EzCatDB: D00062
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DB codeD00062
CATH domainDomain 11.10.520.10 : Peroxidase; domain 1Catalytic domain
Domain 21.10.420.10 : Peroxidase; domain 2Catalytic domain
E.C.1.11.1.14

CATH domainRelated DB codes (homologues)
1.10.420.10 : Peroxidase; domain 2D00060,D00061
1.10.520.10 : Peroxidase; domain 1D00060,D00061

Enzyme Name
UniProtKBKEGG

P06181P49012
Protein nameLigninase H8Ligninase LG2lignin peroxidase
diarylpropane oxygenase
ligninase I
diarylpropane peroxidase
LiP
diarylpropane:oxygen,hydrogen-peroxide oxidoreductase(C-C-bond-cleaving)
SynonymsEC 1.11.1.14
Diarylpropane peroxidase
Lignin peroxidase
EC 1.11.1.14
Diarylpropane peroxidase
Lignin peroxidase
PfamPF11895 (DUF3415)
PF00141 (peroxidase)
[Graphical view]
PF11895 (DUF3415)
PF00141 (peroxidase)
[Graphical view]


UniProtKB:Accession NumberP06181P49012
Entry nameLIG8_PHACHLIG2_PHACH
Activity1,2-bis(3,4-dimethoxyphenyl)propane-1,3-diol + H(2)O(2) = 3,4-dimethoxybenzaldehyde + 1-(3,4- dimethoxyphenyl)ethane-1,2-diol + H(2)O.1,2-bis(3,4-dimethoxyphenyl)propane-1,3-diol + H(2)O(2) = 3,4-dimethoxybenzaldehyde + 1-(3,4- dimethoxyphenyl)ethane-1,2-diol + H(2)O.
Subunit

Subcellular location

CofactorBinds 2 calcium ions per subunit.,Binds 1 heme B (iron-protoporphyrin IX) group per subunit.Binds 2 calcium ions per subunit.,Binds 1 heme B (iron-protoporphyrin IX) group per subunit.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00032C00076C04597C00027C02201C04355C00001
CompoundHemeCalcium1,2-Bis(3,4-dimethoxyphenyl)propane-1,3-diolH2O2Veratraldehyde1-(3,4-Dimethylphenyl)ethane-1,2-diolH2O
Typearomatic ring (with nitrogen atoms),carboxyl group,heavy metaldivalent metal (Ca2+, Mg2+)aromatic ring (only carbon atom),carbohydrateothersaromatic ring (only carbon atom),carbohydratearomatic ring (only carbon atom),carbohydrateH2O
ChEBI17627
26355
29108
27670
16240
17098

15377
PubChem
271
440402
784
22326046
8419

962
22247451
               
1b80A01UnboundBound:_CAUnboundUnboundUnboundUnboundBound:HOH 362
1b80B01UnboundBound:_CAUnboundUnboundUnboundUnboundBound:HOH 361
1b82A01UnboundBound:_CAUnboundUnboundUnboundUnboundBound:HOH 362
1b82B01UnboundBound:_CAUnboundUnboundUnboundUnboundBound:HOH 361
1b85A01UnboundBound:_CAUnboundUnboundUnboundUnboundBound:HOH 362
1b85B01UnboundBound:_CAUnboundUnboundUnboundUnboundBound:HOH 361
1lgaA01UnboundBound:_CAUnboundUnboundUnboundUnboundBound:HOH 99
1lgaB01UnboundBound:_CAUnboundUnboundUnboundUnboundBound:HOH 184
1llpA01UnboundBound:_CAUnboundBound:HOH 398-HOH 399UnboundUnboundUnbound
1b80A02Bound:HEMBound:_CAUnboundUnboundUnboundUnboundUnbound
1b80B02Bound:HEMBound:_CAUnboundUnboundUnboundUnboundUnbound
1b82A02Bound:HEMBound:_CAUnboundUnboundUnboundUnboundUnbound
1b82B02Bound:HEMBound:_CAUnboundUnboundUnboundUnboundUnbound
1b85A02Bound:HEMBound:_CAUnboundUnboundUnboundUnboundUnbound
1b85B02Bound:HEMBound:_CAUnboundUnboundUnboundUnboundUnbound
1lgaA02Bound:HEMBound:_CAUnboundUnboundUnboundUnboundUnbound
1lgaB02Bound:HEMBound:_CAUnboundUnboundUnboundUnboundUnbound
1llpA02Bound:HEMBound:_CAUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P06181 & literature [16], [19]
pdbCatalytic residuesCofactor-binding residuesModified residuescomment
            
1b80A01ARG 43;HIS 47
ASP 48;GLY 66;ASP 68;SER 70(Calcium-1 binding)
 
 
1b80B01ARG 43;HIS 47
ASP 48;GLY 66;ASP 68;SER 70(Calcium-1 binding)
 
