S00546
type: Enzyme
rlcp: p530
cath: Pectate Lyase C-like
ec: https://purl.uniprot.org/enzyme/4.2.2.2
uniprot: P39116
uniprot: P0C1A2
kegg enzyme: pectate lyase
kegg enzyme: polygalacturonic transeliminase
kegg enzyme: pectic acid transeliminase
kegg enzyme: polygalacturonate lyase
kegg enzyme: endopectin methyltranseliminase
kegg enzyme: pectate transeliminase
kegg enzyme: endogalacturonate transeliminase
kegg enzyme: pectic acid lyase
kegg enzyme: pectic lyase
kegg enzyme: alpha-1,4-D-endopolygalacturonic acid lyase
kegg enzyme: PGA lyase
kegg enzyme: PPase-N
kegg enzyme: endo-alpha-1,4-polygalacturonic acid lyase
kegg enzyme: polygalacturonic acid lyase
kegg enzyme: pectin trans-eliminase
kegg enzyme: Polygalacturonic acid trans-eliminase
kegg pathway: Pentose and glucuronate interconversions
kegg cofactor: Calcium
kegg substrate: Pectate
kegg product: 4-(4-Deoxy-alpha-D-gluc-4-enuronosyl)-D-galacturonate
kegg product: Pectate
pdb: 1bn8A
pdb: 2bspA
pdb: 1jrgA
pdb: 1jrgB
pdb: 1jtaA
pdb bound state: Unbound
  compound: Pectate
  pdb: 1bn8A
pdb bound state: Unbound
  compound: Pectate
  pdb: 2bspA
pdb bound state: Unbound
  compound: Pectate
  pdb: 1jrgA
pdb bound state: Unbound
  compound: Pectate
  pdb: 1jrgB
pdb bound state: Unbound
  compound: Pectate
  pdb: 1jtaA
pdb bound state: Unbound
  compound: Calcium
  pdb: 1jrgA
pdb bound state: Unbound
  compound: Calcium
  pdb: 1jrgB
pdb bound state: Unbound
  compound: Calcium
  pdb: 1jtaA
pdb bound state: Unbound
  compound: 4-(4-Deoxy-alpha-D-gluc-4-enuronosyl)-D-galacturonate
  pdb: 1bn8A
pdb bound state: Unbound
  compound: 4-(4-Deoxy-alpha-D-gluc-4-enuronosyl)-D-galacturonate
  pdb: 2bspA
pdb bound state: Unbound
  compound: 4-(4-Deoxy-alpha-D-gluc-4-enuronosyl)-D-galacturonate
  pdb: 1jrgA
pdb bound state: Unbound
  compound: 4-(4-Deoxy-alpha-D-gluc-4-enuronosyl)-D-galacturonate
  pdb: 1jrgB
pdb bound state: Unbound
  compound: 4-(4-Deoxy-alpha-D-gluc-4-enuronosyl)-D-galacturonate
  pdb: 1jtaA
pdb bound state: Unbound
  compound: Pectate
  pdb: 1bn8A
pdb bound state: Unbound
  compound: Pectate
  pdb: 2bspA
pdb bound state: Unbound
  compound: Pectate
  pdb: 1jrgA
pdb bound state: Unbound
  compound: Pectate
  pdb: 1jrgB
pdb bound state: Unbound
  compound: Pectate
  pdb: 1jtaA
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 2
  reference section: p.722
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 4
  reference section: p.361-363
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 5
  reference section: p.163
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 6
  reference section: p.90
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 8
  reference section: p.1086-1088
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 10
  reference section: Fig.2, p.8763-8765
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 11
  reference section: p.1790-1791
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 13
  reference section: p.1012-1013
references: New domain motif: the structure of pectate lyase C, a secreted plant virulence factor.
references: The structure of Bacillus subtilis pectate lyase in complex with calcium.
references: Protein motifs. 3. The parallel beta helix and other coiled folds.
references: The Refined Three-Dimensional Structure of Pectate Lyase C from Erwinia chrysanthemi at 2.2 Angstrom Resolution (Implications for an Enzymatic Mechanism).
references: Role of lysine, tryptophan and calcium in the beta-elimination activity of a low-molecular-mass pectate lyase from Fusarium moniliformae.
references: The refined three-dimensional structure of pectate lyase E from Erwinia chrysanthemi at 2.2-A resolution.
references: 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.
references: Structure of a plant cell wall fragment complexed to pectate lyase C.
references: The stability, structural organization, and denaturation of pectate lyase C, a parallel beta-helix protein.
references: Structure and function of pectic enzymes: virulence factors of plant pathogens.
references: The first structure of pectate lyase belonging to polysaccharide lyase family 3.
references: A new family of rhamnogalacturonan lyases contains an enzyme that binds to cellulose.
references: Structure of pectate lyase A: comparison to other isoforms.
references: Identification of proline residues responsible for the slow folding kinetics in pectate lyase C by mutagenesis.
references: Folding kinetics of the protein pectate lyase C reveal fast-forming intermediates and slow proline isomerization.
references: Differences in the solution structures of the parallel beta-helical pectate lyases as determined by limited proteolysis.
references: CASH--a beta-helix domain widespread among carbohydrate-binding proteins.
references: Characterization and implications of Ca2+ binding to pectate lyase C.
comment: This enzyme is homologous to the counterpart enzyme (S00169), although one of the calcium binding residues, Asp184 (of 1jrg), is different from that (Glu166 of 1air) of its homologous enzyme. According to the literature [8], the catalytic reaction (beta-elimination) involves three process: (1) Neutralization of the carboxyl group adjacent to the deprotonation site of leaving group. (2) Deprotonation at the C-5 atom (deprotonation site of leaving group). (3) Protonation to the glycosidic oxygen (eliminated group). Although calcium ion usually plays a structural role, it is catalytically importnat in this enzyme. The calcium ion at the active site seems to acidify (or lower the pKa of) the alpha-proton at C-5 atom for abstraction by a general base, by polarizing and neutralizing the carboxy group (or uronic acid group) of the substrate (see [4], [5] & [6]). Here, the calcium ion acts as a Lewis acid. The literature [8] proposed that the conserved residue, Arg241 (of 1jrg), might serve as a general base, to abstract the proton at the C-5 atom. Although it is unusual for argnine residues to be a general base, the substrate carboxylate group (uronic acid) makes Arg241 to act as a general base, by lowering its pKa. As for the general acid, which protonates the glycosidic oxygen atom, a water molecule was suggested by the paper [8]. No alternative group has been found for this role. Moreover, during the catalysis, an enolic intermediate is formed and stabilized by Lys208 (of 1jrg) (see [8]).

