1YYD

High Resolution Crystal Structure of Manganese Peroxidase

Summary for 1YYD

• Entry DOI: 10.2210/pdb1yyd/pdb
• Related: 1MN1 1MN2 1MNP
• Descriptor: Peroxidase manganese-dependent I, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, alpha-D-mannopyranose, ... (9 entities in total)
• Functional Keywords: peroxidase, heme enzyme, oxidoreductase
• Biological source: Phanerochaete chrysosporium
• Cellular location: Secreted: Q02567
• Total number of polymer chains: 1
• Total formula weight: 39211.46

Authors

Sundaramoorthy, M.,Youngs, H.L.,Gold, M.H.,Poulos, T.L. (deposition date: 2005-02-24, release date: 2005-05-10, Last modification date: 2023-08-23)

Primary citation

Sundaramoorthy, M.,Youngs, H.L.,Gold, M.H.,Poulos, T.L.
High-Resolution Crystal Structure of Manganese Peroxidase: Substrate and Inhibitor Complexes.
Biochemistry, 44:6463-6470, 2005

PubMed 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.

PubMed: 15850380
DOI: 10.1021/bi047318e

Experimental method

X-RAY DIFFRACTION (1.45 Å)