pdb: 1hjsB00
pdb bound state: Unbound
  compound: Rhamnogalacturonan I
  pdb: 1hjsC00
pdb bound state: Unbound
  compound: Rhamnogalacturonan I
  pdb: 1hjsD00
pdb bound state: Unbound
  compound: Rhamnogalacturonan I
  pdb: 1hjuA00
pdb bound state: Unbound
  compound: Rhamnogalacturonan I
  pdb: 1hjuB00
pdb bound state: Unbound
  compound: Rhamnogalacturonan I
  pdb: 1hjuC00
pdb bound state: Unbound
  compound: Rhamnogalacturonan I
  pdb: 1hjuD00
pdb bound state: Unbound
  compound: Arabinogalactan type I
  pdb: 1fhlA00
pdb bound state: Unbound
  compound: Arabinogalactan type I
  pdb: 1fobA00
pdb bound state: Unbound
  compound: Arabinogalactan type I
  pdb: 1hjqA00
pdb bound state: Unbound
  compound: Arabinogalactan type I
  pdb: 1hjsA00
pdb bound state: Unbound
  compound: Arabinogalactan type I
  pdb: 1hjsB00
pdb bound state: Unbound
  compound: Arabinogalactan type I
  pdb: 1hjsC00
pdb bound state: Unbound
  compound: Arabinogalactan type I
  pdb: 1hjsD00
pdb bound state: Unbound
  compound: Arabinogalactan type I
  pdb: 1hjuA00
pdb bound state: Unbound
  compound: Arabinogalactan type I
  pdb: 1hjuB00
pdb bound state: Unbound
  compound: Arabinogalactan type I
  pdb: 1hjuC00
pdb bound state: Unbound
  compound: Arabinogalactan type I
  pdb: 1hjuD00
pdb bound state: Unbound
  compound: Galactan
  pdb: 1fhlA00
pdb bound state: Unbound
  compound: Galactan
  pdb: 1fobA00
pdb bound state: Unbound
  compound: Galactan
  pdb: 1hjqA00
pdb bound state: Unbound
  compound: Galactan
  pdb: 1hjsA00
pdb bound state: Unbound
  compound: Galactan
  pdb: 1hjsB00
active site residues resources: Purification and characterization of Aspergillus À-Image -galactanases acting on À-1,4- and À-1,3/6-linked arabinogalactans
active site residues resources: The structure of endo-beta-1,4-galactanase from Bacillus licheniformis in complex with two oligosaccharide products.
active site residues resources: Bifidobacterium longum endogalactanase liberates galactotriose from type I galactans.
active site residues resources: http://ezcatdb.cbrc.jp/EzCatDB/reference/S00748#12
active site residues resources: Q65CX5
active site residues resources: P48842
active site residues resources: P83691
active site residues resources: P83692
references: Structure 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.
references: http://ezcatdb.cbrc.jp/EzCatDB/reference/S00748#2
references: Mechanisms of enzymatic glycoside hydrolysis.
references: Structures and mechanisms of glycosyl hydrolases.
references: Evidence that galactanase A from Pseudomonas fluorescens subspecies cellulosa is a retaining family 53 glycosyl hydrolase in which E161 and E270 are the catalytic residues.
references: Aspergillus aculeatus beta-1,4-galactanase: substrate recognition and relations to other glycoside hydrolases in clan GH-A.
references: Purification and characterization of Aspergillus À-Image -galactanases acting on À-1,4- and À-1,3/6-linked arabinogalactans
references: Structure of two fungal beta-1,4-galactanases: searching for the basis for temperature and pH optimum.
references: The structure of endo-beta-1,4-galactanase from Bacillus licheniformis in complex with two oligosaccharide products.
references: Bifidobacterium longum endogalactanase liberates galactotriose from type I galactans.
references: Investigating the binding of beta-1,4-galactan to Bacillus licheniformis beta-1,4-galactanase by crystallography and computational modeling.
comment: 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.

TIM Barrel
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.20.20.80
catalytic domain: index.html

Rhamnogalacturonan I
type: KeggSubstrate
references: KEGG:L00048
compound type: carboxyl group
compound type: polysaccharide
type: KeggProduct

Arabinogalactan type I
type: KeggSubstrate
references: KEGG:L00049
compound type: polysaccharide
type: KeggProduct
label: Arabinogalactan

Galactan
type: KeggSubstrate
references: KEGG:C05796
compound type: polysaccharide
type: KeggProduct

H2O
type: KeggSubstrate
references: KEGG:C00001
compound type: H2O
references: CHEBI:15377
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

Galactose oligosaccharide
type: KeggProduct
references: KEGG:C03611
compound type: polysaccharide

Peptidyl-Glu-galactan
type: KeggIntermediate
references: KEGG:I00121

1fhlA00
type: Pdb
references: 1fhl
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1fhl
catalytic residue: ARG 45;ASN 135;GLU 136;TYR 215;GLU 246

1fobA00
type: Pdb
references: 1fob
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1fob
catalytic residue: ARG 45;ASN 135;GLU 136;TYR 215;GLU 246

1hjqA00
type: Pdb
references: 1hjq
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1hjq
catalytic residue: ARG 45;ASN 134;GLU 135;TYR 214;GLU 245

1hjsA00
type: Pdb
references: 1hjs
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1hjs
catalytic residue: ARG 45;ASN 134;GLU 135;TYR 214;GLU 245

1hjsB00
type: Pdb
references: 1hjs
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1hjs
catalytic residue: ARG 45;ASN 134;GLU 135;TYR 214;GLU 245

1hjsC00
type: Pdb
references: 1hjs
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1hjs
catalytic residue: ARG 45;ASN 134;GLU 135;TYR 214;GLU 245

