Information on EC 4.2.2.2 - pectate lyase

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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria

EC NUMBER
COMMENTARY
4.2.2.2
-
RECOMMENDED NAME
GeneOntology No.
pectate lyase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
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
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
elimination
-
-
-
-
PATHWAY
KEGG Link
MetaCyc Link
Pentose and glucuronate interconversions
-
SYSTEMATIC NAME
IUBMB Comments
(1->4)-alpha-D-galacturonan lyase
Favours pectate, the anion, over pectin, the methyl ester (which is the preferred substrate of EC 4.2.2.10, pectin lyase).
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
alkaline pectate lyase
-
-
alkaline pectate lyase
Bacillus subtilis WSHB04-02
-
-
-
alkaline polygalacturonate lyase
-
-
alpha-1,4-D-endopolygalacturonic acid lyase
-
-
-
-
DKS1 pectate lyase
B2ZFM0
-
DKS1 pectate lyase
Bacillus pumilus DKS1
B2ZFM0
-
-
EC 4.2.99.3
-
-
-
-
endo-alpha-1,4-polygalacturonic acid lyase
-
-
-
-
endo-polygalacturonate trans-eliminase
-
-
endo-polygalacturonate trans-eliminase
Bacillus sp. TS 47
-
-
-
endogalacturonate transeliminase
-
-
-
-
endopectin methyltranseliminase
-
-
-
-
Gr-PEL-2
Q53EK1
-
Gr-PEL2
Q53EK1
-
Hb-PEL-1
B3SXR0
-
Hspel1
A3F5C0
-
Hspel2
A3F5B9
-
lyase, pectate
-
-
-
-
neutral-alkaline pectate lyase
-
-
NPLase
-
-
-
PATE
Pectobacterium carotovorum IFO3830
-
-
-
PCPEL2
G2XKV7
-
pectate lyase
-
-
pectate lyase
-
-
pectate lyase
Q9XDT2
-
pectate lyase
Q9XDT2
-
-
pectate lyase
P39116
-
pectate lyase
-
-
pectate lyase
-
-
pectate lyase
O50325
-
pectate lyase
-
-
pectate lyase
-
-
pectate lyase
B3SXR0
-
pectate lyase
-
-
pectate lyase
Q93J76, Q93RU6
-
pectate lyase
Q9M505
-
pectate lyase
Q8P6Z9, Q8PCR8
-
pectate lyase 10A
-
-
pectate lyase 2
-
-
pectate lyase 2
C8CMI5
-
pectate lyase 2
Q53EK1
-
pectate lyase 2
C8CML7
-
pectate lyase 9A
Q76EC9
-
pectate lyase 9A
Clostridium stercorarium F-9
Q76EC9
-
-
pectate lyase A
-
-
pectate lyase A
Q00645
-
pectate lyase A
Emericella nidulans GR5
Q00645
-
-
pectate lyase A
-
-
pectate lyase A
Erwinia chrysanthemi EC16
-
;
-
pectate lyase B
-
-
pectate lyase B
Erwinia chrysanthemi EC16
-
-
-
pectate lyase C
-
-
pectate lyase C
-
-
pectate lyase C
Erwinia chrysanthemi EC16
-
-
-
pectate lyase C
-
-
pectate lyase E
Q9XDT2
-
pectate lyase E
Q9XDT2
-
-
pectate lyase E
-
-
pectate lyase L
-
-
pectate lyase Pel10A
-
-
pectate lyase Pel9A
-
-
pectate lyase PL 47
-
-
pectate lyase PL 47
Bacillus sp. TS 47
-
-
-
pectate transeliminase
-
-
-
-
pectate transeliminase
Q9XDT1
-
pectate transeliminase
Q9XDT2
-
pectate transeliminase
Q9XDT1, Q9XDT2
-
-
pectic acid lyase
-
-
-
-
pectic acid transeliminase
-
-
-
-
pectic lyase
-
-
-
-
pectic lyase
-
-
Pel
Q9XDT1
-
Pel
-, Q9XDT1
-
-
Pel
Bacillus sp. P4-N, Bacillus sp. TS 47
-
-
-
Pel
Bacillus subtilis 168, Bacillus subtilis SO113
-
-
-
Pel
Q4JLV6
-
Pel I
Aspergillus niger MIUG 16
-
-
-
Pel II
Aspergillus niger MIUG 16
-
-
-
Pel III
Aspergillus niger MIUG 16
-
-
-
Pel SWU
B1B6T1
-
Pel SWU
B1B6T1
-
-
Pel-15
-
-
Pel-15
Q9RHW0
-
Pel-15
-, Q9RHW0
-
-
Pel-15
Bacillus sp. P4-N, Bacillus sp. TS 47
-
-
-
Pel-15E
Q9XDT2
-
Pel-15E
Q9XDT2
-
