EzCatDB: S00168
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DB codeS00168
RLCP classification1.30.260.1001 : Hydrolysis
CATH domainDomain 12.160.20.10 : Pectate Lyase C-likeCatalytic domain
E.C.3.2.1.15
CSA1czf

CATH domainRelated DB codes (homologues)
2.160.20.10 : Pectate Lyase C-likeS00171,S00546,S00837,S00170,S00169,D00803

Enzyme Name
UniProtKBKEGG

P26509O74213P26213P26214P79074Q07181
Protein nameEndo-polygalacturonasePolygalacturonase 1Polygalacturonase-1Endopolygalacturonase-2
Polygalacturonasepolygalacturonase
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
SynonymsEC 3.2.1.15
PG-1
EC 3.2.1.15
Pectinase 1
EC 3.2.1.15
Polygalacturonase I
PG-I
Pectinase 1
EC 3.2.1.15
Endopolygalacturonase II
EPG-II
PG-II
Pectinase-2
Endopolygalacturonase
EC 3.2.1.15
PG
EC 3.2.1.15
FmPG
Pectinase
RefSeqYP_006284264.1 (Protein)
NC_017845.1 (DNA/RNA sequence)





PfamPF00295 (Glyco_hydro_28)
[Graphical view]
PF00295 (Glyco_hydro_28)
[Graphical view]
PF00295 (Glyco_hydro_28)
[Graphical view]
PF00295 (Glyco_hydro_28)
[Graphical view]
PF00295 (Glyco_hydro_28)
[Graphical view]
PF00295 (Glyco_hydro_28)
[Graphical view]
CAZyGH28 (Glycoside Hydrolase Family)
GH28 (Glycoside Hydrolase Family)
GH28 (Glycoside Hydrolase Family)
GH28 (Glycoside Hydrolase Family)
GH28 (Glycoside Hydrolase Family)
GH28 (Glycoside Hydrolase Family)

KEGG pathways
MAP codePathways
MAP00040Pentose and glucuronate interconversions
MAP00500Starch and sucrose metabolism

UniProtKB:Accession NumberP26509O74213P26213P26214P79074Q07181
Entry namePGLR2_PECCCPGLR1_ASPACPGLR1_ASPNGPGLR2_ASPNGP79074_9AGARPGLR_GIBFU
ActivityRandom hydrolysis of (1->4)-alpha-D- galactosiduronic linkages in pectate and other galacturonans.Random hydrolysis of (1->4)-alpha-D- galactosiduronic linkages in pectate and other galacturonans.Random hydrolysis of (1->4)-alpha-D- galactosiduronic linkages in pectate and other galacturonans.Random hydrolysis of (1->4)-alpha-D- galactosiduronic linkages in pectate and other galacturonans.
Random hydrolysis of (1->4)-alpha-D- galactosiduronic linkages in pectate and other galacturonans.
SubunitMonomer.




Subcellular locationSecreted.




Cofactor






Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC00470C00001C00470C00333
CompoundPectateH2OPectateD-Galacturonate
Typecarboxyl group,polysaccharideH2Ocarboxyl group,polysaccharidecarbohydrate,carboxyl group
ChEBI
15377

4153
PubChem24892720
962
22247451
24892720
439215
            
1bheAUnbound UnboundUnbound
1ia5AUnbound UnboundUnbound
1ib4AUnbound UnboundUnbound
1ib4BUnbound UnboundUnbound
1nhcAUnbound UnboundUnbound
1nhcBUnbound UnboundUnbound
1nhcCUnbound UnboundUnbound
1nhcDUnbound UnboundUnbound
1nhcEUnbound UnboundUnbound
1nhcFUnbound UnboundUnbound
1czfAUnbound UnboundUnbound
1czfBUnbound UnboundUnbound
1k5cAUnbound UnboundUnbound
1kccAUnbound UnboundBound:GTR
1kcdAUnbound Analogue:GTR 1001Bound:GTR 1002
1hg8AUnbound UnboundUnbound

Active-site residues
resource
literature [13]
pdbCatalytic residues
         
1bheAASP 202;ASP 205;ASP 223;ASP 224;ARG 280;LYS 282
1ia5AASP 159;ASP 162;ASP 180;ASP 181;ARG 235;LYS 237
1ib4AASP 159;ASP 162;ASP 180;ASP 181;ARG 235;LYS 237
1ib4BASP 159;ASP 162;ASP 180;ASP 181;ARG 235;LYS 237
1nhcAASP 186;ASP 189;ASP 207;ASP 208;ARG 262;LYS 264
1nhcBASP 186;ASP 189;ASP 207;ASP 208;ARG 262;LYS 264
1nhcCASP 186;ASP 189;ASP 207;ASP 208;ARG 262;LYS 264
1nhcDASP 186;ASP 189;ASP 207;ASP 208;ARG 262;LYS 264
1nhcEASP 186;ASP 189;ASP 207;ASP 208;ARG 262;LYS 264
1nhcFASP 186;ASP 189;ASP 207;ASP 208;ARG 262;LYS 264
1czfAASP 180;ASP 183;ASP 201;ASP 202;ARG 256;LYS 258
1czfBASP 180;ASP 183;ASP 201;ASP 202;ARG 256;LYS 258
1k5cAASP 153;ASP 156;ASP 173;ASP 174;ARG 226;LYS 228
1kccAASP 153;ASP 156;ASP 173;ASP 174;ARG 226;LYS 228
1kcdAASP 153;ASP 156;ASP 173;ASP 174;ARG 226;LYS 228
1hg8AASP 191;ASP 194;ASP 212;ASP 213;ARG 267;LYS 269

