DB code: S00168

RLCP classification	1.30.260.1001 : Hydrolysis
CATH domain	2.160.20.10 : Pectate Lyase C-like	Catalytic domain
E.C.	3.2.1.15
CSA	1czf
M-CSA	1czf
MACiE

CATH domain	Related DB codes (homologues)
2.160.20.10 : Pectate Lyase C-like	S00171 S00546 S00837 S00170 S00169 D00803

Uniprot Enzyme Name
UniprotKB	Protein name	Synonyms	RefSeq	CAZy	Pfam
P26509	Endo-polygalacturonase	EC 3.2.1.15	YP_006284264.1 (Protein) NC_017845.1 (DNA/RNA sequence)	GH28 (Glycoside Hydrolase Family 28)	PF00295 (Glyco_hydro_28) [Graphical View]
O74213	Polygalacturonase 1	PG-1 EC 3.2.1.15 Pectinase 1		GH28 (Glycoside Hydrolase Family 28)	PF00295 (Glyco_hydro_28) [Graphical View]
P26213	Polygalacturonase-1	EC 3.2.1.15 Polygalacturonase I PG-I Pectinase 1		GH28 (Glycoside Hydrolase Family 28)	PF00295 (Glyco_hydro_28) [Graphical View]
P26214	Endopolygalacturonase-2	EC 3.2.1.15 Endopolygalacturonase II EPG-II PG-II Pectinase-2		GH28 (Glycoside Hydrolase Family 28)	PF00295 (Glyco_hydro_28) [Graphical View]
P79074		Endopolygalacturonase EC 3.2.1.15		GH28 (Glycoside Hydrolase Family 28)	PF00295 (Glyco_hydro_28) [Graphical View]
Q07181	Polygalacturonase	PG EC 3.2.1.15 FmPG Pectinase		GH28 (Glycoside Hydrolase Family 28)	PF00295 (Glyco_hydro_28) [Graphical View]

KEGG enzyme name
polygalacturonase pectin depolymerase pectinase endopolygalacturonase pectolase pectin hydrolase pectin polygalacturonase endo-polygalacturonase poly-alpha-1,4-galacturonide glycanohydrolase endogalacturonase endo-D-galacturonase poly(1,4-alpha-D-galacturonide) glycanohydrolase

UniprotKB: Accession Number	Entry name	Activity	Subunit	Subcellular location
P26509	PGLR2_PECCC	Random hydrolysis of (1->4)-alpha-D- galactosiduronic linkages in pectate and other galacturonans.	Monomer.	Secreted.
O74213	PGLR1_ASPAC	Random hydrolysis of (1->4)-alpha-D- galactosiduronic linkages in pectate and other galacturonans.
P26213	PGLR1_ASPNG	Random hydrolysis of (1->4)-alpha-D- galactosiduronic linkages in pectate and other galacturonans.
P26214	PGLR2_ASPNG	Random hydrolysis of (1->4)-alpha-D- galactosiduronic linkages in pectate and other galacturonans.
P79074	P79074_9AGAR
Q07181	PGLR_GIBFU	Random hydrolysis of (1->4)-alpha-D- galactosiduronic linkages in pectate and other galacturonans.

KEGG Pathways
Map code	Pathways	E.C.
MAP00040	Pentose and glucuronate interconversions
MAP00500	Starch and sucrose metabolism

Compound table
	Substrates		Products		Intermediates
KEGG-id	C00470	C00001	C00470	C00333
E.C.
Compound	Pectate	H2O	Pectate	D-Galacturonate
Type	carboxyl group,polysaccharide	H2O	carboxyl group,polysaccharide	carbohydrate,carboxyl group
ChEBI		15377 15377		4153 4153
PubChem	24892720 24892720	22247451 962 22247451 962	24892720 24892720	439215 439215

1bheA	Unbound		Unbound	Unbound
1ia5A	Unbound		Unbound	Unbound
1ib4A	Unbound		Unbound	Unbound
1ib4B	Unbound		Unbound	Unbound
1nhcA	Unbound		Unbound	Unbound
1nhcB	Unbound		Unbound	Unbound
1nhcC	Unbound		Unbound	Unbound
1nhcD	Unbound		Unbound	Unbound
1nhcE	Unbound		Unbound	Unbound
1nhcF	Unbound		Unbound	Unbound
1czfA	Unbound		Unbound	Unbound
1czfB	Unbound		Unbound	Unbound
1k5cA	Unbound		Unbound	Unbound
1kccA	Unbound		Unbound	Bound:GTR
1kcdA	Unbound		Analogue:GTR_1001	Bound:GTR_1002
1hg8A	Unbound		Unbound	Unbound

Reference for Active-site residues
resource	references	E.C.
literature [13]

