DB code: D00062

CATH domain 1.10.520.10 : Peroxidase; domain 1 Catalytic domain
1.10.420.10 : Peroxidase; domain 2 Catalytic domain
E.C. 1.11.1.14
CSA
M-CSA
MACiE

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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P06181 Ligninase H8
EC 1.11.1.14
Diarylpropane peroxidase
Lignin peroxidase
PF11895 (DUF3415)
PF00141 (peroxidase)
[Graphical View]
P49012 Ligninase LG2
EC 1.11.1.14
Diarylpropane peroxidase
Lignin peroxidase
PF11895 (DUF3415)
PF00141 (peroxidase)
[Graphical View]

KEGG enzyme name
lignin peroxidase
diarylpropane oxygenase
ligninase I
diarylpropane peroxidase
LiP
diarylpropane:oxygen,hydrogen-peroxide oxidoreductase(C-C-bond-cleaving)

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P49012 LIG2_PHACH 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. Binds 2 calcium ions per subunit. Binds 1 heme B (iron-protoporphyrin IX) group per subunit.
P06181 LIG8_PHACH 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. Binds 2 calcium ions per subunit. Binds 1 heme B (iron-protoporphyrin IX) group per subunit.

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00032 C00076 C04597 C00027 C02201 C04355 C00001
E.C.
Compound Heme Calcium 1,2-Bis(3,4-dimethoxyphenyl)propane-1,3-diol H2O2 Veratraldehyde 1-(3,4-Dimethylphenyl)ethane-1,2-diol H2O
Type aromatic ring (with nitrogen atoms),carboxyl group,heavy metal divalent metal (Ca2+, Mg2+) aromatic ring (only carbon atom),carbohydrate others aromatic ring (only carbon atom),carbohydrate aromatic ring (only carbon atom),carbohydrate H2O
ChEBI 17627
26355
29108
27670
16240
17098
15377
PubChem 271
440402
22326046
784
8419
22247451
962
1b80A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:_CA Unbound Unbound Unbound Unbound Bound:HOH_362
1b80B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:_CA Unbound Unbound Unbound Unbound Bound:HOH_361
1b82A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:_CA Unbound Unbound Unbound Unbound Bound:HOH_362
1b82B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:_CA Unbound Unbound Unbound Unbound Bound:HOH_361
1b85A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:_CA Unbound Unbound Unbound Unbound Bound:HOH_362
1b85B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:_CA Unbound Unbound Unbound Unbound Bound:HOH_361
1lgaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:_CA Unbound Unbound Unbound Unbound Bound:HOH_99
1lgaB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:_CA Unbound Unbound Unbound Unbound Bound:HOH_184
1llpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:_CA Unbound Bound:HOH_398-HOH_399 Unbound Unbound Unbound
1b80A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:HEM Bound:_CA Unbound Unbound Unbound Unbound Unbound
1b80B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:HEM Bound:_CA Unbound Unbound Unbound Unbound Unbound
1b82A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:HEM Bound:_CA Unbound Unbound Unbound Unbound Unbound
1b82B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:HEM Bound:_CA Unbound Unbound Unbound Unbound Unbound
1b85A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:HEM Bound:_CA Unbound Unbound Unbound Unbound Unbound
1b85B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:HEM Bound:_CA Unbound Unbound Unbound Unbound Unbound
1lgaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:HEM Bound:_CA Unbound Unbound Unbound Unbound Unbound
1lgaB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:HEM Bound:_CA Unbound Unbound Unbound Unbound Unbound
1llpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:HEM Bound:_CA Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P06181 & literature [16], [19]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1b80A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 43;HIS 47 ASP 48;GLY 66;ASP 68;SER 70(Calcium-1 binding)
1b80B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 43;HIS 47 ASP 48;GLY 66;ASP 68;SER 70(Calcium-1 binding)
