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PDBsum entry 1yyd

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protein ligands metals links
Oxidoreductase PDB id
1yyd
Jmol
Contents
Protein chain
357 a.a. *
Ligands
NAG-NAG
MAN
SO4
HEM
GOL ×3
Metals
_CA ×2
_MN
Waters ×516
* Residue conservation analysis
PDB id:
1yyd
Name: Oxidoreductase
Title: High resolution crystal structure of manganese peroxidase
Structure: Peroxidase manganese-dependent i. Chain: a. Synonym: mnp-1, mnp1, manganese peroxidase isozyme 1. Ec: 1.11.1.13
Source: Phanerochaete chrysosporium. Organism_taxid: 5306
Resolution:
1.45Å     R-factor:   0.180     R-free:   0.227
Authors: M.Sundaramoorthy,H.L.Youngs,M.H.Gold,T.L.Poulos
Key ref:
M.Sundaramoorthy et al. (2005). High-resolution crystal structure of manganese peroxidase: substrate and inhibitor complexes. Biochemistry, 44, 6463-6470. PubMed id: 15850380 DOI: 10.1021/bi047318e
Date:
24-Feb-05     Release date:   10-May-05    
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

 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: 10.1021/bi047318e Biochemistry 44:6463-6470 (2005)
PubMed id: 15850380  
 
 
High-resolution crystal structure of manganese peroxidase: substrate and inhibitor complexes.
M.Sundaramoorthy, H.L.Youngs, M.H.Gold, T.L.Poulos.
 
  ABSTRACT  
 
Manganese peroxidase (MnP) is an extracellular heme enzyme that catalyzes the peroxide-dependent oxidation of Mn(II) to Mn(III). The Mn(III) is released from the enzyme in complex with oxalate. One heme propionate and the side chains of Glu35, Glu39, and Asp179 were identified as Mn(II) ligands in the 2.0 A resolution crystal structure. The new 1.45 A crystal structure of MnP complexed with Mn(II) provides a more accurate view of the Mn-binding site. New features include possible partial protonation of Glu39 in the Mn-binding site and glycosylation at Ser336. This is also the first report of MnP-inhibitor complex structures. At the Mn-binding site, divalent Cd(II) exhibits octahedral, hexacoordinate ligation geometry similar to that of Mn(II). Cd(II) also binds to a putative second weak metal-binding site with tetrahedral geometry at the C-terminus of the protein. Unlike that for Mn(II) and Cd(II), coordination of trivalent Sm(III) at the Mn-binding site is octacoordinate. Sm(III) was removed from a MnP-Sm(III) crystal by soaking the crystal in oxalate and then reintroduced into the binding site. Thus, direct comparisons of Sm(III)-bound and metal-free structures were made using the same crystal. No ternary complex was observed upon incubation with oxalate. The reversible binding of Sm(III) may be a useful model for the reversible binding of Mn(III) to the enzyme, which is too unstable to allow similar examination.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20495915 M.Hofrichter, R.Ullrich, M.J.Pecyna, C.Liers, and T.Lundell (2010).
New and classic families of secreted fungal heme peroxidases.
  Appl Microbiol Biotechnol, 87, 871-897.  
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.  
18373237 M.Asgher, H.N.Bhatti, M.Ashraf, and R.L.Legge (2008).
Recent developments in biodegradation of industrial pollutants by white rot fungi and their enzyme system.
  Biodegradation, 19, 771-783.  
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
16410517 I.J.Macrae, K.Zhou, F.Li, A.Repic, A.N.Brooks, W.Z.Cande, P.D.Adams, and J.A.Doudna (2006).
Structural basis for double-stranded RNA processing by Dicer.
  Science, 311, 195-198.
PDB code: 2ffl
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.