EzCatDB: D00061
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DB codeD00061
CATH domainDomain 11.10.520.10 : Peroxidase; domain 1Catalytic domain
Domain 21.10.420.10 : Peroxidase; domain 2Catalytic domain
E.C.1.11.1.13

CATH domainRelated DB codes (homologues)
1.10.420.10 : Peroxidase; domain 2D00060,D00062
1.10.520.10 : Peroxidase; domain 1D00060,D00062

Enzyme Name
UniProtKBKEGG

Q02567
Protein namePeroxidase manganese-dependent 1manganese peroxidase
peroxidase-M2
Mn-dependent (NADH-oxidizing) peroxidase
SynonymsEC 1.11.1.13
Peroxidase manganese-dependent I
Manganese peroxidase isozyme 1
MnP-1
MnP1
PfamPF11895 (DUF3415)
PF00141 (peroxidase)
[Graphical view]


UniProtKB:Accession NumberQ02567
Entry namePEM1_PHACH
Activity2 Mn(2+) + 2 H(+) + H(2)O(2) = 2 Mn(3+) + 2 H(2)O.
Subunit
Subcellular locationSecreted.
CofactorBinds 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-idC00032C00076C00034C00080C00027C00034C00001
CompoundHemeCalciumMn(II)H+H2O2Mn(III)H2O
Typearomatic ring (with nitrogen atoms),carboxyl group,heavy metaldivalent metal (Ca2+, Mg2+)heavy metalothersothersheavy metalH2O
ChEBI17627
26355
29108
18291
35154
15378
16240
18291
35154
15377
PubChem
271
23930
1038
784
22326046
23930
962
22247451
               
1mn1A01UnboundBound:_CAUnbound UnboundUnbound 
1mn2A01UnboundBound:_CAUnbound UnboundUnbound 
1mnpA01UnboundBound:_CABound:_MN UnboundUnbound 
1yydA01UnboundBound:_CABound:_MN UnboundUnbound 
1yygA01UnboundBound:_CA 372Analogue:_CA 381 UnboundUnbound 
1yzpA01UnboundBound:_CAUnbound UnboundUnbound 
1yzrA01UnboundBound:_CAAnalogue:_SM UnboundUnbound 
1mn1A02Bound:HEMBound:_CAUnbound UnboundUnbound 
1mn2A02Bound:HEMBound:_CAUnbound UnboundUnbound 
1mnpA02Bound:HEMBound:_CAUnbound UnboundUnbound 
1yydA02Bound:HEMBound:_CAUnbound UnboundUnbound 
1yygA02Bound:HEMBound:_CA 371Unbound UnboundUnbound 
1yzpA02Bound:HEMBound:_CAUnbound UnboundUnbound 
1yzrA02Bound:HEMBound:_CAUnbound UnboundUnbound 

Active-site residues
resource
Swiss-prot;Q02567 & literature [37]
pdbCatalytic residuesCofactor-binding residuescomment
           
1mn1A01ARG 42;PHE 45;HIS 46;GLU 74;ASN 80
GLU 35;GLU 39(Manganese binding);ASP 47;GLY 62;ASP 64;SER 66(Calcium-1 binding)
 
1mn2A01ARG 42;PHE 45;HIS 46;GLU 74;ASN 80
      ;GLU 39(Manganese binding);ASP 47;GLY 62;ASP 64;SER 66(Calcium-1 binding)
mutant E35Q
1mnpA01ARG 42;PHE 45;HIS 46;GLU 74;ASN 80
GLU 35;GLU 39(Manganese binding);ASP 47;GLY 62;ASP 64;SER 66(Calcium-1 binding)
 
1yydA01ARG 42;PHE 45;HIS 46;GLU 74;ASN 80
GLU 35;GLU 39(Manganese binding);ASP 47;GLY 62;ASP 64;SER 66(Calcium-1 binding)
 
1yygA01ARG 42;PHE 45;HIS 46;GLU 74;ASN 80
GLU 35;GLU 39(Manganese binding);ASP 47;GLY 62;ASP 64;SER 66(Calcium-1 binding)
 