1b82A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 43;HIS 47 ASP 48;GLY 66;ASP 68;SER 70(Calcium-1 binding)
1b82B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 43;HIS 47 ASP 48;GLY 66;ASP 68;SER 70(Calcium-1 binding)
1b85A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 43;HIS 47 ASP 48;GLY 66;ASP 68;SER 70(Calcium-1 binding)
1b85B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 43;HIS 47 ASP 48;GLY 66;ASP 68;SER 70(Calcium-1 binding)
1lgaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 43;HIS 47 ASP 48;GLY 66;ASP 68;SER 70(Calcium-1 binding)
1lgaB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 43;HIS 47 ASP 48;GLY 66;ASP 68;SER 70(Calcium-1 binding)
1llpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 43;HIS 47 ASP 48;GLY 66;ASP 68;SER 70(Calcium-1 binding)
1b80A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 176(Fe binding);SER 177;ASP 194;THR 196;ILE 199;ASP 201(Calcium-2 binding) HTR 171 HTR, hydroxylated Trp
1b80B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 176(Fe binding);SER 177;ASP 194;THR 196;ILE 199;ASP 201(Calcium-2 binding) HTR 171 HTR, hydroxylated Trp
1b82A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 176(Fe binding);SER 177;ASP 194;THR 196;ILE 199;ASP 201(Calcium-2 binding) TRP 171
1b82B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 176(Fe binding);SER 177;ASP 194;THR 196;ILE 199;ASP 201(Calcium-2 binding) TRP 171
1b85A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 176(Fe binding);SER 177;ASP 194;THR 196;ILE 199;ASP 201(Calcium-2 binding) mutant W171F
1b85B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 176(Fe binding);SER 177;ASP 194;THR 196;ILE 199;ASP 201(Calcium-2 binding) mutant W171F
1lgaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 176(Fe binding);SER 177;ASP 194;THR 196;ILE 199;ASP 201(Calcium-2 binding) TRP 171
1lgaB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 176(Fe binding);SER 177;ASP 194;THR 196;ILE 199;ASP 201(Calcium-2 binding) TRP 171
1llpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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
References Sections No. 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]
Resource
Comments
Medline ID
PubMed ID 1336201
Journal Protein Eng
Year 1992
Volume 5
Pages 679-91
Authors Du P, Collins JR, Loew GH
Title Homology modeling of a heme protein, lignin peroxidase, from the crystal structure of cytochrome c peroxidase.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 8417967
Journal FEBS Lett
Year 1993
Volume 315
Pages 119-24
Authors Piontek K, Glumoff T, Winterhalter K
Title Low pH crystal structure of glycosylated lignin peroxidase from Phanerochaete chrysosporium at 2.5 A resolution.
Related PDB
Related UniProtKB
[3]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS)
Medline ID 93179455
PubMed ID 8440725
Journal J Biol Chem
Year 1993
Volume 268
Pages 4429-40
Authors Poulos TL, Edwards SL, Wariishi H, Gold MH
Title Crystallographic refinement of lignin peroxidase at 2 A.
Related PDB 1lga
Related UniProtKB P06181
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS)
Medline ID 21519514
PubMed ID 11607355
Journal Proc Natl Acad Sci U S A
Year 1993
Volume 90
Pages 750-4
Authors Edwards SL, Raag R, Wariishi H, Gold MH, Poulos TL
Title Crystal structure of lignin peroxidase.
Related PDB
Related UniProtKB P06181
[5]
Resource
Comments
Medline ID
PubMed ID 8386362
Journal Protein Eng
Year 1993
Volume 6
Pages 177-82
Authors Hoffren AM, Saloheimo M, Thomas P, Overington JP, Johnson MS, Knowles JK, Blundell TL
Title Modelling of the lignin peroxidase LIII of Phlebia radiata: use of a sequence template generated from a 3-D structure.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 7918458
Journal Biochemistry
Year 1994
Volume 33
Pages 12356-66
Authors Banci L, Carloni P, Savellini GG
Title Molecular dynamics studies on peroxidases: a structural model for horseradish peroxidase and a substrate adduct.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 8000874
Journal Bioorg Med Chem
