EzCatDB D00061

EzCatDB: D00061

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DB code	D00061
CATH domain	Domain 1	1.10.520.10 : Peroxidase; domain 1		Catalytic domain
CATH domain	Domain 2	1.10.420.10 : Peroxidase; domain 2		Catalytic domain
E.C.	1.11.1.13

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

Enzyme Name
UniProtKB		KEGG
	Q02567	KEGG
Protein name	Peroxidase manganese-dependent 1	manganese peroxidase peroxidase-M2 Mn-dependent (NADH-oxidizing) peroxidase
Synonyms	EC 1.11.1.13 Peroxidase manganese-dependent I Manganese peroxidase isozyme 1 MnP-1 MnP1
Pfam	PF11895 (DUF3415) PF00141 (peroxidase) [Graphical view]

UniProtKB:Accession Number	Q02567
Entry name	PEM1_PHACH
Activity	2 Mn(2+) + 2 H(+) + H(2)O(2) = 2 Mn(3+) + 2 H(2)O.
Subunit
Subcellular location	Secreted.
Cofactor	Binds 2 calcium ions per subunit.,Binds 1 heme B (iron-protoporphyrin IX) group per subunit.

Compound table: links to PDB-related databases & PoSSuM
								Cofactors		Substrates			Products
KEGG-id								C00032	C00076	C00034	C00080	C00027	C00034	C00001
Compound								Heme	Calcium	Mn(II)	H+	H2O2	Mn(III)	H2O
Type								aromatic ring (with nitrogen atoms),carboxyl group,heavy metal	divalent metal (Ca2+, Mg2+)	heavy metal	others	others	heavy metal	H2O
ChEBI								17627 26355	29108	18291 35154	15378	16240	18291 35154	15377
PubChem									271	23930	1038	784 22326046	23930	962 22247451

1mn1A01								Unbound	Bound:_CA	Unbound		Unbound	Unbound
1mn2A01								Unbound	Bound:_CA	Unbound		Unbound	Unbound
1mnpA01								Unbound	Bound:_CA	Bound:_MN		Unbound	Unbound
1yydA01								Unbound	Bound:_CA	Bound:_MN		Unbound	Unbound
1yygA01								Unbound	Bound:_CA 372	Analogue:_CA 381		Unbound	Unbound
1yzpA01								Unbound	Bound:_CA	Unbound		Unbound	Unbound
1yzrA01								Unbound	Bound:_CA	Analogue:_SM		Unbound	Unbound
1mn1A02								Bound:HEM	Bound:_CA	Unbound		Unbound	Unbound
1mn2A02								Bound:HEM	Bound:_CA	Unbound		Unbound	Unbound
1mnpA02								Bound:HEM	Bound:_CA	Unbound		Unbound	Unbound
1yydA02								Bound:HEM	Bound:_CA	Unbound		Unbound	Unbound
1yygA02								Bound:HEM	Bound:_CA 371	Unbound		Unbound	Unbound
1yzpA02								Bound:HEM	Bound:_CA	Unbound		Unbound	Unbound
1yzrA02								Bound:HEM	Bound:_CA	Unbound		Unbound	Unbound

Active-site residues
resource
Swiss-prot;Q02567 & literature [37]
pdb								Catalytic residues	Cofactor-binding residues	comment