1hjsD00
type: Pdb
references: 1hjs
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1hjs
catalytic residue: ARG 45;ASN 134;GLU 135;TYR 214;GLU 245

1hjuA00
type: Pdb
references: 1hju
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1hju
catalytic residue: ARG 45;ASN 134;GLU 135;TYR 214;GLU 245

1hjuB00
type: Pdb
references: 1hju
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1hju
catalytic residue: ARG 45;ASN 134;GLU 135;TYR 214;GLU 245

1hjuC00
type: Pdb
references: 1hju
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1hju
catalytic residue: ARG 45;ASN 134;GLU 135;TYR 214;GLU 245

1hjuD00
type: Pdb
references: 1hju
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1hju
catalytic residue: ARG 45;ASN 134;GLU 135;TYR 214;GLU 245

Structure 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.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/823153
journal: J Biol Chem
volume: 251
pages: 5904-10
published year: 1976
authors:
  item: Labavitch JM
  item: Freeman LE
  item: Albersheim P

http://ezcatdb.cbrc.jp/EzCatDB/reference/S00748#2
type: BibliographicResource
journal: Carbohydr Polym
volume: 16
pages: 167-87
published year: 1991
authors:
  item: van de Visa JW
  item: Searle-van Leeuwena MJF
  item: Silihaa HA
  item: Kormelinka FJM
  item: Voragena AGJ
title: Purification and characterization of Endo-1,4-À-D-galactanases from Aspergillus niger and Aspergillus aculeatus: Use in combination with arabinanases from Aspergillus niger in enzymic conversion of potato arabinogalactan

Mechanisms of enzymatic glycoside hydrolysis.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/7712292
journal: Curr Opin Struct Biol
volume: 4
pages: 885-92
published year: 1994
authors:
  item: McCarter JD
  item: Withers SG

Structures and mechanisms of glycosyl hydrolases.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8535779
journal: Structure
volume: 3
pages: 853-9
published year: 1995
authors:
  item: Davies G
  item: Henrissat B

Evidence that galactanase A from Pseudomonas fluorescens subspecies cellulosa is a retaining family 53 glycosyl hydrolase in which E161 and E270 are the catalytic residues.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9398278
journal: Biochemistry
volume: 36
pages: 15489-500
published year: 1997
authors:
  item: Braithwaite KL
  item: Barna T
  item: Spurway TD
  item: Charnock SJ
  item: Black GW
  item: Hughes N
  item: Lakey JH
  item: Virden R
  item: Hazlewood GP
  item: Henrissat B
  item: Gilbert HJ

Aspergillus aculeatus beta-1,4-galactanase: substrate recognition and relations to other glycoside hydrolases in clan GH-A.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
references: http://www.ncbi.nlm.nih.gov/pubmed/12484750
journal: Biochemistry
volume: 41
pages: 15135-43
published year: 2002
authors:
  item: Ryttersgaard C
  item: Lo Leggio L
  item: Coutinho PM
  item: Henrissat B
  item: Larsen S
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P48842

Purification and characterization of Aspergillus À-Image -galactanases acting on À-1,4- and À-1,3/6-linked arabinogalactans
type: BibliographicResource
journal: Carbohydr Polym
volume: 53
pages: 155-68
published year: 2003
authors:
  item: Luonteria E
  item: Laineb C
  item: Uusitaloa S
  item: Telemanc A
  item: Siika-ahoa M
  item: Tenkanen M

Structure of two fungal beta-1,4-galactanases: searching for the basis for temperature and pH optimum.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS), CATALYTIC ACTIVITY, GLYCOSYLATION AT ASN-111.
references: http://www.ncbi.nlm.nih.gov/pubmed/12761390
journal: Protein Sci
volume: 12
pages: 1195-204
published year: 2003
authors:
  item: Le Nours J
  item: Ryttersgaard C
  item: Lo Leggio L
  item: Ostergaard PR
  item: Borchert TV
  item: Christensen LL
  item: Larsen S
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P83691
references: P83692

The structure of endo-beta-1,4-galactanase from Bacillus licheniformis in complex with two oligosaccharide products.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 28-424 IN COMPLEX WITH CALCIUM IONS AND SUBSTRATE ANALOGS, COFACTOR.
references: http://www.ncbi.nlm.nih.gov/pubmed/15312766
journal: J Mol Biol
volume: 341
pages: 107-17
published year: 2004
authors:
  item: Ryttersgaard C
  item: Le Nours J
  item: Lo Leggio L
  item: Jorgensen CT
  item: Christensen LL
  item: Bjornvad M
  item: Larsen S
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: Q65CX5

Bifidobacterium longum endogalactanase liberates galactotriose from type I galactans.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/16151143
journal: Appl Environ Microbiol
volume: 71
pages: 5501-10
published year: 2005
authors:
  item: Hinz SW
  item: Pastink MI
  item: van den Broek LA
  item: Vincken JP
  item: Voragen AG

Investigating the binding of beta-1,4-galactan to Bacillus licheniformis beta-1,4-galactanase by crystallography and computational modeling.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/19089956
journal: Proteins
volume: 75
pages: 977-89
published year: 2009
authors:
  item: Le Nours J
  item: De Maria L
  item: Welner D
  item: Jorgensen CT
  item: Christensen LL
  item: Borchert TV
  item: Larsen S
  item: Lo Leggio L
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: Q65CX5

ReferenceForCatalyticMechanism
reference index: 6
reference section: FIGURE 3, p.15138-15141

ReferenceForCatalyticMechanism
reference index: 8
reference section: Figure 5

ReferenceForCatalyticMechanism
reference index: 9
reference section: p.109

ReferenceForCatalyticMechanism
reference index: 11
reference section: p.978