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

1bheA	ASP 202;ASP 205;ASP 223;ASP 224;ARG 280;LYS 282
1ia5A	ASP 159;ASP 162;ASP 180;ASP 181;ARG 235;LYS 237
1ib4A	ASP 159;ASP 162;ASP 180;ASP 181;ARG 235;LYS 237
1ib4B	ASP 159;ASP 162;ASP 180;ASP 181;ARG 235;LYS 237
1nhcA	ASP 186;ASP 189;ASP 207;ASP 208;ARG 262;LYS 264
1nhcB	ASP 186;ASP 189;ASP 207;ASP 208;ARG 262;LYS 264
1nhcC	ASP 186;ASP 189;ASP 207;ASP 208;ARG 262;LYS 264
1nhcD	ASP 186;ASP 189;ASP 207;ASP 208;ARG 262;LYS 264
1nhcE	ASP 186;ASP 189;ASP 207;ASP 208;ARG 262;LYS 264
1nhcF	ASP 186;ASP 189;ASP 207;ASP 208;ARG 262;LYS 264
1czfA	ASP 180;ASP 183;ASP 201;ASP 202;ARG 256;LYS 258
1czfB	ASP 180;ASP 183;ASP 201;ASP 202;ARG 256;LYS 258
1k5cA	ASP 153;ASP 156;ASP 173;ASP 174;ARG 226;LYS 228
1kccA	ASP 153;ASP 156;ASP 173;ASP 174;ARG 226;LYS 228
1kcdA	ASP 153;ASP 156;ASP 173;ASP 174;ARG 226;LYS 228
1hg8A	ASP 191;ASP 194;ASP 212;ASP 213;ARG 267;LYS 269

References for Catalytic Mechanism
References	Sections	No. of steps in catalysis
[1]	Scheme 1, p.171-172
[3]	p.538-539
[4]	p.24664
[5]	Fig.3, p.30477-30479
[6]	p.695-696
[10]	p.870-874
[11]	p.13429-13430
[13]	Fig.7, p.6656-6658
[15]	p.60-61

References
[1]
Resource
Comments
Medline ID
PubMed ID	1416030
Journal	Anal Biochem
Year	1992
Volume	203
Pages	335-9
Authors	Bach E, Schollmeyer E
Title	An ultraviolet-spectrophotometric method with 2-cyanoacetamide for the determination of the enzymatic degradation of reducing polysaccharides.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID	8814223
Journal	Biochim Biophys Acta
Year	1996
Volume	1296
Pages	167-73
Authors	Rao MN, Kembhavi AA, Pant A
Title	Implication of tryptophan and histidine in the active site of endo-polygalacturonase from Aspergillus ustus: elucidation of the reaction mechanism.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID	9115442
Journal	Structure
Year	1997
Volume	5
Pages	533-44
Authors	Petersen TN, Kauppinen S, Larsen S
Title	The crystal structure of rhamnogalacturonase A from Aspergillus aculeatus: a right-handed parallel beta helix.
Related PDB
Related UniProtKB
[4]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
Medline ID	98406113
PubMed ID	9733763
Journal	J Biol Chem
Year	1998
Volume	273
Pages	24660-4
Authors	Pickersgill R, Smith D, Worboys K, Jenkins J
Title	Crystal structure of polygalacturonase from Erwinia carotovora ssp. carotovora.
Related PDB	1bhe
Related UniProtKB	P26509
[5]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (1.68 ANGSTROMS), AND MUTAGENESIS OF ASP-180; ASP-201; ASP-202; HIS-223; ARG-256 AND LYS-258.
Medline ID
PubMed ID	10521427
Journal	J Biol Chem
Year	1999
Volume	274
Pages	30474-80
Authors	van Santen Y, Benen JA, Schroter KH, Kalk KH, Armand S, Visser J, Dijkstra BW
Title	1.68-A crystal structure of endopolygalacturonase II from Aspergillus niger and identification of active site residues by site-directed mutagenesis.
Related PDB	1czf
Related UniProtKB	P26214
[6]
Resource
Comments
Medline ID
PubMed ID	10617668
Journal	J Biol Chem
Year	2000
Volume	275
Pages	691-6
Authors	Armand S, Wagemaker MJ, Sanchez-Torres P, Kester HC, van Santen Y, Dijkstra BW, Visser J, Benen JA
Title	The active site topology of Aspergillus niger endopolygalacturonase II as studied by site-directed mutagenesis.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID	10893426
Journal	J Biol Chem
Year	2000
Volume	275
Pages	29348-53
Authors	Pages S, Heijne WH, Kester HC, Visser J, Benen JA
Title	Subsite mapping of Aspergillus niger endopolygalacturonase II by site-directed mutagenesis.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID	11168425
Journal	Eur J Biochem
Year	2001
Volume	268
Pages	832-40
Authors	Niture SK, Pant A, Kumar AR
Title	Active site characterization of the single endo-polygalacturonase produced by Fusarium moniliforme NCIM 1276.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID	11445590
Journal	J Biol Chem
Year	2001
Volume	276
Pages	33652-6
Authors	Pages S, Kester HC, Visser J, Benen JA
Title	Changing a single amino acid residue switches processive and non-processive behavior of Aspergillus niger endopolygalacturonase I and II.
Related PDB
Related UniProtKB
[10]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 40-378, AND GLYCOSYLATION AT THR-44; SER-46; SER-48; SER-52; SER-53; SER-55; SER-57; SER-62; THR-63; SER-73 AND ASN-249.
Medline ID
PubMed ID	11518536
Journal	J Mol Biol
Year	2001
Volume	311
Pages	863-78
Authors	Cho SW, Lee S, Shin W
Title	The X-ray structure of Aspergillus aculeatus polygalacturonase and a modeled structure of the polygalacturonase-octagalacturonate complex.
Related PDB	1ia5 1ib4
Related UniProtKB	O74213
[11]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (1.73 ANGSTROMS) OF 25-373, AND MUTAGENESIS OF HIS-188; ASP-191; 212-ASP-ASP-213; ARG-267 AND LYS-269.
Medline ID
PubMed ID	11687632
Journal	Proc Natl Acad Sci U S A
Year	2001
Volume	98
Pages	13425-30
Authors	Federici L, Caprari C, Mattei B, Savino C, Di Matteo A, De Lorenzo G, Cervone F, Tsernoglou D
Title	Structural requirements of endopolygalacturonase for the interaction with PGIP (polygalacturonase-inhibiting protein).
Related PDB	1hg8
Related UniProtKB	Q07181
[12]
Resource
Comments
Medline ID
PubMed ID	11707607
Journal	Protein Eng
Year	2001
Volume	14
Pages	615-31
Authors	Markovic O, Janecek S
Title	Pectin degrading glycoside hydrolases of family 28: sequence-structural features, specificities and evolution.
Related PDB
Related UniProtKB
[13]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (0.96 ANGSTROMS) OF 25-359.
Medline ID
PubMed ID	12022868
Journal	Biochemistry
Year	2002
Volume	41
Pages	6651-9
Authors	Shimizu T, Nakatsu T, Miyairi K, Okuno T, Kato H
Title	Active-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution.
Related PDB	1k5c 1kcc 1kcd
Related UniProtKB	P79074
[14]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 33-368, AND GLYCOSYLATION AT SER-44; SER-46 AND ASN-246.
Medline ID
PubMed ID	14623112
Journal	FEBS Lett
Year	2003
Volume	554
Pages	462-6
Authors	van Pouderoyen G, Snijder HJ, Benen JA, Dijkstra BW
Title	Structural insights into the processivity of endopolygalacturonase I from Aspergillus niger.
Related PDB	1nhc
Related UniProtKB	P26213
[15]
Resource
Comments
Medline ID
PubMed ID	15848136
Journal	Biochim Biophys Acta
Year	2005
Volume	1749
Pages	53-64
Authors	Andre-Leroux G, Tessier D, Bonnin E
Title	Action pattern of Fusarium moniliforme endopolygalacturonase towards pectin fragments: Comprehension and prediction.
Related PDB
Related UniProtKB