1mn1A01								`ARG 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)`
1mn2A01								`ARG 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`
1mnpA01								`ARG 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)`
1yydA01								`ARG 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)`
1yygA01								`ARG 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)`
1yzpA01								`ARG 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)`
1yzrA01								`ARG 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
References	Sections	No. 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 ID	2925681
Journal	J Biol Chem
Year	1989
Volume	264
Pages	5036-40
Authors	Pribnow D, Mayfield MB, Nipper VJ, Brown JA, Gold MH
Title	Characterization of a cDNA encoding a manganese peroxidase, from the lignin-degrading basidiomycete Phanerochaete chrysosporium.
[2]
PubMed ID	1851156
Journal	J Biol Chem
Year	1991
Volume	266
Pages	8751-8
Authors	Harris RZ, Wariishi H, Gold MH, Ortiz de Montellano PR
Title	The catalytic site of manganese peroxidase. Regiospecific addition of sodium azide and alkylhydrazines to the heme group.
[3]
PubMed ID	1327129
Journal	Biochemistry
Year	1992
Volume	31
Pages	10009-17
Authors	Banci L, Bertini I, Pease EA, Tien M, Turano P
Title	1H NMR investigation of manganese peroxidase from Phanerochaete chrysosporium. A comparison with other peroxidases.
[4]
PubMed ID	8393660
Journal	Biochem J
Year	1993
Volume	293
Pages	431-5
Authors	Ander P, Sena-Martins G, Duarte JC
Title	Influence of cellobiose oxidase on peroxidases from Phanerochaete chrysosporium.
[5]
PubMed ID	7763834
Journal	J Biotechnol
Year	1993
Volume	30
Pages	79-90
Authors	Cai D, Tien M
Title	Lignin-degrading peroxidases of Phanerochaete chrysosporium.
[6]
PubMed ID	8034057
Journal	FEBS Lett
Year	1994
Volume	348
Pages	291-6
Authors	Lundell T, Hatakka A
Title	Participation of Mn(II) in the catalysis of laccase, manganese peroxidase and lignin peroxidase from Phelbia radiata.
[7]
Comments	X-RAY CRYSTALLOGRAPHY (2.06 ANGSTROMS)
Medline ID	95105154
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 UniProtKB	Q02567
[8]
Comments	X-ray crystallography
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	1mnp
[9]
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.
[10]
PubMed ID	7672248
Journal	Biochem Soc Trans
Year	1995
Volume	23
Pages	228-32
Authors	Poulos TL, Patterson WR, Sundaramoorthy M
Title	The crystal structure of ascorbate and manganese peroxidases: the role of non-haem metal in the catalytic mechanism.
[11]
PubMed ID	7654716
Journal	Biochemistry
Year	1995
Volume	34
Pages	10620-7
Authors	Kusters-van Someren M, Kishi K, Lundell T, Gold MH
Title	The manganese binding site of manganese peroxidase: characterization of an Asp179Asn site-directed mutant protein.
[12]
PubMed ID	7548080
Journal	Biochemistry
Year	1995
Volume	34
Pages	13176-82
Authors	Sinclair R, Copeland B, Yamazaki I, Powers L
Title	X-ray absorption spectroscopy comparison of the active site structures of Phanerochaete chrysosporium lignin peroxidase isoenzymes H2, H3, H4, H5, H8, and H10.
[13]
PubMed ID	7737200
Journal	Eur J Biochem
Year	1995
Volume	228
Pages	955-61
Authors	Selvaggini C, Salmona M, De Gioia L
Title	Manganese peroxidase from Phanerochaete chrysosporium. A homology-based molecular model.
[14]
PubMed ID	8806717
Journal	Arch Biochem Biophys
Year	1996
Volume	332
Pages	128-34
Authors	Sutherland GR, Aust SD
Title	The effects of calcium on the thermal stability and activity of manganese peroxidase.
[15]
Comments	METAL-BINDING
Medline ID	96280658
PubMed ID	8688436
Journal	Biochemistry
Year	1996
Volume	35
Pages	8986-94
Authors	Kishi K, Kusters-van Someren M, Mayfield MB, Sun J, Loehr TM, Gold MH