1yzpA01ARG 42;PHE 45;HIS 46;GLU 74;ASN 80
GLU 35;GLU 39(Manganese binding);ASP 47;GLY 62;ASP 64;SER 66(Calcium-1 binding)
 
1yzrA01ARG 42;PHE 45;HIS 46;GLU 74;ASN 80
GLU 35;GLU 39(Manganese binding);ASP 47;GLY 62;ASP 64;SER 66(Calcium-1 binding)
 
1mn1A02 
HIS 173(Heme binding);                          ;SER 174;ASP 191;THR 193;THR 196;ASP 198(Calcium-2 binding)
mutant D179N
1mn2A02 
HIS 173(Heme binding);                          ;SER 174;ASP 191;THR 193;THR 196;ASP 198(Calcium-2 binding)
mutant D179N
1mnpA02 
HIS 173(Heme binding);ASP 179(Manganese binding);SER 174;ASP 191;THR 193;THR 196;ASP 198(Calcium-2 binding)
 
1yydA02 
HIS 173(Heme binding);ASP 179(Manganese binding);SER 174;ASP 191;THR 193;THR 196;ASP 198(Calcium-2 binding)
 
1yygA02 
HIS 173(Heme binding);ASP 179(Manganese binding);SER 174;ASP 191;THR 193;THR 196;ASP 198(Calcium-2 binding)
 
1yzpA02 
HIS 173(Heme binding);ASP 179(Manganese binding);SER 174;ASP 191;THR 193;THR 196;ASP 198(Calcium-2 binding)
 
1yzrA02 
HIS 173(Heme binding);ASP 179(Manganese binding);SER 174;ASP 191;THR 193;THR 196;ASP 198(Calcium-2 binding)
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[7]

[10]

[19]p.3659
[20]

[22]SCHEME 1
[23]

[25]