-
Pel-15H
Q9XDT1
-
Pel-15H
Q9XDT1
-
-
pel-2
C8CMI5
-
pel-2
C8CML7
-
Pel-22
D8X181
-
Pel-22
Bacillus pumilus BS22
D8X181
-
-
Pel-66
D8X180
-
Pel-66
Bacillus subtilis BS66
D8X180
-
-
Pel-BL11
Paenibacillus campinasensis BL11
D8WN00
-
-
Pel1
Penicillium occitanis CT1
-
-
-
PelA
Bacillus pumilus BK2
-
-
-
PelA
-
-
PelA
D0VP31
-
PelA
D0VP31
-
-
PelA
Bacillus sp. P4-N, Bacillus sp. TS 47
-
-
-
PelA
Bacillus subtilis 168, Bacillus subtilis SO113
-
-
-
PelA
Q00645
-
PelA
Emericella nidulans GR5
Q00645
-
-
PelA
-
isoform
PelA
Erwinia chrysanthemi EC16
-
-
-
PelA
Paenibacillus amylolyticus 27C64
D3JTC1
-
-
PelA
Streptomyces thermocarboxydus B1
C6L867
-
-
PelB
P04959
isoform
PelB
Paenibacillus amylolyticus 27C64
D3JTC2
-
-
pelC
P11073
isoform
PelD
P18209
isoform
PelE
-
isoform
PGA lyase
-
-
-
-
PL
Bacillus sp. TS 47
-
-
-
PL I
C6L867
an endo-acting family 3 pectate lyase
PL I
Streptomyces thermocarboxydus B1
C6L867
an endo-acting family 3 pectate lyase
-
Pla
-
-
-
-
PLB
-
-
-
-
PLB
Erwinia chrysanthemi EC16
-
-
-
PLC
-
-
-
-
PLC
Erwinia chrysanthemi EC16
-
-
-
PLE
Erwinia chrysanthemi EC16
-
-
-
poly(1,4-alpha-D-galacturonide) lyase
-
-
-
-
poly-galacturonic acid trans-eliminase
-
-
poly-galacturonic acid trans-eliminase
Pectobacterium carotovorum IFO3830
-
-
-
polygalacturonate lyase
-
-
-
-
polygalacturonic acid lyase
-
-
-
-
polygalacturonic transeliminase
-
-
-
-
PPase-N
-
-
-
-
ScPL NP_626147
Q93RU6
-
ScPL NP_627050
Q93J76
-
XcPL NP_636037
Q8PCR8
-
XcPL NP_638163
Q8P6Z9
-
additional information
B2ZFM0
the enzyme belongs to the polysaccharide family 1
additional information
Bacillus pumilus DKS1
B2ZFM0
the enzyme belongs to the polysaccharide family 1
-
CAS REGISTRY NUMBER
COMMENTARY
9015-75-2
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
L. Heynh. ecotype Columbia
-
-
Manually annotated by BRENDA team
strain MIUG 16
-
-
Manually annotated by BRENDA team
Aspergillus niger MIUG 16
strain MIUG 16
-
-
Manually annotated by BRENDA team
gene pelB
UniProt
Manually annotated by BRENDA team
isolated from fermenting cocoa beans
UniProt
Manually annotated by BRENDA team
strain DKS1
-
-
Manually annotated by BRENDA team
Bacillus pumilus BK2
strain BK2
-
-
Manually annotated by BRENDA team
Bacillus pumilus BS22
isolated from fermenting cocoa beans
UniProt
Manually annotated by BRENDA team
Bacillus pumilus DKS1
gene pelB
UniProt
Manually annotated by BRENDA team
Bacillus pumilus DKS1
strain DKS1
-
-
Manually annotated by BRENDA team
an endo-pectate lyase produced by a genetically modified Bacillus sp. is used
-
-
Manually annotated by BRENDA team
BP-23
SwissProt
Manually annotated by BRENDA team
KSM-P15
Swissprot
Manually annotated by BRENDA team
strain BP-7
-
-
Manually annotated by BRENDA team
strain KSM-P15
-
-
Manually annotated by BRENDA team
strain KSM-P15
SwissProt
Manually annotated by BRENDA team
strain KSM-P15
Swissprot
Manually annotated by BRENDA team
strain KSM-P15; strain P4-N; strain TS 47
-
-
Manually annotated by BRENDA team
strain KSM-P7
-
-
Manually annotated by BRENDA team
strain N16-5
UniProt
Manually annotated by BRENDA team
strain RN1
UniProt
Manually annotated by BRENDA team
Bacillus sp. BP-23
BP-23
SwissProt
Manually annotated by BRENDA team