Pectate Lyase C-like
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/2.160.20.10
catalytic domain: index.html

Pentose and glucuronate interconversions
type: KeggPathway
references: KEGG:MAP00040

Calcium
type: KeggCofactor
references: KEGG:C00076
compound type: divalent metal (Ca2+, Mg2+)
references: CHEBI:29108
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

Pectate
type: KeggSubstrate
references: KEGG:C00470
compound type: carboxyl group
compound type: polysaccharide
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi
type: KeggProduct

4-(4-Deoxy-alpha-D-gluc-4-enuronosyl)-D-galacturonate
type: KeggProduct
references: KEGG:C06118
compound type: carboxyl group
compound type: polysaccharide
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

1bn8A
type: Pdb
references: 1bn8
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1bn8
catalytic residue: LYS 247;ARG 279
cofactor binding residue: ASP 184;ASP 223;ASP 227(Calcium binding)

2bspA
type: Pdb
references: 2bsp
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:2bsp
catalytic residue: LYS 247;
cofactor binding residue: ASP 184;ASP 223;ASP 227(Calcium binding)
comment: mutant R279K

1jrgA
type: Pdb
references: 1jrg
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1jrg
catalytic residue: LYS 208;ARG 241
cofactor binding residue: ASP 144;ASP 184;ASP 188(Calcium binding)

1jrgB
type: Pdb
references: 1jrg
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1jrg
catalytic residue: LYS 208;ARG 241
cofactor binding residue: ASP 144;ASP 184;ASP 188(Calcium binding)

1jtaA
type: Pdb
references: 1jta
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1jta
catalytic residue: LYS 208;ARG 241
cofactor binding residue: ASP 144;ASP 184;ASP 188(Calcium binding)

New domain motif: the structure of pectate lyase C, a secreted plant virulence factor.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
medline id: 93276270
references: http://www.ncbi.nlm.nih.gov/pubmed/8502994
journal: Science
volume: 260
pages: 1503-7
published year: 1993
authors:
  item: Yoder MD
  item: Keen NT
  item: Jurnak F
references: P11073

The structure of Bacillus subtilis pectate lyase in complex with calcium.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
medline id: 95360717
references: http://www.ncbi.nlm.nih.gov/pubmed/7634076
journal: Nat Struct Biol
volume: 1
pages: 717-23
published year: 1994
authors:
  item: Pickersgill R
  item: Jenkins J
  item: Harris G
  item: Nasser W
  item: Robert-Baudouy J
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P39116

Protein motifs. 3. The parallel beta helix and other coiled folds.
type: BibliographicResource
comment: X-ray crystallography
references: http://www.ncbi.nlm.nih.gov/pubmed/7896002
journal: FASEB J
volume: 9
pages: 335-42
published year: 1995
authors:
  item: Yoder MD
  item: Jurnak F
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