[37]Fig.2, p.563-565, Fig.5, Fig.6, p.571-574

references
[1]
PubMed ID2925681
JournalJ Biol Chem
Year1989
Volume264
Pages5036-40
AuthorsPribnow D, Mayfield MB, Nipper VJ, Brown JA, Gold MH
TitleCharacterization of a cDNA encoding a manganese peroxidase, from the lignin-degrading basidiomycete Phanerochaete chrysosporium.
[2]
PubMed ID1851156
JournalJ Biol Chem
Year1991
Volume266
Pages8751-8
AuthorsHarris RZ, Wariishi H, Gold MH, Ortiz de Montellano PR
TitleThe catalytic site of manganese peroxidase. Regiospecific addition of sodium azide and alkylhydrazines to the heme group.
[3]
PubMed ID1327129
JournalBiochemistry
Year1992
Volume31
Pages10009-17
AuthorsBanci L, Bertini I, Pease EA, Tien M, Turano P
Title1H NMR investigation of manganese peroxidase from Phanerochaete chrysosporium. A comparison with other peroxidases.
[4]
PubMed ID8393660
JournalBiochem J
Year1993
Volume293
Pages431-5
AuthorsAnder P, Sena-Martins G, Duarte JC
TitleInfluence of cellobiose oxidase on peroxidases from Phanerochaete chrysosporium.
[5]
PubMed ID7763834
JournalJ Biotechnol
Year1993
Volume30
Pages79-90
AuthorsCai D, Tien M
TitleLignin-degrading peroxidases of Phanerochaete chrysosporium.
[6]
PubMed ID8034057
JournalFEBS Lett
Year1994
Volume348
Pages291-6
AuthorsLundell T, Hatakka A
TitleParticipation of Mn(II) in the catalysis of laccase, manganese peroxidase and lignin peroxidase from Phelbia radiata.
[7]
CommentsX-RAY CRYSTALLOGRAPHY (2.06 ANGSTROMS)
Medline ID95105154
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.
Related UniProtKBQ02567
[8]
CommentsX-ray crystallography
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.
Related PDB1mnp
[9]
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.
[10]
PubMed ID7672248
JournalBiochem Soc Trans
Year1995
Volume23
Pages228-32
AuthorsPoulos TL, Patterson WR, Sundaramoorthy M
TitleThe crystal structure of ascorbate and manganese peroxidases: the role of non-haem metal in the catalytic mechanism.
[11]
PubMed ID7654716
JournalBiochemistry
Year1995
Volume34
Pages10620-7
AuthorsKusters-van Someren M, Kishi K, Lundell T, Gold MH
TitleThe manganese binding site of manganese peroxidase: characterization of an Asp179Asn site-directed mutant protein.
[12]
PubMed ID7548080
JournalBiochemistry
Year1995
Volume34
Pages13176-82
AuthorsSinclair R, Copeland B, Yamazaki I, Powers L
TitleX-ray absorption spectroscopy comparison of the active site structures of Phanerochaete chrysosporium lignin peroxidase isoenzymes H2, H3, H4, H5, H8, and H10.
[13]
PubMed ID7737200
JournalEur J Biochem
Year1995
Volume228
Pages955-61
AuthorsSelvaggini C, Salmona M, De Gioia L
TitleManganese peroxidase from Phanerochaete chrysosporium. A homology-based molecular model.
[14]
PubMed ID8806717
JournalArch Biochem Biophys
Year1996
Volume332
Pages128-34
AuthorsSutherland GR, Aust SD
TitleThe effects of calcium on the thermal stability and activity of manganese peroxidase.
[15]
CommentsMETAL-BINDING
Medline ID96280658
PubMed ID8688436
JournalBiochemistry
Year1996
Volume35
Pages8986-94
AuthorsKishi K, Kusters-van Someren M, Mayfield MB, Sun J, Loehr TM, Gold MH
TitleCharacterization of manganese(II) binding site mutants of manganese peroxidase.
Related UniProtKBQ02567
[16]
PubMed ID8647081
JournalEur J Biochem
Year1996
Volume237
Pages424-32
AuthorsMartinez MJ, Ruiz-Duenas FJ, Guillen F, Martinez AT
TitlePurification and catalytic properties of two manganese peroxidase isoenzymes from Pleurotus eryngii.
[17]
PubMed ID9100022
JournalBiochemistry
Year1997
Volume36
Pages4268-77
AuthorsKishi K, Hildebrand DP, Kusters-van Someren M, Gettemy J, Mauk AG, Gold MH
TitleSite-directed mutations at phenylalanine-190 of manganese peroxidase: effects on stability, function, and coordination.
[18]
PubMed ID9214302
JournalBiochemistry