Title	Characterization of manganese(II) binding site mutants of manganese peroxidase.
Related UniProtKB	Q02567
[16]
PubMed ID	8647081
Journal	Eur J Biochem
Year	1996
Volume	237
Pages	424-32
Authors	Martinez MJ, Ruiz-Duenas FJ, Guillen F, Martinez AT
Title	Purification and catalytic properties of two manganese peroxidase isoenzymes from Pleurotus eryngii.
[17]
PubMed ID	9100022
Journal	Biochemistry
Year	1997
Volume	36
Pages	4268-77
Authors	Kishi K, Hildebrand DP, Kusters-van Someren M, Gettemy J, Mauk AG, Gold MH
Title	Site-directed mutations at phenylalanine-190 of manganese peroxidase: effects on stability, function, and coordination.
[18]
PubMed ID	9214302
Journal	Biochemistry
Year	1997
Volume	36
Pages	8567-73
Authors	Sutherland GR, Aust SD
Title	Thermodynamics of binding of the distal calcium to manganese peroxidase.
[19]
PubMed ID	9132018
Journal	Biochemistry
Year	1997
Volume	36
Pages	3654-62
Authors	Sutherland GR, Zapanta LS, Tien M, Aust SD
Title	Role of calcium in maintaining the heme environment of manganese peroxidase.
[20]
PubMed ID	9245408
Journal	Biochemistry
Year	1997
Volume	36
Pages	9766-73
Authors	Whitwam RE, Brown KR, Musick M, Natan MJ, Tien M
Title	Mutagenesis of the Mn2+-binding site of manganese peroxidase affects oxidation of Mn2+ by both compound I and compound II.
[21]
Comments	X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF MUTANTS
Medline ID	97362247
PubMed ID	9211904
Journal	J Biol Chem
Year	1997
Volume	272
Pages	17574-80
Authors	Sundaramoorthy M, Kishi K, Gold MH, Poulos TL
Title	Crystal structures of substrate binding site mutants of manganese peroxidase.
Related PDB	1mn1,1mn2
Related UniProtKB	Q02567
[22]
PubMed ID	9705219
Journal	Arch Biochem Biophys
Year	1998
Volume	356
Pages	287-95
Authors	Timofeevski SL, Reading NS, Aust SD
Title	Mechanisms for protection against inactivation of manganese peroxidase by hydrogen peroxide.
[23]
PubMed ID	9636044
Journal	Biochemistry
Year	1998
Volume	37
Pages	9009-15
Authors	Banci L, Bertini I, Dal Pozzo L, Del Conte R, Tien M
Title	Monitoring the role of oxalate in manganese peroxidase.
[24]
PubMed ID	10099422
Journal	Biotechnol Bioeng
Year	1998
Volume	60
Pages	204-15
Authors	Grabski AC, Grimek HJ, Burgess RR
Title	Immobilization of manganese peroxidase from Lentinula edodes and its biocatalytic generation of MnIII-chelate as a chemical oxidant of chlorophenols.
[25]
PubMed ID	9742955
Journal	FEBS Lett
Year	1998
Volume	434
Pages	362-6
Authors	Hofrichter M, Ziegenhagen D, Vares T, Friedrich M, Jager MG, Fritsche W, Hatakka A
Title	Oxidative decomposition of malonic acid as basis for the action of manganese peroxidase in the absence of hydrogen peroxide.
[26]
PubMed ID	9469932
Journal	Gene
Year	1998
Volume	206
Pages	185-93
Authors	Lobos S, Larrondo L, Salas L, Karahanian E, Vicuna R
Title	Cloning 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 ID	9624124
Journal	J Biol Chem
Year	1998
Volume	273
Pages	15412-7
Authors	Mester T, Field JA
Title	Characterization of a novel manganese peroxidase-lignin peroxidase hybrid isozyme produced by Bjerkandera species strain BOS55 in the absence of manganese.
[28]
PubMed ID	10423239
Journal	Biochemistry
Year	1999
Volume	38
Pages	9617-25
Authors	Banci L, Bertini I, Capannoli C, Del Conte R, Tien M
Title	Spectroscopic characterization of active mutants of manganese peroxidase: mutations on the proximal side affect calcium binding of the distal side.
[29]
PubMed ID	10074376
Journal	Biochemistry
Year	1999
Volume	38
Pages	3205-10
Authors	Banci L, Ciofi-Baffoni S, Tien M
Title	Lignin and Mn peroxidase-catalyzed oxidation of phenolic lignin oligomers.
[30]
PubMed ID	10471300