References for Catalytic Mechanism
ReferencesSectionsNo. 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]
PubMed ID1416030
JournalAnal Biochem
Year1992
Volume203
Pages335-9
AuthorsBach E, Schollmeyer E
TitleAn ultraviolet-spectrophotometric method with 2-cyanoacetamide for the determination of the enzymatic degradation of reducing polysaccharides.
[2]
PubMed ID8814223
JournalBiochim Biophys Acta
Year1996
Volume1296
Pages167-73
AuthorsRao MN, Kembhavi AA, Pant A
TitleImplication of tryptophan and histidine in the active site of endo-polygalacturonase from Aspergillus ustus: elucidation of the reaction mechanism.
[3]
PubMed ID9115442
JournalStructure
Year1997
Volume5
Pages533-44
AuthorsPetersen TN, Kauppinen S, Larsen S
TitleThe crystal structure of rhamnogalacturonase A from Aspergillus aculeatus: a right-handed parallel beta helix.
[4]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
Medline ID98406113
PubMed ID9733763
JournalJ Biol Chem
Year1998
Volume273
Pages24660-4
AuthorsPickersgill R, Smith D, Worboys K, Jenkins J
TitleCrystal structure of polygalacturonase from Erwinia carotovora ssp. carotovora.
Related PDB1bhe
Related UniProtKBP26509
[5]
CommentsX-RAY CRYSTALLOGRAPHY (1.68 ANGSTROMS), AND MUTAGENESIS OF ASP-180; ASP-201; ASP-202; HIS-223; ARG-256 AND LYS-258.
PubMed ID10521427
JournalJ Biol Chem
Year1999
Volume274
Pages30474-80
Authorsvan Santen Y, Benen JA, Schroter KH, Kalk KH, Armand S, Visser J, Dijkstra BW
Title1.68-A crystal structure of endopolygalacturonase II from Aspergillus niger and identification of active site residues by site-directed mutagenesis.
Related PDB1czf
Related UniProtKBP26214
[6]
PubMed ID10617668
JournalJ Biol Chem
Year2000
Volume275
Pages691-6
AuthorsArmand S, Wagemaker MJ, Sanchez-Torres P, Kester HC, van Santen Y, Dijkstra BW, Visser J, Benen JA
TitleThe active site topology of Aspergillus niger endopolygalacturonase II as studied by site-directed mutagenesis.
[7]
PubMed ID10893426
JournalJ Biol Chem
Year2000
Volume275
Pages29348-53
AuthorsPages S, Heijne WH, Kester HC, Visser J, Benen JA
TitleSubsite mapping of Aspergillus niger endopolygalacturonase II by site-directed mutagenesis.
[8]
PubMed ID11168425
JournalEur J Biochem
Year2001
Volume268
Pages832-40
AuthorsNiture SK, Pant A, Kumar AR
TitleActive site characterization of the single endo-polygalacturonase produced by Fusarium moniliforme NCIM 1276.
[9]
PubMed ID11445590
JournalJ Biol Chem
Year2001
Volume276
Pages33652-6
AuthorsPages S, Kester HC, Visser J, Benen JA
TitleChanging a single amino acid residue switches processive and non-processive behavior of Aspergillus niger endopolygalacturonase I and II.
[10]
CommentsX-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.
PubMed ID11518536
JournalJ Mol Biol
Year2001
Volume311
Pages863-78
AuthorsCho SW, Lee S, Shin W
TitleThe X-ray structure of Aspergillus aculeatus polygalacturonase and a modeled structure of the polygalacturonase-octagalacturonate complex.
Related PDB1ia5,1ib4
Related UniProtKBO74213
[11]
CommentsX-RAY CRYSTALLOGRAPHY (1.73 ANGSTROMS) OF 25-373, AND MUTAGENESIS OF HIS-188; ASP-191; 212-ASP-ASP-213; ARG-267 AND LYS-269.
PubMed ID11687632
JournalProc Natl Acad Sci U S A
Year2001
Volume98
Pages13425-30
AuthorsFederici L, Caprari C, Mattei B, Savino C, Di Matteo A, De Lorenzo G, Cervone F, Tsernoglou D
TitleStructural requirements of endopolygalacturonase for the interaction with PGIP (polygalacturonase-inhibiting protein).
Related PDB1hg8
Related UniProtKBQ07181
[12]
PubMed ID11707607
JournalProtein Eng
Year2001
Volume14
Pages615-31
AuthorsMarkovic O, Janecek S
TitlePectin degrading glycoside hydrolases of family 28: sequence-structural features, specificities and evolution.
[13]
CommentsX-RAY CRYSTALLOGRAPHY (0.96 ANGSTROMS) OF 25-359.
PubMed ID12022868
JournalBiochemistry
Year2002
Volume41
Pages6651-9
AuthorsShimizu T, Nakatsu T, Miyairi K, Okuno T, Kato H
TitleActive-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution.
Related PDB1k5c,1kcc,1kcd
Related UniProtKBP79074
[14]
CommentsX-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 33-368, AND GLYCOSYLATION AT SER-44; SER-46 AND ASN-246.
PubMed ID14623112
JournalFEBS Lett
Year2003
Volume554
Pages462-6
Authorsvan Pouderoyen G, Snijder HJ, Benen JA, Dijkstra BW
TitleStructural insights into the processivity of endopolygalacturonase I from Aspergillus niger.
Related PDB1nhc
Related UniProtKBP26213
[15]
PubMed ID15848136
JournalBiochim Biophys Acta
Year2005
Volume1749
Pages53-64
AuthorsAndre-Leroux G, Tessier D, Bonnin E
TitleAction pattern of Fusarium moniliforme endopolygalacturonase towards pectin fragments: Comprehension and prediction.

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.

createdupdated
2007-01-052009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
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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