DB code: S00546

RLCP classification 5.20.1710000.530 : Elimination
CATH domain 2.160.20.10 : Pectate Lyase C-like Catalytic domain
E.C. 4.2.2.2
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
2.160.20.10 : Pectate Lyase C-like S00168 S00171 S00837 S00170 S00169 D00803

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq CAZy Pfam
P39116 Pectate lyase
PL
EC 4.2.2.2
NP_388637.1 (Protein)
NC_000964.3 (DNA/RNA sequence)
PL1 (Polysaccharide Lyase Family 1)
PF00544 (Pec_lyase_C)
[Graphical View]
P0C1A2 Pectate lyase A
EC 4.2.2.2
PL1 (Polysaccharide Lyase Family 1)
PF00544 (Pec_lyase_C)
[Graphical View]

KEGG enzyme name
pectate lyase
polygalacturonic transeliminase
pectic acid transeliminase
polygalacturonate lyase
endopectin methyltranseliminase
pectate transeliminase
endogalacturonate transeliminase
pectic acid lyase
pectic lyase
alpha-1,4-D-endopolygalacturonic acid lyase
PGA lyase
PPase-N
endo-alpha-1,4-polygalacturonic acid lyase
polygalacturonic acid lyase
pectin trans-eliminase
Polygalacturonic acid trans-eliminase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P39116 PEL_BACSU Eliminative cleavage of (1->4)-alpha-D- galacturonan to give oligosaccharides with 4-deoxy-alpha-D-galact- 4-enuronosyl groups at their non-reducing ends. Monomer. Secreted. Binds 1 calcium ion per subunit.
P0C1A2 PELA_ERWCH Eliminative cleavage of (1->4)-alpha-D- galacturonan to give oligosaccharides with 4-deoxy-alpha-D-galact- 4-enuronosyl groups at their non-reducing ends. Secreted. Binds 1 calcium ion per subunit.

KEGG Pathways
Map code Pathways E.C.
MAP00040 Pentose and glucuronate interconversions

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00076 C00470 C06118 C00470
E.C.
Compound Calcium Pectate 4-(4-Deoxy-alpha-D-gluc-4-enuronosyl)-D-galacturonate Pectate
Type divalent metal (Ca2+, Mg2+) carboxyl group,polysaccharide carboxyl group,polysaccharide carboxyl group,polysaccharide
ChEBI 29108
 29108
PubChem 271
 271
 		24892720
 24892720
 		440470
 440470
 		24892720
 24892720
1bn8A Bound:_CA Unbound Unbound Unbound
2bspA Bound:_CA Unbound Unbound Unbound
1jrgA Unbound Unbound Unbound Unbound
1jrgB Unbound Unbound Unbound Unbound
1jtaA Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
see S00169

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1bn8A LYS 247;ARG 279 ASP 184;ASP 223;ASP 227(Calcium binding)
2bspA LYS 247; ASP 184;ASP 223;ASP 227(Calcium binding) mutant R279K
1jrgA LYS 208;ARG 241 ASP 144;ASP 184;ASP 188(Calcium binding)
1jrgB LYS 208;ARG 241 ASP 144;ASP 184;ASP 188(Calcium binding)
1jtaA LYS 208;ARG 241 ASP 144;ASP 184;ASP 188(Calcium binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[2]
p.722
[4]
p.361-363
[5]
p.163
[6]
p.90
[8]
p.1086-1088
[10]
Fig.2, p.8763-8765
[11]
p.1790-1791
[13]
p.1012-1013