strain BP-7
-
-
Manually annotated by BRENDA team
KSM-P15
Swissprot
Manually annotated by BRENDA team
strain KSM-P15
SwissProt
Manually annotated by BRENDA team
strain KSM-P15
Swissprot
Manually annotated by BRENDA team
Bacillus sp. KSM-P7
strain KSM-P7
-
-
Manually annotated by BRENDA team
strain N16-5
UniProt
Manually annotated by BRENDA team
Bacillus sp. P4-N
strain P4-N
-
-
Manually annotated by BRENDA team
Bacillus sp. RK9
RK9
-
-
Manually annotated by BRENDA team
strain RN1
UniProt
Manually annotated by BRENDA team
Bacillus sp. TS 47
strain TS 47
-
-
Manually annotated by BRENDA team
Bacillus sp. TS 47
TS 47
-
-
Manually annotated by BRENDA team
IFO 3134
-
-
Manually annotated by BRENDA team
isolated from fermenting cocoa beans
UniProt
Manually annotated by BRENDA team
strain 168; strain SO113
-
-
Manually annotated by BRENDA team
strain WSHB04-02
-
-
Manually annotated by BRENDA team
Bacillus subtilis 168
strain 168
-
-
Manually annotated by BRENDA team
Bacillus subtilis BS66
isolated from fermenting cocoa beans
UniProt
Manually annotated by BRENDA team
Bacillus subtilis IFO3134
IFO3134
-
-
Manually annotated by BRENDA team
Bacillus subtilis SO113
SO113
-
-
Manually annotated by BRENDA team
Bacillus subtilis SO113
strain SO113
-
-
Manually annotated by BRENDA team
Bacillus subtilis WSHB04-02
strain WSHB04-02
-
-
Manually annotated by BRENDA team
; pectate lyase precursor
SwissProt
Manually annotated by BRENDA team
strain F-9
SwissProt
Manually annotated by BRENDA team
Clostridium stercorarium F-9
strain F-9
SwissProt
Manually annotated by BRENDA team
nine pel genes, pelA to pelE, pelI, pelL, pelX, and pelZ
-
-
Manually annotated by BRENDA team
nine pel genes, pelA to pelE, pelI, pelL, pelX, and pelZ
-
-
Manually annotated by BRENDA team
Erwinia aroidea
-
-
-
Manually annotated by BRENDA team
3937; 5 isoenzymes: PelA, PelB, PelD, PelI and PelL
-
-
Manually annotated by BRENDA team
3937; at least 7 isoenzymes, 5 major isoenzymes, PelA, PelB, PelC, PelD, Pel E and two minor isoenzyme PelL and PelZ
-
-
Manually annotated by BRENDA team
5 isoenzymes: PelA, PelB, PelC, PelD, PelE
-
-
Manually annotated by BRENDA team
at least 4 isoenzymes
-
-
Manually annotated by BRENDA team
isoform PelB
UniProt
Manually annotated by BRENDA team
isoform PelC
UniProt
Manually annotated by BRENDA team
isoform PelD
UniProt
Manually annotated by BRENDA team
Erwinia chrysanthemi 3937
3937
-
-
Manually annotated by BRENDA team
Erwinia chrysanthemi EC16
EC16
-
-
Manually annotated by BRENDA team
cultivar Chandler
-
-
Manually annotated by BRENDA team
f. sp. lycopersici
-
-
Manually annotated by BRENDA team
f. sp. pisi
-
-
Manually annotated by BRENDA team
f. sp. pisi; Nectria haematococca mating type VI; pectate lyase B
-
-
Manually annotated by BRENDA team
f. sp. pisi; Nectria haematococca mating type VI; pectate lyase C
-
-
Manually annotated by BRENDA team
f. sp. pisi; Nectria haematococca mating type VI; pectate lyase D
-
-
Manually annotated by BRENDA team
strain NCIM 1276
-
-
Manually annotated by BRENDA team
Gibberella moniliformis NCIM 1276
strain NCIM 1276
-
-
Manually annotated by BRENDA team
gene pel-2
-
-
Manually annotated by BRENDA team
gene pel-2
UniProt
