DB code: S00170

CATH domain 2.160.20.10 : Pectate Lyase C-like Catalytic domain
E.C. 4.2.2.10
CSA 1idj
M-CSA 1idj
MACiE

CATH domain Related DB codes (homologues)
2.160.20.10 : Pectate Lyase C-like S00168 S00171 S00546 S00837 S00169 D00803

Uniprot Enzyme Name
UniprotKB Protein name Synonyms CAZy Pfam
Q01172 Pectin lyase A
PLA
EC 4.2.2.10
Pectin lyase II
PLII
PL1 (Polysaccharide Lyase Family 1)
PF00544 (Pec_lyase_C)
[Graphical View]
Q00205 Pectin lyase B
PLB
EC 4.2.2.10
PL1 (Polysaccharide Lyase Family 1)
PF00544 (Pec_lyase_C)
[Graphical View]

KEGG enzyme name
pectin lyase
pectin trans-eliminase
endo-pectin lyase
polymethylgalacturonic transeliminase
pectin methyltranseliminase
pectolyase
PL
PNL
PMGL

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q01172 PLYA_ASPNG Eliminative cleavage of (1->4)-alpha-D- galacturonan methyl ester to give oligosaccharides with 4-deoxy-6- O-methyl-alpha-D-galact-4-enuronosyl groups at their non-reducing ends.
Q00205 PLYB_ASPNG Eliminative cleavage of (1->4)-alpha-D- galacturonan methyl ester to give oligosaccharides with 4-deoxy-6- O-methyl-alpha-D-galact-4-enuronosyl groups at their non-reducing ends.

KEGG Pathways
Map code Pathways E.C.

Compound table
Substrates Products Intermediates
KEGG-id C00714 C00714 C04898
E.C.
Compound Pectin Pectin Oligosaccharides with terminal 4-deoxy-6-methyl-alpha-D-galact-4-enuronosyl groups
Type carboxyl group,polysaccharide carboxyl group,polysaccharide carbohydrate,polysaccharide
ChEBI
PubChem
1idjA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1idjB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1idkA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1qcxA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;Q01172, Q00205 & literature [5]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1idjA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 176;ARG 236;LYS 239
1idjB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 176;ARG 236;LYS 239
1idkA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 176;ARG 236;LYS 239
1qcxA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 176;ARG 236;LYS 239

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[5]
p.333-334

References
[1]
Resource
Comments
Medline ID
PubMed ID 2018526
Journal Biochem Biophys Res Commun
Year 1991
Volume 176
Pages 321-7
Authors Ohnishi H, Nishida T, Yoshida A, Kamio Y, Izaki K
Title Nucleotide sequence of pnl gene from Erwinia carotovora Er.
Related PDB
Related UniProtKB
[2]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
Medline ID 97341230
PubMed ID 9195887
Journal Structure
Year 1997
Volume 5
Pages 677-89
Authors Mayans O, Scott M, Connerton I, Gravesen T, Benen J, Visser J, Pickersgill R, Jenkins J
Title Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases.
Related PDB 1idj 1idk
Related UniProtKB Q01172
[3]
Resource
Comments
Medline ID
PubMed ID 9724625
Journal J Struct Biol
Year 1998
Volume 122
Pages 236-46
Authors Jenkins J, Mayans O, Pickersgill R
Title Structure and evolution of parallel beta-helix proteins.
Related PDB
Related UniProtKB
[4]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 9449837
Journal Plant Physiol
Year 1998
Volume 116
Pages 69-80
Authors Vitali J, Schick B, Kester HC, Visser J, Jurnak F
Title The tree-dimensional structure of aspergillus niger pectin lyase B at 1.7-A resolution.
Related PDB 1qcx
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 12418964
Journal Biochem J
Year 2003
Volume 370
Pages 331-7
Authors Sanchez-Torres P, Visser J, Benen JA
Title Identification of amino acid residues critical for catalysis and stability in Aspergillus niger family 1 pectin lyase A.
Related PDB
Related UniProtKB

Comments

Created Updated
2004-04-04 2009-02-26