EzCatDB: S00546
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DB codeS00546
RLCP classification5.20.1710000.530 : Elimination
CATH domainDomain 12.160.20.10 : Pectate Lyase C-likeCatalytic domain
E.C.4.2.2.2

CATH domainRelated DB codes (homologues)
2.160.20.10 : Pectate Lyase C-likeS00168,S00171,S00837,S00170,S00169,D00803

Enzyme Name
UniProtKBKEGG

P39116P0C1A2
Protein namePectate lyasePectate lyase Apectate 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
SynonymsPL
EC 4.2.2.2
EC 4.2.2.2
RefSeqNP_388637.1 (Protein)
NC_000964.3 (DNA/RNA sequence)

PfamPF00544 (Pec_lyase_C)
[Graphical view]
PF00544 (Pec_lyase_C)
[Graphical view]
CAZyPL1 (Polysaccharide Lyase Family)
PL1 (Polysaccharide Lyase Family)

KEGG pathways
MAP codePathways
MAP00040Pentose and glucuronate interconversions

UniProtKB:Accession NumberP39116P0C1A2
Entry namePEL_BACSUPELA_ERWCH
ActivityEliminative cleavage of (1->4)-alpha-D- galacturonan to give oligosaccharides with 4-deoxy-alpha-D-galact- 4-enuronosyl groups at their non-reducing ends.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.
SubunitMonomer.
Subcellular locationSecreted.Secreted.
CofactorBinds 1 calcium ion per subunit.Binds 1 calcium ion per subunit.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00076C00470C06118C00470
CompoundCalciumPectate4-(4-Deoxy-alpha-D-gluc-4-enuronosyl)-D-galacturonatePectate
Typedivalent metal (Ca2+, Mg2+)carboxyl group,polysaccharidecarboxyl group,polysaccharidecarboxyl group,polysaccharide
ChEBI29108



PubChem271
24892720
440470
24892720
            
1bn8ABound:_CAUnboundUnboundUnbound
2bspABound:_CAUnboundUnboundUnbound
1jrgAUnboundUnboundUnboundUnbound
1jrgBUnboundUnboundUnboundUnbound
1jtaAUnboundUnboundUnboundUnbound

Active-site residues
resource
see S00169
pdbCatalytic residuesCofactor-binding residuescomment
           
1bn8ALYS 247;ARG 279
ASP 184;ASP 223;ASP 227(Calcium binding)
 
2bspALYS 247;       
ASP 184;ASP 223;ASP 227(Calcium binding)
mutant R279K
1jrgALYS 208;ARG 241
ASP 144;ASP 184;ASP 188(Calcium binding)
 
1jrgBLYS 208;ARG 241
ASP 144;ASP 184;ASP 188(Calcium binding)
 
1jtaALYS 208;ARG 241
ASP 144;ASP 184;ASP 188(Calcium binding)
 