Manually annotated by BRENDA team
subsp. tabacum, gene pel-2
UniProt
Manually annotated by BRENDA team
variant acc 7235
UniProt
Manually annotated by BRENDA team
strain D32
-
-
Manually annotated by BRENDA team
Lachnospira multipara D32
strain D32
-
-
Manually annotated by BRENDA team
Lysinibacillus fusiformis, isolated from fermenting cocoa beans
UniProt
Manually annotated by BRENDA team
Alpine strain A15; Siberian strain AG25
-
-
Manually annotated by BRENDA team
strain Harichhal
-
-
Manually annotated by BRENDA team
Musa acuminata Harichhal
strain Harichhal
-
-
Manually annotated by BRENDA team
Musa acuminata Nangka
-
-
-
Manually annotated by BRENDA team
PelA; gene pelA
UniProt
Manually annotated by BRENDA team
Paenibacillus amylolyticus 27C64
gene pelB
UniProt
Manually annotated by BRENDA team
Paenibacillus amylolyticus 27C64
PelA; gene pelA
UniProt
Manually annotated by BRENDA team
Paenibacillus campinasensis BL11
-
UniProt
Manually annotated by BRENDA team
strain BP-23
-
-
Manually annotated by BRENDA team
Paenibacillus sp. BP-23
strain BP-23
-
-
Manually annotated by BRENDA team
3 isoenzymes; subsp. atroseptica, 3 isoenzymes; subsp. carotovora
-
-
Manually annotated by BRENDA team
formerly Erwinia aroideae; pectate lyase I and pectate lyase II
-
-
Manually annotated by BRENDA team
isoenzyme PL I and PL II
-
-
Manually annotated by BRENDA team
pectate lyase B; subsp. carotovora
-
-
Manually annotated by BRENDA team
pectate lyase III
-
-
Manually annotated by BRENDA team
subsp. carotovorum
-
-
Manually annotated by BRENDA team
Pectobacterium carotovorum IFO3830
IFO3830
-
-
Manually annotated by BRENDA team
Pectobacterium carotovorum ZT0505
subsp. carotovorum
-
-
Manually annotated by BRENDA team
Penicillium occitanis CT1
-
-
-
Manually annotated by BRENDA team
gene Pcpel2
UniProt
Manually annotated by BRENDA team
pv. glycinea
-
-
Manually annotated by BRENDA team
pv. lachrymans, isoenzyme PelS
-
-
Manually annotated by BRENDA team
strain B1
C6L867
UniProt
Manually annotated by BRENDA team
Streptomyces thermocarboxydus B1
strain B1
C6L867
UniProt
Manually annotated by BRENDA team
nov., pectate lyase a and pectate lyase b
-
-
Manually annotated by BRENDA team
DSM 3109
SwissProt
Manually annotated by BRENDA team
strain MSB8
-
-
Manually annotated by BRENDA team
ATCC 33768
SwissProt
Manually annotated by BRENDA team
ATCC 49397, ATCC 35669 (low activity), and JB580v
SwissProt
Manually annotated by BRENDA team
ACTIVATING COMPOUND
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
cystine
-
25% activation at 1 mM, 73% activation at 5 mM
Tris-HCl buffer
B1B6T1
enzyme activity increases with increasing concentration of the buffer (20 mM to 1 M) and has highest activity at 1 M
Ki VALUE [mM]
Ki VALUE [mM] Maximum
INHIBITOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.0022
-
2-mercaptoethanol
-
-
0.0104
-
dithiothreitol
-
-
PDB
SCOP
CATH
ORGANISM
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Caldicellulosiruptor bescii (strain ATCC BAA-1888 / DSM 6725 / Z-1320)
Caldicellulosiruptor bescii (strain ATCC BAA-1888 / DSM 6725 / Z-1320)
Dickeya dadantii (strain 3937)
Xanthomonas campestris pv. campestris (strain ATCC 33913 / NCPPB 528 / LMG 568)