Comments
This enzyme belongs to the glycosidase family-28, with an inverting mechanism. According to the literature [13], the distances between the three catalytic residues with a carboxy group in the sidechain (Asp153, Asp173, Asp174) are all approximately 5 A, although the distances between the catalytic carboxy groups should be approximately 10 A in the ordinary inverting glycosidases. The difference of the catalytic site of this glycosidase enzyme from those of the other enzymes might suggest some differenes in its catalytic mechanism from those by other enzymes. According to the literature [13], the reaction proceeds by SN2-like reaction, for this enzyme, unlike the other glycosidase enzymes. According to the literature [13], the reaction of this enzyme proceeds as follows: (0) Lys228 and Arg226 (of 1k5c) modulate and decrease the pKa of Asp174, one of general bases, whilst Asp156 modulate the pKa of Asp153, another base. (1) Asp174 and Asp153 act as general bases, which deprotonate and activate the hydrolytic water. (Asp174 is more likely to be a general base than Asp153.) (2) The activated water makes a nucleophilic attack on anomeric carbon of the scissile bond. The reaction proceeds by an SN2-like mechanism. (3) Asp173 acts as a general acid to protonate the leaving group, the glycosidic oxygen, completing the hydrolysis.

Comments

This enzyme belongs to the glycosidase family-28, with an inverting mechanism.
According to the literature [13], the distances between the three catalytic residues with a carboxy group in the sidechain (Asp153, Asp173, Asp174) are all approximately 5 A, although the distances between the catalytic carboxy groups should be approximately 10 A in the ordinary inverting glycosidases. The difference of the catalytic site of this glycosidase enzyme from those of the other enzymes might suggest some differenes in its catalytic mechanism from those by other enzymes. According to the literature [13], the reaction proceeds by SN2-like reaction, for this enzyme, unlike the other glycosidase enzymes.
According to the literature [13], the reaction of this enzyme proceeds as follows:
(0) Lys228 and Arg226 (of 1k5c) modulate and decrease the pKa of Asp174, one of general bases, whilst Asp156 modulate the pKa of Asp153, another base.
(1) Asp174 and Asp153 act as general bases, which deprotonate and activate the hydrolytic water. (Asp174 is more likely to be a general base than Asp153.)
(2) The activated water makes a nucleophilic attack on anomeric carbon of the scissile bond. The reaction proceeds by an SN2-like mechanism.
(3) Asp173 acts as a general acid to protonate the leaving group, the glycosidic oxygen, completing the hydrolysis.

Created	Updated
2007-01-05	2009-02-26