 
1b82A01ARG 43;HIS 47
ASP 48;GLY 66;ASP 68;SER 70(Calcium-1 binding)
 
 
1b82B01ARG 43;HIS 47
ASP 48;GLY 66;ASP 68;SER 70(Calcium-1 binding)
 
 
1b85A01ARG 43;HIS 47
ASP 48;GLY 66;ASP 68;SER 70(Calcium-1 binding)
 
 
1b85B01ARG 43;HIS 47
ASP 48;GLY 66;ASP 68;SER 70(Calcium-1 binding)
 
 
1lgaA01ARG 43;HIS 47
ASP 48;GLY 66;ASP 68;SER 70(Calcium-1 binding)
 
 
1lgaB01ARG 43;HIS 47
ASP 48;GLY 66;ASP 68;SER 70(Calcium-1 binding)
 
 
1llpA01ARG 43;HIS 47
ASP 48;GLY 66;ASP 68;SER 70(Calcium-1 binding)
 
 
1b80A02 
HIS 176(Fe binding);SER 177;ASP 194;THR 196;ILE 199;ASP 201(Calcium-2 binding)
HTR 171
HTR, hydroxylated Trp
1b80B02 
HIS 176(Fe binding);SER 177;ASP 194;THR 196;ILE 199;ASP 201(Calcium-2 binding)
HTR 171
HTR, hydroxylated Trp
1b82A02 
HIS 176(Fe binding);SER 177;ASP 194;THR 196;ILE 199;ASP 201(Calcium-2 binding)
TRP 171
 
1b82B02 
HIS 176(Fe binding);SER 177;ASP 194;THR 196;ILE 199;ASP 201(Calcium-2 binding)
TRP 171
 
1b85A02 
HIS 176(Fe binding);SER 177;ASP 194;THR 196;ILE 199;ASP 201(Calcium-2 binding)
       
mutant W171F
1b85B02 
HIS 176(Fe binding);SER 177;ASP 194;THR 196;ILE 199;ASP 201(Calcium-2 binding)
       
mutant W171F
1lgaA02 
HIS 176(Fe binding);SER 177;ASP 194;THR 196;ILE 199;ASP 201(Calcium-2 binding)
TRP 171
 
1lgaB02 
HIS 176(Fe binding);SER 177;ASP 194;THR 196;ILE 199;ASP 201(Calcium-2 binding)
TRP 171
 
1llpA02 
HIS 176(Fe binding);SER 177;ASP 194;THR 196;ILE 199;ASP 201(Calcium-2 binding)
TRP 171
HYD, hydroxylated W171

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]p.4435-4436
[7]Fig.4, p.513-
[13]Fig.8, p.5118
[14]Scheme 1, Scheme 2, p.8836-8837
[15]