Year1997
Volume36
Pages8567-73
AuthorsSutherland GR, Aust SD
TitleThermodynamics of binding of the distal calcium to manganese peroxidase.
[19]
PubMed ID9132018
JournalBiochemistry
Year1997
Volume36
Pages3654-62
AuthorsSutherland GR, Zapanta LS, Tien M, Aust SD
TitleRole of calcium in maintaining the heme environment of manganese peroxidase.
[20]
PubMed ID9245408
JournalBiochemistry
Year1997
Volume36
Pages9766-73
AuthorsWhitwam RE, Brown KR, Musick M, Natan MJ, Tien M
TitleMutagenesis of the Mn2+-binding site of manganese peroxidase affects oxidation of Mn2+ by both compound I and compound II.
[21]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF MUTANTS
Medline ID97362247
PubMed ID9211904
JournalJ Biol Chem
Year1997
Volume272
Pages17574-80
AuthorsSundaramoorthy M, Kishi K, Gold MH, Poulos TL
TitleCrystal structures of substrate binding site mutants of manganese peroxidase.
Related PDB1mn1,1mn2
Related UniProtKBQ02567
[22]
PubMed ID9705219
JournalArch Biochem Biophys
Year1998
Volume356
Pages287-95
AuthorsTimofeevski SL, Reading NS, Aust SD
TitleMechanisms for protection against inactivation of manganese peroxidase by hydrogen peroxide.
[23]
PubMed ID9636044
JournalBiochemistry
Year1998
Volume37
Pages9009-15
AuthorsBanci L, Bertini I, Dal Pozzo L, Del Conte R, Tien M
TitleMonitoring the role of oxalate in manganese peroxidase.
[24]
PubMed ID10099422
JournalBiotechnol Bioeng
Year1998
Volume60
Pages204-15
AuthorsGrabski AC, Grimek HJ, Burgess RR
TitleImmobilization of manganese peroxidase from Lentinula edodes and its biocatalytic generation of MnIII-chelate as a chemical oxidant of chlorophenols.
[25]
PubMed ID9742955
JournalFEBS Lett
Year1998
Volume434
Pages362-6
AuthorsHofrichter M, Ziegenhagen D, Vares T, Friedrich M, Jager MG, Fritsche W, Hatakka A
TitleOxidative decomposition of malonic acid as basis for the action of manganese peroxidase in the absence of hydrogen peroxide.
[26]
PubMed ID9469932
JournalGene
Year1998
Volume206
Pages185-93
AuthorsLobos S, Larrondo L, Salas L, Karahanian E, Vicuna R
TitleCloning and molecular analysis of a cDNA and the Cs-mnp1 gene encoding a manganese peroxidase isoenzyme from the lignin-degrading basidiomycete Ceriporiopsis subvermispora.
[27]
PubMed ID9624124
JournalJ Biol Chem
Year1998
Volume273
Pages15412-7
AuthorsMester T, Field JA
TitleCharacterization of a novel manganese peroxidase-lignin peroxidase hybrid isozyme produced by Bjerkandera species strain BOS55 in the absence of manganese.
[28]
PubMed ID10423239
JournalBiochemistry
Year1999
Volume38
Pages9617-25
AuthorsBanci L, Bertini I, Capannoli C, Del Conte R, Tien M
TitleSpectroscopic characterization of active mutants of manganese peroxidase: mutations on the proximal side affect calcium binding of the distal side.
[29]
PubMed ID10074376
JournalBiochemistry
Year1999
Volume38
Pages3205-10
AuthorsBanci L, Ciofi-Baffoni S, Tien M
TitleLignin and Mn peroxidase-catalyzed oxidation of phenolic lignin oligomers.
[30]
PubMed ID10471300
JournalBiochemistry
Year1999
Volume38
Pages11482-9
AuthorsSollewijn Gelpke MD, Moenne-Loccoz P, Gold MH
TitleArginine 177 is involved in Mn(II) binding by manganese peroxidase.
[31]
PubMed ID10413489
JournalBiochemistry
Year1999
Volume38
Pages9146-57
AuthorsWang X, Lu Y
TitleProton NMR investigation of the heme active site structure of an engineered cytochrome c peroxidase that mimics manganese peroxidase.
[32]
PubMed ID11051101
JournalArch Biochem Biophys
Year2000
Volume382
Pages89-94
AuthorsAmbert-Balay K, Dougherty M, Tien M
TitleReactivity of manganese peroxidase: site-directed mutagenesis of residues in proximity to the porphyrin ring.
[33]
PubMed ID10620333
JournalArch Biochem Biophys
Year2000
Volume373
Pages147-53
AuthorsTimofeevski SL, Nie G, Reading NS, Aust SD
