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PDBsum entry 1mn1

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protein ligands metals links
Peroxidase PDB id
1mn1
Jmol
Contents
Protein chain
357 a.a. *
Ligands
NAG-NAG
HEM
Metals
_CA ×2
Waters ×251
* Residue conservation analysis
PDB id:
1mn1
Name: Peroxidase
Title: Manganese peroxidase substrate binding site mutant d179n
Structure: Manganese peroxidase. Chain: a. Engineered: yes. Mutation: yes
Source: Phanerochaete chrysosporium. Organism_taxid: 5306. Strain: ogc101. Variant: ogc107-1. Cellular_location: extracellular. Gene: mnp1. Expressed in: phanerochaete chrysosporium. Expression_system_taxid: 5306. Expression_system_variant: d179n-6.
Resolution:
2.00Å     R-factor:   0.187    
Authors: M.Sundaramoorthy,T.L.Poulos
Key ref:
M.Sundaramoorthy et al. (1997). Crystal structures of substrate binding site mutants of manganese peroxidase. J Biol Chem, 272, 17574-17580. PubMed id: 9211904 DOI: 10.1074/jbc.272.28.17574
Date:
26-Apr-97     Release date:   04-Sep-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q02567  (PEM1_PHACH) -  Manganese peroxidase 1
Seq:
Struc:
378 a.a.
357 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.1.11.1.13  - Manganese peroxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 Mn2+ + 2 H+ + H2O2 = 2 Mn3+ + 2 H2O
2 × Mn(2+)
+ 2 × H(+)
+ H(2)O(2)
= 2 × Mn(3+)
+ 2 × H(2)O
      Cofactor: Heme
Heme
Bound ligand (Het Group name = HEM) matches with 95.45% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     oxidation-reduction process   4 terms 
  Biochemical function     oxidoreductase activity     5 terms  

 

 
    Added reference    
 
 
DOI no: 10.1074/jbc.272.28.17574 J Biol Chem 272:17574-17580 (1997)
PubMed id: 9211904  
 
 
Crystal structures of substrate binding site mutants of manganese peroxidase.
M.Sundaramoorthy, K.Kishi, M.H.Gold, T.L.Poulos.
 
