1YYD image
Deposition Date 2005-02-24
Release Date 2005-05-10
Last Version Date 2024-11-20
Entry Detail
PDB ID:
1YYD
Keywords:
Title:
High Resolution Crystal Structure of Manganese Peroxidase
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
1.45 Å
R-Value Free:
0.22
R-Value Work:
0.14
R-Value Observed:
0.18
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Peroxidase manganese-dependent I
Gene (Uniprot):MNP1
Chain IDs:A
Chain Length:357
Number of Molecules:1
Biological Source:Phanerochaete chrysosporium
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
ASN A ASN GLYCOSYLATION SITE
SER A SER GLYCOSYLATION SITE
Primary Citation
High-Resolution Crystal Structure of Manganese Peroxidase: Substrate and Inhibitor Complexes.
Biochemistry 44 6463 6470 (2005)
PMID: 15850380 DOI: 10.1021/bi047318e

Abstact

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.

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Primary Citation of related structures