DB code: S00171

RLCP classification 1.12.30190.70 : Hydrolysis
CATH domain 2.160.20.10 : Pectate Lyase C-like Catalytic domain
E.C. 3.1.1.11
CSA 1gq8
M-CSA 1gq8
MACiE

CATH domain Related DB codes (homologues)
2.160.20.10 : Pectate Lyase C-like S00168 S00546 S00837 S00170 S00169 D00803

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P0C1A8 Pectinesterase A
PE A
EC 3.1.1.11
Pectin methylesterase A
PF01095 (Pectinesterase)
[Graphical View]
P83218 Pectinesterase
PE
EC 3.1.1.11
Pectin methylesterase
PF01095 (Pectinesterase)
[Graphical View]

KEGG enzyme name
pectinesterase
pectin demethoxylase
pectin methoxylase
pectin methylesterase
pectase
pectin methyl esterase
pectinoesterase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P0C1A8 PMEA_ERWCH Pectin + n H(2)O = n methanol + pectate. Monomer (By similarity). Secreted (By similarity).
P83218 PME_DAUCA Pectin + n H(2)O = n methanol + pectate. Secreted, cell wall (Probable).

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

Compound table
Substrates Products Intermediates
KEGG-id C00714 C00001 C00132 C00470
E.C.
Compound Pectin H2O Methanol Pectate
Type carbohydrate,polysaccharide H2O carbohydrate carboxyl group,polysaccharide
ChEBI 15377
17790
PubChem 22247451
962
887
24892720
1qjvA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1qjvB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1gq8A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
PDB;1qjv & Swiss-prot;P07863

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1qjvA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLN 153;GLN 177;ASP 178;ASP 199;ARG 267
1qjvB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLN 153;GLN 177;ASP 178;ASP 199;ARG 267
1gq8A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLN 113;GLN 135;ASP 136;ASP 157;ARG 225

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[2]
Scheme 1, p.347-349
[8]
p.955-957
[11]
p.248

References
[1]
Resource
Comments
Medline ID
PubMed ID 2837615
Journal Mol Microbiol
Year 1988
Volume 2
Pages 247-54
Authors Plastow GS
Title Molecular cloning and nucleotide sequence of the pectin methyl esterase gene of Erwinia chrysanthemi B374.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 1953633
Journal Biochem J
Year 1991
Volume 279
Pages 343-50
Authors Nari J, Noat G, Ricard J
Title Pectin methylesterase, metal ions and plant cell-wall extension. Hydrolysis of pectin by plant cell-wall pectin methylesterase.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 1868195
Journal Plant Mol Biol
Year 1991
Volume 16
Pages 501-13
Authors Albani D, Altosaar I, Arnison PG, Fabijanski SF
Title A 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.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 8370537
Journal Gene
Year 1993
Volume 131
Pages 17-25
Authors Laurent F, Kotoujansky A, Labesse G, Bertheau Y
Title Characterization and overexpression of the pem gene encoding pectin methylesterase of Erwinia chrysanthemi strain 3937.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 10564001
Journal J Agric Food Chem
Year 1999
Volume 47
Pages 1471-5
Authors Sun D, Wicker L
Title Kinetic compensation and the role of cations in pectinesterase catalysis.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 10956097
Journal J Agric Food Chem
Year 2000
Volume 48
Pages 3238-44
Authors Corredig M, Wicker L
Title Role of cations in the catalysis of thermostable pectinmethylesterase extracted from Marsh grapefruit pulp.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 11120736
Journal J Biol Chem
Year 2001
Volume 276
Pages 8841-7
Authors Goldberg R, Pierron M, Bordenave M, Breton C, Morvan C, du Penhoat CH
Title Control of Mung bean pectinmethylesterase isoform activities. Influence of pH and carboxyl group distribution along the pectic chains.
Related PDB
Related UniProtKB
[8]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 11162105
Journal J Mol Biol
Year 2001
Volume 305
Pages 951-60
Authors Jenkins J, Mayans O, Smith D, Worboys K, Pickersgill RW
Title Three-dimensional structure of Erwinia chrysanthemi pectin methylesterase reveals a novel esterase active site.
Related PDB 1qjv
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 11544130
Journal Trends Plant Sci
Year 2001
Volume 6
Pages 414-9
Authors Micheli F
Title Pectin methylesterases: cell wall enzymes with important roles in plant physiology.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 11934288
Journal Biotechnol Prog
Year 2002
Volume 18
Pages 221-8
Authors Terefe NS, Hendrickx M
Title Kinetics of the pectin methylesterase catalyzed de-esterification of pectin in frozen food model systems.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 11943159
Journal FEBS Lett
Year 2002
Volume 514
Pages 243-9
Authors Johansson K, El-Ahmad M, Friemann R, Jornvall H, Markovic O, Eklund H
Title Crystal structure of plant pectin methylesterase.
Related PDB 1gq8
Related UniProtKB

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.

Created Updated
2004-03-22 2009-02-26