TitleSubstrate specificity of lignin peroxidase and a S168W variant of manganese peroxidase.
[34]
PubMed ID10835231
JournalBiotechnol Prog
Year2000
Volume16
Pages326-33
AuthorsReading NS, Aust SD
TitleEngineering a disulfide bond in recombinant manganese peroxidase results in increased thermostability.
[35]
PubMed ID11106414
JournalEur J Biochem
Year2000
Volume267
Pages7038-45
AuthorsGelpke MD, Youngs HL, Gold MH
TitleRole of arginine 177 in the MnII binding site of manganese peroxidase. Studies with R177D, R177E, R177N, and R177Q mutants.
[36]
PubMed ID10806381
JournalEur J Biochem
Year2000
Volume267
Pages2840-9
AuthorsZou P, Schrempf H
TitleThe heme-independent manganese-peroxidase activity depends on the presence of the C-terminal domain within the Streptomyces reticuli catalase-peroxidase CpeB.
[37]
PubMed ID10693145
JournalMet Ions Biol Syst
Year2000
Volume37
Pages559-86
AuthorsGold MH, Youngs HL, Gelpke MD
TitleManganese peroxidase.
[38]
PubMed ID11329293
JournalBiochemistry
Year2001
Volume40
Pages2243-50
AuthorsYoungs HL, Sollewijn Gelpke MD, Li D, Sundaramoorthy M, Gold MH
TitleThe role of Glu39 in MnII binding and oxidation by manganese peroxidase from Phanerochaete chrysoporium.
[39]
PubMed ID11734216
JournalFEBS Lett
Year2001
Volume509
Pages111-4
AuthorsMiyazaki C, Takahashi H
TitleEngineering of the H2O2-binding pocket region of a recombinant manganese peroxidase to be resistant to H2O2.
[40]
PubMed ID12089036
JournalAppl Environ Microbiol
Year2002
Volume68
Pages3514-21
AuthorsSchlosser D, Hofer C
TitleLaccase-catalyzed oxidation of Mn(2+) in the presence of natural Mn(3+) chelators as a novel source of extracellular H(2)O(2) production and its impact on manganese peroxidase.
[41]
PubMed ID12172033
JournalPlant Cell
Year2002
Volume14
Pages1953-62
AuthorsOnnerud H, Zhang L, Gellerstedt G, Henriksson G
TitlePolymerization of monolignols by redox shuttle-mediated enzymatic oxidation: a new model in lignin biosynthesis I.
[42]
PubMed ID12400090
JournalBiopolymers
Year2003
Volume72
Pages38-47
AuthorsBanci L, Bartalesi I, Ciofi-Baffoni S, Tien M
TitleUnfolding and pH studies on manganese peroxidase: role of heme and calcium on secondary structure stability.
[43]
PubMed ID15766255
JournalBiochemistry
Year2005
Volume44
Pages4267-74
AuthorsPogni R, Baratto MC, Giansanti S, Teutloff C, Verdin J, Valderrama B, Lendzian F, Lubitz W, Vazquez-Duhalt R, Basosi R
TitleTryptophan-based radical in the catalytic mechanism of versatile peroxidase from Bjerkandera adusta.
[44]
PubMed ID15850380
JournalBiochemistry
Year2005
Volume44
Pages6463-70
AuthorsSundaramoorthy M, Youngs HL, Gold MH, Poulos TL
TitleHigh-resolution crystal structure of manganese peroxidase: substrate and i
Related PDB1yyd,1yyg,1yzp,1yzr

comments
Although this enzyme binds two calcium ions, they are not involved in catalysis.
According to the literature, this enzyme catalyzes three reactions as follows:
(1) P-Fe3+ + H2O2 = Compound I + H2O ; Compound I = [P+-Fe4+=O] (two-electron transfer)
(2) Compound I + Mn2+ = Compound II + Mn3+ ; Compound II = [P-Fe4+=O] (one-electron transfer)
(3) Compound II + Mn2+ = P-Fe3+ + Mn3+ (one-electron transfer)
Here, "P" and "P+" indicate "a porphyrin" and "a porphyrin pi cation radical", respectively.
Thus, Compound I is a two-electron-oxidized intermediate, containing an oxyferryl center, Fe4+=O, and a porphyrin pi cation radical. Compound II is one-electron-oxidized intermediate, containing an oxyferryl center, Fe4+=O, and a porphyrin.
During the reaction (2), this enzyme can oxidze a phenolic or aromatic amine substrate, such as lignin, instead of manganese (see [37]).

createdupdated
2005-06-022009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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