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
glycoprotein
-, Q9C2Z0
purification of the recombinant enzyme results in identification of two enzyme forms of which one appears to be N-glycosylated and the other appears to be free of N-glycosylation. The two enzyme forms show identical specific activies
glycoprotein
-
-
side-chain modification
-
one putative N-glycosylation site
side-chain modification
-
glycoprotein
side-chain modification
-
neutral sugar content : 2.5% for pectate lyase I and 4.8% for pectate lyase II
glycoprotein
-
Pel1 is 7.7% glycosylated
glycoprotein
Penicillium occitanis CT1
-
Pel1 is 7.7% glycosylated
-
no modification
-
contains no carbohydrate
side-chain modification
-
contains 0.195 mg of glucose equivalents per mg of protein
GENERAL STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
Ca2+, Mn2+ or polygalacturonate increase thermostability
-
complete unfolding in 6 M guanidine-HCl
-
pectate lyase B, C and E are denatured by guanidine hydrochloride with transition midpoint concentrations of 1.3 mM, 1.1 mM and 1.8 mM
-
the enzyme is reversibly unfolded by urea and guanidine-HCl at its optimal pH of 8.5
-
UV-C light blanching (13.8Wm-2UV-C light for 5 min at 4°C) allows to non-thermally increase the enzymatic stability of the surface of fresh-cut fruit and vegetables.
-
enzyme from Alpine strain A15 is stable up to fourfold freezing and thawing
-
enzyme from Siberian strain AG25 is stable up to fourfold freezing and thawing
-
OXIDATION STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
bubbling O2 through the enzyme preparation increases activity 63%
-
37377
EXPRESSION
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
the production of enzyme increases significantly with increasing calcium-alginate concentration and reaches a maximum enzyme yield of 38.5 units/ml at 18 g/l
-
the production of enzyme increases significantly with increasing calcium-alginate concentration and reaches a maximum enzyme yield of 38.5 units/ml at 18 g/l
Bacillus pumilus DKS1
-
-
RpoS downregulates pelD expression of in planta, RpoS negatively regulates pelD promoter activity
-
RpoS downregulates pelD expression of in planta, RpoS negatively regulates pelD promoter activity
-
-
the PEL gene is preferentially expressed in fibers at 10 days-post anthesis
-, Q4JLV6
isolate Phytophthora capsici SD33 shows an approximately 8fold increase of pectate lyase activity grown on pepper extract plus pectin compared with those on pectin alone as carbon source
-
polygalacturonic acid and CaCl2 induce the expression of the pelA1 gene, cAMP receptor protein-like protein and RpfF (an enoyl-CoA hydratase homologue that is required for the synthesis of cis-11-methyl-2-dodecenoic acid) positively regulate pelA1 transcription
-
Renatured/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
after complete unfolding in 6 M guanidine-HCl and removal of the denaturant by dialysis, the enzymatic activity of pelC is regained and is identical to that of freshly purified enzyme. Thermal denaturation is not reversible
-
thermal denaturation at 75°C for 10 min is reversible. The enzyme is reversibly unfolded by urea and guanidine-HCl at its optimal pH of 8.5
-