References
[1]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
Medline ID 93276270
PubMed ID 8502994
Journal Science
Year 1993
Volume 260
Pages 1503-7
Authors Yoder MD, Keen NT, Jurnak F
Title New domain motif: the structure of pectate lyase C, a secreted plant virulence factor.
Related PDB
Related UniProtKB P11073
[2]
Resource
Comments X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
Medline ID 95360717
PubMed ID 7634076
Journal Nat Struct Biol
Year 1994
Volume 1
Pages 717-23
Authors Pickersgill R, Jenkins J, Harris G, Nasser W, Robert-Baudouy J
Title The structure of Bacillus subtilis pectate lyase in complex with calcium.
Related PDB 1bn8
Related UniProtKB P39116
[3]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 7896002
Journal FASEB J
Year 1995
Volume 9
Pages 335-42
Authors Yoder MD, Jurnak F
Title Protein motifs. 3. The parallel beta helix and other coiled folds.
Related PDB 2pec
Related UniProtKB
[4]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 12228363
Journal Plant Physiol
Year 1995
Volume 107
Pages 349-364
Authors Yoder MD, Jurnak F
Title The Refined Three-Dimensional Structure of Pectate Lyase C from Erwinia chrysanthemi at 2.2 Angstrom Resolution (Implications for an Enzymatic Mechanism).
Related PDB 1plu
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 8870663
Journal Biochem J
Year 1996
Volume 319
Pages 159-64
Authors Rao MN, Kembhavi AA, Pant A
Title Role of lysine, tryptophan and calcium in the beta-elimination activity of a low-molecular-mass pectate lyase from Fusarium moniliformae.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS)
Medline ID
PubMed ID
Journal Plant Physiol
Year 1996
Volume 111
Pages 73-92
Authors Lietzke SE, Scavetta RD, Yoder MD, Jurnak FA
Title The refined three-dimensional structure of pectate lyase E from Erwinia chrysanthemi at 2.2-A resolution.
Related PDB 1air
Related UniProtKB P11073
[7]
Resource
Comments
Medline ID
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
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 10368179
Journal Plant Cell
Year 1999
Volume 11
Pages 1081-92
Authors Scavetta RD, Herron SR, Hotchkiss AT, Kita N, Keen NT, Benen JA, Kester HC, Visser J, Jurnak F
Title Structure of a plant cell wall fragment complexed to pectate lyase C.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 11123920
Journal Biochemistry
Year 2000
Volume 39
Pages 15932-43
Authors Kamen DE, Griko Y, Woody RW
Title The stability, structural organization, and denaturation of pectate lyase C, a parallel beta-helix protein.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 10922032
Journal Proc Natl Acad Sci U S A
Year 2000
Volume 97
Pages 8762-9
Authors Herron SR, Benen JA, Scavetta RD, Visser J, Jurnak F
Title Structure and function of pectic enzymes: virulence factors of plant pathogens.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 11717490
Journal Acta Crystallogr D Biol Crystallogr
Year 2001
Volume 57
Pages 1786-92
Authors Akita M, Suzuki A, Kobayashi T, Ito S, Yamane T
Title The first structure of pectate lyase belonging to polysaccharide lyase family 3.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 11256961
Journal Biochem J
Year 2001
Volume 355
Pages 167-77
Authors McKie VA, Vincken JP, Voragen AG, van den Broek LA, Stimson E, Gilbert HJ
Title A new family of rhamnogalacturonan lyases contains an enzyme that binds to cellulose.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 12037303
Journal Acta Crystallogr D Biol Crystallogr
Year 2002
Volume 58
Pages 1008-15
Authors Thomas LM, Doan CN, Oliver RL, Yoder MD
Title Structure of pectate lyase A: comparison to other isoforms.
Related PDB 1jrg 1jta
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 11926835
Journal Biochemistry
Year 2002
Volume 41
Pages 4724-32
Authors Kamen DE, Woody RW
Title Identification of proline residues responsible for the slow folding kinetics in pectate lyase C by mutagenesis.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 11926834
Journal Biochemistry
Year 2002
Volume 41
Pages 4713-23
Authors Kamen DE, Woody RW
Title Folding kinetics of the protein pectate lyase C reveal fast-forming intermediates and slow proline isomerization.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 12479401
Journal Biochim Biophys Acta
Year 2002
Volume 1599
Pages 9-20
Authors Hurlbert JC, Preston JF 2nd
Title Differences in the solution structures of the parallel beta-helical pectate lyases as determined by limited proteolysis.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 11852237
Journal Trends Biochem Sci
Year 2002
Volume 27
Pages 59-62
Authors Ciccarelli FD, Copley RR, Doerks T, Russell RB, Bork P
Title CASH--a beta-helix domain widespread among carbohydrate-binding proteins.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 12540845
Journal J Biol Chem
Year 2003
Volume 278
Pages 12271-7
Authors Herron SR, Scavetta RD, Garrett M, Legner M, Jurnak F
Title Characterization and implications of Ca2+ binding to pectate lyase C.
Related PDB 1o88 1o8d 1o8e 1o8f 1o8g 1o8h 1o8i 1o8j 1o8k 1o8l 1o8m
Related UniProtKB

Comments
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]).

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