[16]SCHEME 1, p.89-91
[17]Scheme 2, p.819-823
[18]p.1993-1994
[20]p.858-859

references
[1]
PubMed ID1336201
JournalProtein Eng
Year1992
Volume5
Pages679-91
AuthorsDu P, Collins JR, Loew GH
TitleHomology modeling of a heme protein, lignin peroxidase, from the crystal structure of cytochrome c peroxidase.
[2]
PubMed ID8417967
JournalFEBS Lett
Year1993
Volume315
Pages119-24
AuthorsPiontek K, Glumoff T, Winterhalter K
TitleLow pH crystal structure of glycosylated lignin peroxidase from Phanerochaete chrysosporium at 2.5 A resolution.
[3]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS)
Medline ID93179455
PubMed ID8440725
JournalJ Biol Chem
Year1993
Volume268
Pages4429-40
AuthorsPoulos TL, Edwards SL, Wariishi H, Gold MH
TitleCrystallographic refinement of lignin peroxidase at 2 A.
Related PDB1lga
Related UniProtKBP06181
[4]
CommentsX-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS)
Medline ID21519514
PubMed ID11607355
JournalProc Natl Acad Sci U S A
Year1993
Volume90
Pages750-4
AuthorsEdwards SL, Raag R, Wariishi H, Gold MH, Poulos TL
TitleCrystal structure of lignin peroxidase.
Related UniProtKBP06181
[5]
PubMed ID8386362
JournalProtein Eng
Year1993
Volume6
Pages177-82
AuthorsHoffren AM, Saloheimo M, Thomas P, Overington JP, Johnson MS, Knowles JK, Blundell TL
TitleModelling of the lignin peroxidase LIII of Phlebia radiata: use of a sequence template generated from a 3-D structure.
[6]
PubMed ID7918458
JournalBiochemistry
Year1994
Volume33
Pages12356-66
AuthorsBanci L, Carloni P, Savellini GG
TitleMolecular dynamics studies on peroxidases: a structural model for horseradish peroxidase and a substrate adduct.
[7]
PubMed ID8000874
JournalBioorg Med Chem
Year1994
Volume2
Pages509-19
AuthorsSchoemaker HE, Lundell TK, Floris R, Glumoff T, Winterhalter KH, Piontek K
TitleDo carbohydrates play a role in the lignin peroxidase cycle? Redox catalysis in the endergonic region of the driving force.
[8]
PubMed ID7806497
JournalJ Biol Chem
Year1994
Volume269
Pages32759-67
AuthorsSundaramoorthy M, Kishi K, Gold MH, Poulos TL
TitleThe crystal structure of manganese peroxidase from Phanerochaete chrysosporium at 2.06-A resolution.
[9]
PubMed ID8289254
JournalJ Mol Biol
Year1994
Volume235
Pages331-44
AuthorsKunishima N, Fukuyama K, Matsubara H, Hatanaka H, Shibano Y, Amachi T
TitleCrystal structure of the fungal peroxidase from Arthromyces ramosus at 1.9 A resolution. Structural comparisons with the lignin and cytochrome c peroxidases.
[10]
PubMed ID8182752
JournalJ Mol Biol
Year1994
Volume238
Pages845-8
AuthorsSundaramoorthy M, Kishi K, Gold MH, Poulos TL
TitlePreliminary crystallographic analysis of manganese peroxidase from Phanerochaete chrysosporium.
[11]
PubMed ID7731950
JournalProteins
Year1994
Volume20
Pages312-9
AuthorsJohnson F, Loew GH, Du P
TitleHomology models of two isozymes of manganese peroxidase: prediction of a Mn(II) binding site.
[12]
PubMed ID7922023
JournalStructure
Year1994
Volume2
Pages461-4
AuthorsLi H, Poulos TL
TitleStructural variation in heme enzymes: a comparative analysis of peroxidase and P450 crystal structures.
[13]
PubMed ID9136871
JournalBiochemistry
Year1997
Volume36
Pages5113-9
AuthorsNie G, Aust SD
TitleSpectral changes of lignin peroxidase during reversible inactivation.
[14]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS)
Medline ID98301364
PubMed ID9636023
JournalBiochemistry
Year1998
Volume37
Pages8832-8
AuthorsBlodig W, Doyle WA, Smith AT, Winterhalter K, Choinowski T, Piontek K
TitleAutocatalytic formation of a hydroxy group at C beta of trp171 in lignin peroxidase.
Related UniProtKBP06181
[15]
PubMed ID9790672
JournalBiochemistry
Year1998
Volume37
Pages15097-105
AuthorsDoyle WA, Blodig W, Veitch NC, Piontek K, Smith AT
TitleTwo substrate interaction sites in lignin peroxidase revealed by site-directed mutagenesis.
[16]
PubMed ID10496980
JournalArch Biochem Biophys
Year1999
Volume370
Pages86-92
AuthorsBlodig W, Smith AT, Winterhalter K, Piontek K
TitleEvidence from spin-trapping for a transient radical on tryptophan residue 171 of lignin peroxidase.
[17]
PubMed ID10024453
JournalJ Mol Biol
Year1999
Volume286
Pages809-27
AuthorsChoinowski T, Blodig W, Winterhalter KH, Piontek K
TitleThe crystal structure of lignin peroxidase at 1.70 A resolution reveals a hydroxy group on the cbeta of tryptophan 171: a novel radical site formed during the redox cycle.
Related PDB1llp
[18]
PubMed ID10051582
JournalProc Natl Acad Sci U S A
Year1999
Volume96
Pages1989-94
AuthorsJohjima T, Itoh N, Kabuto M, Tokimura F, Nakagawa T, Wariishi H, Tanaka H
TitleDirect interaction of lignin and lignin peroxidase from Phanerochaete chrysosporium.
[19]
PubMed ID10713531
JournalActa Crystallogr D Biol Crystallogr
Year2000
Volume56
Pages372-5
AuthorsMirza O, Henriksen A, Ostergaard L, Welinder KG, Gajhede M
TitleArabidopsis thaliana peroxidase N: structure of a novel neutral peroxidase.
[20]
CommentsX-ray crystallography
PubMed ID11162097
JournalJ Mol Biol
Year2001
Volume305
Pages851-61
AuthorsBlodig W, Smith AT, Doyle WA, Piontek K
TitleCrystal structures of pristine and oxidatively processed lignin peroxidase expressed in Escherichia coli and of the W171F variant that eliminates the redox active tryptophan 171. Implications for the reaction mechanism.
Related PDB1b80,1b82,1b85

comments
Trp171 is rather distant from the heme iron (more than 10 angstrom) at the active site. However, Trp171 seems to be involved in catalysis, as it forms an indole radical by an electron transfer from substrates to the heme cofactor (see [16], [17]).

createdupdated
2004-10-182009-02-26


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