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 Cofactor
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
4153
PubChem 24892720
22247451
962
24892720
439215
1bheA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1ia5A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1ib4A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1ib4B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1nhcA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1nhcB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1nhcC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1nhcD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1nhcE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1nhcF Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1czfA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1czfB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1k5cA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1kccA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:GTR
1kcdA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:GTR_1001 Bound:GTR_1002
1hg8A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 202;ASP 205;ASP 223;ASP 224;ARG 280;LYS 282
1ia5A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 159;ASP 162;ASP 180;ASP 181;ARG 235;LYS 237
1ib4A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 159;ASP 162;ASP 180;ASP 181;ARG 235;LYS 237
1ib4B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 159;ASP 162;ASP 180;ASP 181;ARG 235;LYS 237
1nhcA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 186;ASP 189;ASP 207;ASP 208;ARG 262;LYS 264
1nhcB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 186;ASP 189;ASP 207;ASP 208;ARG 262;LYS 264
1nhcC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 186;ASP 189;ASP 207;ASP 208;ARG 262;LYS 264
1nhcD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 186;ASP 189;ASP 207;ASP 208;ARG 262;LYS 264
1nhcE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 186;ASP 189;ASP 207;ASP 208;ARG 262;LYS 264
1nhcF Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 186;ASP 189;ASP 207;ASP 208;ARG 262;LYS 264
1czfA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 180;ASP 183;ASP 201;ASP 202;ARG 256;LYS 258
1czfB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 180;ASP 183;ASP 201;ASP 202;ARG 256;LYS 258
1k5cA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 153;ASP 156;ASP 173;ASP 174;ARG 226;LYS 228
1kccA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 153;ASP 156;ASP 173;ASP 174;ARG 226;LYS 228
1kcdA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 153;ASP 156;ASP 173;ASP 174;ARG 226;LYS 228
1hg8A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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.

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