DB code: S00748

RLCP classification	1.30.35880.983 : Hydrolysis
CATH domain	3.20.20.80 : TIM Barrel	Catalytic domain
E.C.	3.2.1.89
CSA	1fhl 1fob
M-CSA	1fhl 1fob
MACiE

CATH domain	Related DB codes (homologues)
3.20.20.80 : TIM Barrel	S00202 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

Uniprot Enzyme Name
UniprotKB	Protein name	Synonyms	CAZy	Pfam
P48842	Arabinogalactan endo-1,4-beta-galactosidase	EC 3.2.1.89 Endo-1,4-beta-galactanase Galactanase	GH53 (Glycoside Hydrolase Family 53)	PF07745 (Glyco_hydro_53) [Graphical View]
P83691	Arabinogalactan endo-1,4-beta-galactosidase	EC 3.2.1.89 Endo-1,4-beta-galactanase Galactanase	GH53 (Glycoside Hydrolase Family 53)	PF07745 (Glyco_hydro_53) [Graphical View]
P83692	Arabinogalactan endo-1,4-beta-galactosidase	EC 3.2.1.89 Endo-1,4-beta-galactanase Galactanase	GH53 (Glycoside Hydrolase Family 53)	PF07745 (Glyco_hydro_53) [Graphical View]

KEGG enzyme name
Arabinogalactan endo-1,4-beta-galactosidase Endo-1,4-beta-galactanase Galactanase Arabinogalactanase

UniprotKB: Accession Number	Entry name	Activity
P48842	GANA_ASPAC	Endohydrolysis of 1,4-beta-D-galactosidic linkages in arabinogalactans.
P83691	GANA_HUMIN	Endohydrolysis of 1,4-beta-D-galactosidic linkages in arabinogalactans.
P83692	GANA_THIHE	Endohydrolysis of 1,4-beta-D-galactosidic linkages in arabinogalactans.

KEGG Pathways
Map code	Pathways	E.C.

Compound table
	Substrates				Products				Intermediates
KEGG-id	L00048	L00049	C05796	C00001	L00048	L00049	C05796	C03611	I00121
E.C.
Compound	Rhamnogalacturonan I	Arabinogalactan type I	Galactan	H2O	Rhamnogalacturonan I	Arabinogalactan	Galactan	Galactose oligosaccharide	Peptidyl-Glu-galactan
Type	carboxyl group,polysaccharide	polysaccharide	polysaccharide	H2O	carboxyl group,polysaccharide	polysaccharide	polysaccharide	polysaccharide
ChEBI				15377 15377
PubChem				22247451 962 22247451 962

1fhlA00	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound	Unbound	Unbound
1fobA00	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound	Unbound	Unbound
1hjqA00	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound	Unbound	Unbound
1hjsA00	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound	Unbound	Unbound
1hjsB00	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound	Unbound	Unbound
1hjsC00	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound	Unbound	Unbound
1hjsD00	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound	Unbound	Unbound
1hjuA00	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound	Unbound	Unbound
1hjuB00	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound	Unbound	Unbound
1hjuC00	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound	Unbound	Unbound
1hjuD00	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound	Unbound	Unbound

Reference for Active-site residues
resource	references	E.C.
Literature [6], [8], [9], [11], Swiss-prot;Q65CX5, P48842, P83691 & P83692

Active-site residues
PDB	Catalytic residues	Cofactor-binding residues	Modified residues	Main-chain involved in catalysis	Comment

1fhlA00	ARG 45;ASN 135;GLU 136;TYR 215;GLU 246
1fobA00	ARG 45;ASN 135;GLU 136;TYR 215;GLU 246
1hjqA00	ARG 45;ASN 134;GLU 135;TYR 214;GLU 245
1hjsA00	ARG 45;ASN 134;GLU 135;TYR 214;GLU 245
1hjsB00	ARG 45;ASN 134;GLU 135;TYR 214;GLU 245
1hjsC00	ARG 45;ASN 134;GLU 135;TYR 214;GLU 245
1hjsD00	ARG 45;ASN 134;GLU 135;TYR 214;GLU 245
1hjuA00	ARG 45;ASN 134;GLU 135;TYR 214;GLU 245
1hjuB00	ARG 45;ASN 134;GLU 135;TYR 214;GLU 245
1hjuC00	ARG 45;ASN 134;GLU 135;TYR 214;GLU 245
1hjuD00	ARG 45;ASN 134;GLU 135;TYR 214;GLU 245