References for Catalytic Mechanism
ReferencesSectionsNo. 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]
CommentsX-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
Medline ID93276270
PubMed ID8502994
JournalScience
Year1993
Volume260
Pages1503-7
AuthorsYoder MD, Keen NT, Jurnak F
TitleNew domain motif: the structure of pectate lyase C, a secreted plant virulence factor.
Related UniProtKBP11073
[2]
CommentsX-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
Medline ID95360717
PubMed ID7634076
JournalNat Struct Biol
Year1994
Volume1
Pages717-23
AuthorsPickersgill R, Jenkins J, Harris G, Nasser W, Robert-Baudouy J
TitleThe structure of Bacillus subtilis pectate lyase in complex with calcium.
Related PDB1bn8
Related UniProtKBP39116
[3]
CommentsX-ray crystallography
PubMed ID7896002
JournalFASEB J
Year1995
Volume9
Pages335-42
AuthorsYoder MD, Jurnak F
TitleProtein motifs. 3. The parallel beta helix and other coiled folds.
Related PDB2pec
[4]
CommentsX-ray crystallography
PubMed ID12228363
JournalPlant Physiol
Year1995
Volume107
Pages349-364
AuthorsYoder MD, Jurnak F
TitleThe Refined Three-Dimensional Structure of Pectate Lyase C from Erwinia chrysanthemi at 2.2 Angstrom Resolution (Implications for an Enzymatic Mechanism).
Related PDB1plu
[5]
PubMed ID8870663
JournalBiochem J
Year1996
Volume319
Pages159-64
AuthorsRao MN, Kembhavi AA, Pant A
TitleRole of lysine, tryptophan and calcium in the beta-elimination activity of a low-molecular-mass pectate lyase from Fusarium moniliformae.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS)
JournalPlant Physiol
Year1996
Volume111
Pages73-92
AuthorsLietzke SE, Scavetta RD, Yoder MD, Jurnak FA
TitleThe refined three-dimensional structure of pectate lyase E from Erwinia chrysanthemi at 2.2-A resolution.
Related PDB1air
Related UniProtKBP11073
[7]
PubMed ID9195887
JournalStructure
Year1997
Volume5
Pages677-89
AuthorsMayans O, Scott M, Connerton I, Gravesen T, Benen J, Visser J, Pickersgill R, Jenkins J
TitleTwo 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.
[8]
PubMed ID10368179
JournalPlant Cell
Year1999
Volume11
Pages1081-92
AuthorsScavetta RD, Herron SR, Hotchkiss AT, Kita N, Keen NT, Benen JA, Kester HC, Visser J, Jurnak F
TitleStructure of a plant cell wall fragment complexed to pectate lyase C.
[9]
PubMed ID11123920
JournalBiochemistry
Year2000
Volume39
Pages15932-43
AuthorsKamen DE, Griko Y, Woody RW
TitleThe stability, structural organization, and denaturation of pectate lyase C, a parallel beta-helix protein.
[10]
PubMed ID10922032
JournalProc Natl Acad Sci U S A
Year2000
Volume97
Pages8762-9
AuthorsHerron SR, Benen JA, Scavetta RD, Visser J, Jurnak F
TitleStructure and function of pectic enzymes: virulence factors of plant pathogens.
[11]
PubMed ID11717490
JournalActa Crystallogr D Biol Crystallogr
Year2001
Volume57
Pages1786-92
AuthorsAkita M, Suzuki A, Kobayashi T, Ito S, Yamane T
TitleThe first structure of pectate lyase belonging to polysaccharide lyase family 3.
[12]
PubMed ID11256961
JournalBiochem J
Year2001
Volume355
Pages167-77
AuthorsMcKie VA, Vincken JP, Voragen AG, van den Broek LA, Stimson E, Gilbert HJ
TitleA new family of rhamnogalacturonan lyases contains an enzyme that binds to cellulose.
[13]
PubMed ID12037303
JournalActa Crystallogr D Biol Crystallogr
Year2002
Volume58
Pages1008-15
AuthorsThomas LM, Doan CN, Oliver RL, Yoder MD
TitleStructure of pectate lyase A: comparison to other isoforms.
Related PDB1jrg,1jta
[14]
PubMed ID11926835
JournalBiochemistry
Year2002
Volume41
Pages4724-32
AuthorsKamen DE, Woody RW
TitleIdentification of proline residues responsible for the slow folding kinetics in pectate lyase C by mutagenesis.
[15]
PubMed ID11926834
JournalBiochemistry
Year2002
Volume41
Pages4713-23
AuthorsKamen DE, Woody RW
TitleFolding kinetics of the protein pectate lyase C reveal fast-forming intermediates and slow proline isomerization.
[16]
PubMed ID12479401
JournalBiochim Biophys Acta
Year2002
Volume1599
Pages9-20
AuthorsHurlbert JC, Preston JF 2nd
TitleDifferences in the solution structures of the parallel beta-helical pectate lyases as determined by limited proteolysis.
[17]
PubMed ID11852237
JournalTrends Biochem Sci
Year2002
Volume27
Pages59-62
AuthorsCiccarelli FD, Copley RR, Doerks T, Russell RB, Bork P
TitleCASH--a beta-helix domain widespread among carbohydrate-binding proteins.
[18]
PubMed ID12540845
JournalJ Biol Chem
Year2003
Volume278
Pages12271-7
AuthorsHerron SR, Scavetta RD, Garrett M, Legner M, Jurnak F
TitleCharacterization and implications of Ca2+ binding to pectate lyase C.
Related PDB1o88,1o8d,1o8e,1o8f,1o8g,1o8h,1o8i,1o8j,1o8k,1o8l,1o8m

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]).

createdupdated
2004-04-042009-02-26


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