Journal	Biochemistry
Year	1999
Volume	38
Pages	11482-9
Authors	Sollewijn Gelpke MD, Moenne-Loccoz P, Gold MH
Title	Arginine 177 is involved in Mn(II) binding by manganese peroxidase.
[31]
PubMed ID	10413489
Journal	Biochemistry
Year	1999
Volume	38
Pages	9146-57
Authors	Wang X, Lu Y
Title	Proton NMR investigation of the heme active site structure of an engineered cytochrome c peroxidase that mimics manganese peroxidase.
[32]
PubMed ID	11051101
Journal	Arch Biochem Biophys
Year	2000
Volume	382
Pages	89-94
Authors	Ambert-Balay K, Dougherty M, Tien M
Title	Reactivity of manganese peroxidase: site-directed mutagenesis of residues in proximity to the porphyrin ring.
[33]
PubMed ID	10620333
Journal	Arch Biochem Biophys
Year	2000
Volume	373
Pages	147-53
Authors	Timofeevski SL, Nie G, Reading NS, Aust SD
Title	Substrate specificity of lignin peroxidase and a S168W variant of manganese peroxidase.
[34]
PubMed ID	10835231
Journal	Biotechnol Prog
Year	2000
Volume	16
Pages	326-33
Authors	Reading NS, Aust SD
Title	Engineering a disulfide bond in recombinant manganese peroxidase results in increased thermostability.
[35]
PubMed ID	11106414
Journal	Eur J Biochem
Year	2000
Volume	267
Pages	7038-45
Authors	Gelpke MD, Youngs HL, Gold MH
Title	Role of arginine 177 in the MnII binding site of manganese peroxidase. Studies with R177D, R177E, R177N, and R177Q mutants.
[36]
PubMed ID	10806381
Journal	Eur J Biochem
Year	2000
Volume	267
Pages	2840-9
Authors	Zou P, Schrempf H
Title	The heme-independent manganese-peroxidase activity depends on the presence of the C-terminal domain within the Streptomyces reticuli catalase-peroxidase CpeB.
[37]
PubMed ID	10693145
Journal	Met Ions Biol Syst
Year	2000
Volume	37
Pages	559-86
Authors	Gold MH, Youngs HL, Gelpke MD
Title	Manganese peroxidase.
[38]
PubMed ID	11329293
Journal	Biochemistry
Year	2001
Volume	40
Pages	2243-50
Authors	Youngs HL, Sollewijn Gelpke MD, Li D, Sundaramoorthy M, Gold MH
Title	The role of Glu39 in MnII binding and oxidation by manganese peroxidase from Phanerochaete chrysoporium.
[39]
PubMed ID	11734216
Journal	FEBS Lett
Year	2001
Volume	509
Pages	111-4
Authors	Miyazaki C, Takahashi H
Title	Engineering of the H2O2-binding pocket region of a recombinant manganese peroxidase to be resistant to H2O2.
[40]
PubMed ID	12089036
Journal	Appl Environ Microbiol
Year	2002
Volume	68
Pages	3514-21
Authors	Schlosser D, Hofer C
Title	Laccase-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 ID	12172033
Journal	Plant Cell
Year	2002
Volume	14
Pages	1953-62
Authors	Onnerud H, Zhang L, Gellerstedt G, Henriksson G
Title	Polymerization of monolignols by redox shuttle-mediated enzymatic oxidation: a new model in lignin biosynthesis I.
[42]
PubMed ID	12400090
Journal	Biopolymers
Year	2003
Volume	72
Pages	38-47
Authors	Banci L, Bartalesi I, Ciofi-Baffoni S, Tien M
Title	Unfolding and pH studies on manganese peroxidase: role of heme and calcium on secondary structure stability.
[43]
PubMed ID	15766255
Journal	Biochemistry
Year	2005
Volume	44
Pages	4267-74
Authors	Pogni R, Baratto MC, Giansanti S, Teutloff C, Verdin J, Valderrama B, Lendzian F, Lubitz W, Vazquez-Duhalt R, Basosi R
Title	Tryptophan-based radical in the catalytic mechanism of versatile peroxidase from Bjerkandera adusta.
[44]
PubMed ID	15850380
Journal	Biochemistry
Year	2005
Volume	44
Pages	6463-70
Authors	Sundaramoorthy M, Youngs HL, Gold MH, Poulos TL
Title	High-resolution crystal structure of manganese peroxidase: substrate and i
Related PDB	1yyd,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]).

created	updated
2005-06-02	2009-02-26

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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