EzCatDB: S00171

DB codeS00171
RLCP classification1.12.30190.70
CATH domainDomain 12.160.20.10Catalytic domain
E.C.3.1.1.11
CSA1gq8

CATH domainRelated DB codes (homologues)
2.160.20.10S00168,S00546,S00837,S00170,S00169,D00803

Enzyme Name
Swiss-protKEGG

P0C1A8P83218
Protein namePectinesterase APectinesterasepectinesterase
pectin demethoxylase
pectin methoxylase
pectin methylesterase
pectase
pectin methyl esterase
pectinoesterase
SynonymsPE A
EC 3.1.1.11
Pectin methylesterase A
PE
EC 3.1.1.11
Pectin methylesterase

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

Swiss-prot:Accession NumberP0C1A8P83218
Entry namePMEA_ERWCHPME_DAUCA
ActivityPectin + n H(2)O = n methanol + pectate.Pectin + n H(2)O = n methanol + pectate.
SubunitMonomer (By similarity).
Subcellular locationSecreted (By similarity).Secreted, cell wall (Probable).
Cofactor



SubstratesProducts
KEGG-idC00714C00001C00132C00470
CompoundPectinH2OMethanolPectate
Typecarbohydrate,polysaccharideH2Ocarbohydratecarboxyl group,polysaccharide
1qjvAUnbound
UnboundUnbound
1qjvBUnbound
UnboundUnbound
1gq8AUnbound
UnboundUnbound

Active-site residues
resource
PDB;1qjv & Swiss-prot;P07863
pdbCatalytic residues
1qjvAGLN 153;GLN 177;ASP 178;ASP 199;ARG 267
1qjvBGLN 153;GLN 177;ASP 178;ASP 199;ARG 267
1gq8AGLN 113;GLN 135;ASP 136;ASP 157;ARG 225

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]Scheme 1, p.347-349
[8]p.955-957
[11]p.248

references
[1]
PubMed ID2837615
JournalMol Microbiol
Year1988
Volume2
Pages247-54
AuthorsPlastow GS
TitleMolecular cloning and nucleotide sequence of the pectin methyl esterase gene of Erwinia chrysanthemi B374.
[2]
PubMed ID1953633
JournalBiochem J
Year1991
Volume279
Pages343-50
AuthorsNari J, Noat G, Ricard J
TitlePectin methylesterase, metal ions and plant cell-wall extension. Hydrolysis of pectin by plant cell-wall pectin methylesterase.
[3]
PubMed ID1868195
JournalPlant Mol Biol
Year1991
Volume16
Pages501-13
AuthorsAlbani D, Altosaar I, Arnison PG, Fabijanski SF
TitleA gene showing sequence similarity to pectin esterase is specifically expressed in developing pollen of Brassica napus. Sequences in its 5' flanking region are conserved in other pollen-specific promoters.
[4]
PubMed ID8370537
JournalGene
Year1993
Volume131
Pages17-25
AuthorsLaurent F, Kotoujansky A, Labesse G, Bertheau Y
TitleCharacterization and overexpression of the pem gene encoding pectin methylesterase of Erwinia chrysanthemi strain 3937.
[5]
PubMed ID10564001
JournalJ Agric Food Chem
Year1999
Volume47
Pages1471-5
AuthorsSun D, Wicker L
TitleKinetic compensation and the role of cations in pectinesterase catalysis.
[6]
PubMed ID10956097
JournalJ Agric Food Chem
Year2000
Volume48
Pages3238-44
AuthorsCorredig M, Wicker L
TitleRole of cations in the catalysis of thermostable pectinmethylesterase extracted from Marsh grapefruit pulp.
[7]
PubMed ID11120736
JournalJ Biol Chem
Year2001
Volume276
Pages8841-7
AuthorsGoldberg R, Pierron M, Bordenave M, Breton C, Morvan C, du Penhoat CH
TitleControl of Mung bean pectinmethylesterase isoform activities. Influence of pH and carboxyl group distribution along the pectic chains.
[8]
CommentsX-ray crystallography
PubMed ID11162105
JournalJ Mol Biol
Year2001
Volume305
Pages951-60
AuthorsJenkins J, Mayans O, Smith D, Worboys K, Pickersgill RW
TitleThree-dimensional structure of Erwinia chrysanthemi pectin methylesterase reveals a novel esterase active site.
Related PDB1qjv
[9]
PubMed ID11544130
JournalTrends Plant Sci
Year2001
Volume6
Pages414-9
AuthorsMicheli F
TitlePectin methylesterases: cell wall enzymes with important roles in plant physiology.
[10]
PubMed ID11934288
JournalBiotechnol Prog
Year2002
Volume18
Pages221-8
AuthorsTerefe NS, Hendrickx M
TitleKinetics of the pectin methylesterase catalyzed de-esterification of pectin in frozen food model systems.
[11]
PubMed ID11943159
JournalFEBS Lett
Year2002
Volume514
Pages243-9
AuthorsJohansson K, El-Ahmad M, Friemann R, Jornvall H, Markovic O, Eklund H
TitleCrystal structure of plant pectin methylesterase.
Related PDB1gq8

comments
According to the literature [11], the catalytic reaction proceeds as follwos:
(1) Arg225 (of PDB;1gq8) enhances the nucleophilicity of Asp157 by its interaction.
(2) Asp157 makes a nucleophilic attack on the carbonyl carbon, resulting in the covalent bond formation leading to a negatively charged tetrahedral intermediate. Here, Asp136 acts as a general acid to protonate the leaving group, methanol.
(3) Gln113 and Gln135 stabilize the negative charge of the tetrahedral intermediate.
(4) Asp136 acts as a general base to activate a water molecule, which would attack on the tetrahedral intermediate, to complete the reaction.

createdupdated
2004-03-222009-02-26


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 2010)
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)

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