References for Catalytic Mechanism
References	Sections	No. of steps in catalysis
[6]	FIGURE 3, p.15138-15141
[8]	Figure 5
[9]	p.109
[11]	p.978

References
[1]
Resource
Comments
Medline ID
PubMed ID	823153
Journal	J Biol Chem
Year	1976
Volume	251
Pages	5904-10
Authors	Labavitch JM, Freeman LE, Albersheim P
Title	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.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID
Journal	Carbohydr Polym
Year	1991
Volume	16
Pages	167-87
Authors	van de Visa JW, Searle-van Leeuwena MJF, Silihaa HA, Kormelinka FJM, 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
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID	7712292
Journal	Curr Opin Struct Biol
Year	1994
Volume	4
Pages	885-92
Authors	McCarter JD, Withers SG
Title	Mechanisms of enzymatic glycoside hydrolysis.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID	8535779
Journal	Structure
Year	1995
Volume	3
Pages	853-9
Authors	Davies G, Henrissat B
Title	Structures and mechanisms of glycosyl hydrolases.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID	9398278
Journal	Biochemistry
Year	1997
Volume	36
Pages	15489-500
Authors	Braithwaite KL, Barna T, Spurway TD, Charnock SJ, Black GW, Hughes N, Lakey JH, Virden R, Hazlewood GP, Henrissat B, Gilbert HJ
Title	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.
Related PDB
Related UniProtKB
[6]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
Medline ID
PubMed ID	12484750
Journal	Biochemistry
Year	2002
Volume	41
Pages	15135-43
Authors	Ryttersgaard C, Lo Leggio L, Coutinho PM, Henrissat B, Larsen S
Title	Aspergillus aculeatus beta-1,4-galactanase: substrate recognition and relations to other glycoside hydrolases in clan GH-A.
Related PDB	1fhl 1fob
Related UniProtKB	P48842
[7]
Resource
Comments
Medline ID
PubMed ID
Journal	Carbohydr Polym
Year	2003
Volume	53
Pages	155-68
Authors	Luonteria E, Laineb C, Uusitaloa S, Telemanc A, Siika-ahoa M, Tenkanen M
Title	Purification and characterization of Aspergillus À-Image -galactanases acting on À-1,4- and À-1,3/6-linked arabinogalactans
Related PDB
Related UniProtKB
[8]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS), CATALYTIC ACTIVITY, GLYCOSYLATION AT ASN-111.
Medline ID
PubMed ID	12761390
Journal	Protein Sci
Year	2003
Volume	12
Pages	1195-204
Authors	Le Nours J, Ryttersgaard C, Lo Leggio L, Ostergaard PR, Borchert TV, Christensen LL, Larsen S
Title	Structure of two fungal beta-1,4-galactanases: searching for the basis for temperature and pH optimum.
Related PDB	1hjq 1hjs 1hju
Related UniProtKB	P83691 P83692
[9]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 28-424 IN COMPLEX WITH CALCIUM IONS AND SUBSTRATE ANALOGS, COFACTOR.
Medline ID
PubMed ID	15312766
Journal	J Mol Biol
Year	2004
Volume	341
Pages	107-17
Authors	Ryttersgaard C, Le Nours J, Lo Leggio L, Jorgensen CT, Christensen LL, Bjornvad M, Larsen S
Title	The structure of endo-beta-1,4-galactanase from Bacillus licheniformis in complex with two oligosaccharide products.
Related PDB	1r8l 1ur0 1ur4
Related UniProtKB	Q65CX5
[10]
Resource
Comments
Medline ID
PubMed ID	16151143
Journal	Appl Environ Microbiol
Year	2005
Volume	71
Pages	5501-10
Authors	Hinz SW, Pastink MI, van den Broek LA, Vincken JP, Voragen AG
Title	Bifidobacterium longum endogalactanase liberates galactotriose from type I galactans.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID	19089956
Journal	Proteins
Year	2009
Volume	75
Pages	977-89
Authors	Le Nours J, De Maria L, Welner D, Jorgensen CT, Christensen LL, Borchert TV, Larsen S, Lo Leggio L
Title	Investigating the binding of beta-1,4-galactan to Bacillus licheniformis beta-1,4-galactanase by crystallography and computational modeling.
Related PDB	2ccr 2j74
Related UniProtKB	Q65CX5

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.

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.

Created	Updated
2010-04-08	2012-01-26