  ABSTRACT  
 
Manganese peroxidase (MnP), an extracellular heme enzyme from the lignin-degrading basidiomycetous fungus, Phanerochaete chrysosporium, catalyzes the oxidation of MnII to MnIII. The latter, acting as a diffusible redox mediator, is capable of oxidizing a variety of lignin model compounds. The proposed MnII binding site of MnP consists of a heme propionate, three acidic ligands (Glu-35, Glu-39, and Asp-179), and two water molecules. Using crystallographic methods, this binding site was probed by altering the amount of MnII bound to the protein. Crystals grown in the absence of MnII, or in the presence of EDTA, exhibited diminished electron density at this site. Crystals grown in excess MnII exhibited increased electron density at the proposed binding site but nowhere else in the protein. This suggests that there is only one major MnII binding site in MnP. Crystal structures of a single mutant (D179N) and a double mutant (E35Q,D179N) at this site were determined. The mutant structures lack a cation at the MnII binding site. The structure of the MnII binding site is altered significantly in both mutants, resulting in increased access to the solvent and substrate.
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. Stereo representations of refined structures and interactions around the MnII binding site in the D179N single mutant (A) and in the E35Q,D179N double mutant (B). In E35Q,D179N, Gln-35 is modeled in two conformations, and Wat-653 is present only in the open conformation of Gln-35. In D179N Wat-653 is fully occupied, and the extra space^ left by the movement of Glu-35 is occupied by Wat-441. Wat-653^ forms hydrogen bond interaction with the heme propionate, Glu-39, Asn-179, and a solvent (Wat-441 in the single mutant and Wat-650^ in the double mutant).
Figure 5.
Fig. 5. Edge-on view of van der Waals surface representations of native MnP (A), the D179N single mutant, down the MnII binding site (B), and the E35Q,D179N double mutant (C). The^ color coding is as follows: heme, red; side chain ligands, green; MnII, yellow; and mutated side chains, purple.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1997, 272, 17574-17580) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20607227 A.Goudopoulou, A.Krimitzas, and M.A.Typas (2010).
Differential gene expression of ligninolytic enzymes in Pleurotus ostreatus grown on olive oil mill wastewater.
  Appl Microbiol Biotechnol, 88, 541-551.  
18581264 D.W.Wong (2009).
Structure and action mechanism of ligninolytic enzymes.
  Appl Biochem Biotechnol, 157, 174-209.  
18987391 F.J.Ruiz-Dueñas, M.Morales, E.García, Y.Miki, M.J.Martínez, and A.T.Martínez (2009).
Substrate oxidation sites in versatile peroxidase and other basidiomycete peroxidases.
  J Exp Bot, 60, 441-452.  
18292958 I.Morgenstern, S.Klopman, and D.S.Hibbett (2008).
Molecular evolution and diversity of lignin degrading heme peroxidases in the Agaricomycetes.
  J Mol Evol, 66, 243-257.  
18038130 M.Scheibner, B.Hülsdau, K.Zelena, M.Nimtz, L.de Boer, R.G.Berger, and H.Zorn (2008).
Novel peroxidases of Marasmius scorodonius degrade beta-carotene.
  Appl Microbiol Biotechnol, 77, 1241-1250.  
17021923 T.D.Pfister, A.Y.Mirarefi, A.J.Gengenbach, X.Zhao, C.Danstrom, N.Conatser, Y.G.Gao, H.Robinson, C.F.Zukoski, A.H.Wang, and Y.Lu (2007).
Kinetic and crystallographic studies of a redesigned manganese-binding site in cytochrome c peroxidase.
  J Biol Inorg Chem, 12, 126-137.
PDB codes: 2ia8 2icv
12829271 D.G.Kehres, and M.E.Maguire (2003).
Emerging themes in manganese transport, biochemistry and pathogenesis in bacteria.
  FEMS Microbiol Rev, 27, 263-290.  
11157267 B.Ma, M.B.Mayfield, and M.H.Gold (2001).
The green fluorescent protein gene functions as a reporter of gene expression in Phanerochaete chrysosporium.
  Appl Environ Microbiol, 67, 948-955.  
10712608 H.L.Youngs, M.Sundaramoorthy, and M.H.Gold (2000).
Effects of cadmium on manganese peroxidase competitive inhibition of MnII oxidation and thermal stabilization of the enzyme.
  Eur J Biochem, 267, 1761-1769.  
10933820 H.L.Youngs, P.Moënne-Loccoz, T.M.Loehr, and M.H.Gold (2000).
Formation of a bis(histidyl) heme iron complex in manganese peroxidase at high pH and restoration of the native enzyme structure by calcium.
  Biochemistry, 39, 9994.  
11106414 M.D.Gelpke, H.L.Youngs, and M.H.Gold (2000).
Role of arginine 177 in the MnII binding site of manganese peroxidase. Studies with R177D, R177E, R177N, and R177Q mutants.
  Eur J Biochem, 267, 7038-7045.  
11004397 S.Camarero, F.J.Ruiz-Dueñas, S.Sarkar, M.J.Martínez, and A.T.Martínez (2000).
The cloning of a new peroxidase found in lignocellulose cultures of Pleurotus eryngii and sequence comparison with other fungal peroxidases.
  FEMS Microbiol Lett, 191, 37-43.  
9987124 F.J.Ruiz-Dueñas, M.J.Martínez, and A.T.Martínez (1999).
Molecular characterization of a novel peroxidase isolated from the ligninolytic fungus Pleurotus eryngii.
  Mol Microbiol, 31, 223-235.
PDB code: 1a20
10348620 T.L.Poulos, H.Li, and C.S.Raman (1999).
Heme-mediated oxygen activation in biology: cytochrome c oxidase and nitric oxide synthase.
  Curr Opin Chem Biol, 3, 131-137.  
10413489 X.Wang, and Y.Lu (1999).
Proton NMR investigation of the heme active site structure of an engineered cytochrome c peroxidase that mimics manganese peroxidase.
  Biochemistry, 38, 9146-9157.  
9667928 A.T.Smith, and N.C.Veitch (1998).
Substrate binding and catalysis in heme peroxidases.
  Curr Opin Chem Biol, 2, 269-278.  
9578561 M.R.Mauk, K.Kishi, M.H.Gold, and A.G.Mauk (1998).
pH-linked binding of Mn(II) to manganese peroxidase.
  Biochemistry, 37, 6767-6771.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.