Year 1994
Volume 2
Pages 509-19
Authors Schoemaker HE, Lundell TK, Floris R, Glumoff T, Winterhalter KH, Piontek K
Title Do carbohydrates play a role in the lignin peroxidase cycle? Redox catalysis in the endergonic region of the driving force.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 7806497
Journal J Biol Chem
Year 1994
Volume 269
Pages 32759-67
Authors Sundaramoorthy M, Kishi K, Gold MH, Poulos TL
Title The crystal structure of manganese peroxidase from Phanerochaete chrysosporium at 2.06-A resolution.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 8289254
Journal J Mol Biol
Year 1994
Volume 235
Pages 331-44
Authors Kunishima N, Fukuyama K, Matsubara H, Hatanaka H, Shibano Y, Amachi T
Title Crystal structure of the fungal peroxidase from Arthromyces ramosus at 1.9 A resolution. Structural comparisons with the lignin and cytochrome c peroxidases.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 8182752
Journal J Mol Biol
Year 1994
Volume 238
Pages 845-8
Authors Sundaramoorthy M, Kishi K, Gold MH, Poulos TL
Title Preliminary crystallographic analysis of manganese peroxidase from Phanerochaete chrysosporium.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 7731950
Journal Proteins
Year 1994
Volume 20
Pages 312-9
Authors Johnson F, Loew GH, Du P
Title Homology models of two isozymes of manganese peroxidase: prediction of a Mn(II) binding site.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 7922023
Journal Structure
Year 1994
Volume 2
Pages 461-4
Authors Li H, Poulos TL
Title Structural variation in heme enzymes: a comparative analysis of peroxidase and P450 crystal structures.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 9136871
Journal Biochemistry
Year 1997
Volume 36
Pages 5113-9
Authors Nie G, Aust SD
Title Spectral changes of lignin peroxidase during reversible inactivation.
Related PDB
Related UniProtKB
[14]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS)
Medline ID 98301364
PubMed ID 9636023
Journal Biochemistry
Year 1998
Volume 37
Pages 8832-8
Authors Blodig W, Doyle WA, Smith AT, Winterhalter K, Choinowski T, Piontek K
Title Autocatalytic formation of a hydroxy group at C beta of trp171 in lignin peroxidase.
Related PDB
Related UniProtKB P06181
[15]
Resource
Comments
Medline ID
PubMed ID 9790672
Journal Biochemistry
Year 1998
Volume 37
Pages 15097-105
Authors Doyle WA, Blodig W, Veitch NC, Piontek K, Smith AT
Title Two substrate interaction sites in lignin peroxidase revealed by site-directed mutagenesis.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 10496980
Journal Arch Biochem Biophys
Year 1999
Volume 370
Pages 86-92
Authors Blodig W, Smith AT, Winterhalter K, Piontek K
Title Evidence from spin-trapping for a transient radical on tryptophan residue 171 of lignin peroxidase.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 10024453
Journal J Mol Biol
Year 1999
Volume 286
Pages 809-27
Authors Choinowski T, Blodig W, Winterhalter KH, Piontek K
Title The 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 PDB 1llp
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 10051582
Journal Proc Natl Acad Sci U S A
Year 1999
Volume 96
Pages 1989-94
Authors Johjima T, Itoh N, Kabuto M, Tokimura F, Nakagawa T, Wariishi H, Tanaka H
Title Direct interaction of lignin and lignin peroxidase from Phanerochaete chrysosporium.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 10713531
Journal Acta Crystallogr D Biol Crystallogr
Year 2000
Volume 56
Pages 372-5
Authors Mirza O, Henriksen A, Ostergaard L, Welinder KG, Gajhede M
Title Arabidopsis thaliana peroxidase N: structure of a novel neutral peroxidase.
Related PDB
Related UniProtKB
[20]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 11162097
Journal J Mol Biol
Year 2001
Volume 305
Pages 851-61
Authors Blodig W, Smith AT, Doyle WA, Piontek K
Title Crystal 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 PDB 1b80 1b82 1b85
Related UniProtKB

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]).

Created Updated
2004-10-18 2009-02-26