1YYD

High Resolution Crystal Structure of Manganese Peroxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.141 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

High-Resolution Crystal Structure of Manganese Peroxidase: Substrate and Inhibitor Complexes.

Sundaramoorthy, M.Youngs, H.L.Gold, M.H.Poulos, T.L.

(2005) Biochemistry 44: 6463-6470

  • DOI: 10.1021/bi047318e
  • Primary Citation of Related Structures:  
  • Also Cited By: 3M8M, 3M5Q

  • 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, ...

    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.


    Related Citations: 
    • Crystal structures of substrate binding site mutants of manganese peroxidase
      Sundaramoorthy, M.,Kishi, K.,Gold, M.H.,Poulos, T.L.
      (1997) J.Biol.Chem. 272: 17574
    • The crystal structure of manganese peroxidase from Phanerochaete chrysosporium at 2.06 A resolution
      Sundaramoorthy, M.,Kishi, K.,Gold, M.H.,Poulos, T.L.
      (1994) J.Biol.Chem. 269: 32759


    Organizational Affiliation

    Division of Nephrology, Department of Medicine, Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232-2372, USA. m.sundaramoorthy@ vanderbilt.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxidase manganese-dependent I
A
357Phanerochaete chrysosporiumMutation(s): 0 
Gene Names: MNP1
EC: 1.11.1.13
Find proteins for Q02567 (Phanerochaete chrysosporium)
Go to UniProtKB:  Q02567
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
HEM
Query on HEM

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A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
NAG
Query on NAG

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A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.141 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 160.967α = 90.00
b = 45.423β = 96.89
c = 52.930γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
X-GENdata scaling
X-PLORphasing
X-GENdata reduction
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-10
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description