The Refined Three-Dimensional Structure of Pectate Lyase C from Erwinia chrysanthemi at 2.2 Angstrom Resolution (Implications for an Enzymatic Mechanism).
type: BibliographicResource
comment: X-ray crystallography
references: http://www.ncbi.nlm.nih.gov/pubmed/12228363
journal: Plant Physiol
volume: 107
pages: 349-364
published year: 1995
authors:
  item: Yoder MD
  item: Jurnak F
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Role of lysine, tryptophan and calcium in the beta-elimination activity of a low-molecular-mass pectate lyase from Fusarium moniliformae.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8870663
journal: Biochem J
volume: 319
pages: 159-64
published year: 1996
authors:
  item: Rao MN
  item: Kembhavi AA
  item: Pant A

The refined three-dimensional structure of pectate lyase E from Erwinia chrysanthemi at 2.2-A resolution.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS)
journal: Plant Physiol
volume: 111
pages: 73-92
published year: 1996
authors:
  item: Lietzke SE
  item: Scavetta RD
  item: Yoder MD
  item: Jurnak FA
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P11073

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.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9195887
journal: Structure
volume: 5
pages: 677-89
published year: 1997
authors:
  item: Mayans O
  item: Scott M
  item: Connerton I
  item: Gravesen T
  item: Benen J
  item: Visser J
  item: Pickersgill R
  item: Jenkins J

Structure of a plant cell wall fragment complexed to pectate lyase C.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10368179
journal: Plant Cell
volume: 11
pages: 1081-92
published year: 1999
authors:
  item: Scavetta RD
  item: Herron SR
  item: Hotchkiss AT
  item: Kita N
  item: Keen NT
  item: Benen JA
  item: Kester HC
  item: Visser J
  item: Jurnak F

The stability, structural organization, and denaturation of pectate lyase C, a parallel beta-helix protein.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11123920
journal: Biochemistry
volume: 39
pages: 15932-43
published year: 2000
authors:
  item: Kamen DE
  item: Griko Y
  item: Woody RW

Structure and function of pectic enzymes: virulence factors of plant pathogens.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10922032
journal: Proc Natl Acad Sci U S A
volume: 97
pages: 8762-9
published year: 2000
authors:
  item: Herron SR
  item: Benen JA
  item: Scavetta RD
  item: Visser J
  item: Jurnak F

The first structure of pectate lyase belonging to polysaccharide lyase family 3.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11717490
journal: Acta Crystallogr D Biol Crystallogr
volume: 57
pages: 1786-92
published year: 2001
authors:
  item: Akita M
  item: Suzuki A
  item: Kobayashi T
  item: Ito S
  item: Yamane T

A new family of rhamnogalacturonan lyases contains an enzyme that binds to cellulose.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11256961
journal: Biochem J
volume: 355
pages: 167-77
published year: 2001
authors:
  item: McKie VA
  item: Vincken JP
  item: Voragen AG
  item: van den Broek LA
  item: Stimson E
  item: Gilbert HJ

Structure of pectate lyase A: comparison to other isoforms.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12037303
journal: Acta Crystallogr D Biol Crystallogr
volume: 58
pages: 1008-15
published year: 2002
authors:
  item: Thomas LM
  item: Doan CN
  item: Oliver RL
  item: Yoder MD
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Identification of proline residues responsible for the slow folding kinetics in pectate lyase C by mutagenesis.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11926835
journal: Biochemistry
volume: 41
pages: 4724-32
published year: 2002
authors:
  item: Kamen DE
  item: Woody RW

Folding kinetics of the protein pectate lyase C reveal fast-forming intermediates and slow proline isomerization.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11926834
journal: Biochemistry
volume: 41
pages: 4713-23
published year: 2002
authors:
  item: Kamen DE
  item: Woody RW

Differences in the solution structures of the parallel beta-helical pectate lyases as determined by limited proteolysis.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12479401
journal: Biochim Biophys Acta
volume: 1599
pages: 9-20
published year: 2002
authors:
  item: Hurlbert JC
  item: Preston JF 2nd

CASH--a beta-helix domain widespread among carbohydrate-binding proteins.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11852237
journal: Trends Biochem Sci
volume: 27
pages: 59-62
published year: 2002
authors:
  item: Ciccarelli FD
  item: Copley RR
  item: Doerks T
  item: Russell RB
  item: Bork P

Characterization and implications of Ca2+ binding to pectate lyase C.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12540845
journal: J Biol Chem
volume: 278
pages: 12271-7
published year: 2003
authors:
  item: Herron SR
  item: Scavetta RD
  item: Garrett M
  item: Legner M
  item: Jurnak F
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl