Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.163 

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This is version 2.0 of the entry. See complete history


Binding of salicylhydroxamic acid and several aromatic donor molecules to Arthromyces ramosus peroxidase, investigated by X-ray crystallography, optical difference spectroscopy, NMR relaxation, molecular dynamics, and kinetics.

Tsukamoto, K.Itakura, H.Sato, K.Fukuyama, K.Miura, S.Takahashi, S.Ikezawa, H.Hosoya, T.

(1999) Biochemistry 38: 12558-12568

  • DOI: 10.1021/bi982925l
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The X-ray crystal structure of the complex of salicylhydroxamic acid (SHA) with Arthromyces ramosus peroxidase (ARP) has been determined at 1.9 A resolution. The position of SHA in the active site of ARP is similar to that of the complex of benzhydroxamic acid (BHA) with ARP [Itakura, H ...

    The X-ray crystal structure of the complex of salicylhydroxamic acid (SHA) with Arthromyces ramosus peroxidase (ARP) has been determined at 1.9 A resolution. The position of SHA in the active site of ARP is similar to that of the complex of benzhydroxamic acid (BHA) with ARP [Itakura, H., et al. (1997) FEBS Lett. 412, 107-110]. The aromatic ring of SHA binds to a hydrophobic region at the opening of the distal pocket, and the hydroxamic acid moiety forms hydrogen bonds with the His56, Arg52, and Pro154 residues but is not asscoiated with the heme iron. X-ray analyses of ARP-resorcinol and ARP-p-cresol complexes failed to identify the aromatic donor molecules, most likely due to the very low affinities of these aromatic donors for ARP. Therefore, we examined the locations of these and other aromatic donors on ARP by the molecular dynamics method and found that the benzene rings are trapped similarly by hydrophobic interactions with the Ala92, Pro156, Leu192, and Phe230 residues at the entrance of the heme pocket, but the dihedral angles between the benzene rings and the heme plane vary from donor to donor. The distances between the heme iron and protons of SHA and resorcinol are similar to those obtained by NMR relaxation. Although SHA and BHA are usually considered potent inhibitors for peroxidase, they were found to reduce compound I and compound II of ARP and horseradish peroxidase C in the same manner as p-cresol and resorcinol. The aforementioned spatial relationships of these aromatic donors to the heme iron in ARP are discussed with respect to the quantum chemical mechanism of electron transfer in peroxidase reactions.

    Related Citations: 
    • Binding mode of benzhydroxamic acid to Arthromyces ramosus peroxidase shown by X-ray crystallographic analysis of the complex at 1.6 A resolution.
      Itakura, H., Oda, Y., Fukuyama, K.
      (1997) FEBS Lett 412: 107
    • Binding of iodide to Arthromyces ramosus peroxidase investigated with X-ray crystallographic analysis, 1H and 127I NMR spectroscopy, and steady-state kinetics.
      Fukuyama, K., Sato, K., Itakura, H., Takahashi, S., Hosoya, T.
      (1997) J Biol Chem 272: 5752
    • Pentacoordination of the heme iron of Arthromyces ramosus peroxidase shown by a 1.8 A resolution crystallographic study at pH 4.5.
      Kunishima, N., Amada, F., Fukuyama, K., Kawamoto, M., Matsunaga, T., Matsubara, H.
      (1996) FEBS Lett 378: 291
    • Crystal structures of cyanide- and triiodide-bound forms of Arthromyces ramosus peroxidase at different pH values. Perturbations of active site residues and their implication in enzyme catalysis.
      Fukuyama, K., Kunishima, N., Amada, F., Kubota, T., Matsubara, H.
      (1995) J Biol Chem 270: 21884
    • Crystal structure of the fungal peroxidase from Arthromyces ramosus at 1.9 A resolution. Structural comparisons with the lignin and cytochrome c peroxidases.
      Kunishima, N., Fukuyama, K., Matsubara, H., Hatanaka, H., Shibano, Y., Amachi, T.
      (1994) J Mol Biol 235: 331
    • Crystallization and preliminary X-ray diffraction studies of peroxidase from a fungus Arthromyces ramosus.
      Kunishima, N., Fukuyama, K., Wakabayashi, S., Sumida, M., Takaya, M., Shibano, Y., Amachi, T., Matsubara, H.
      (1993) Proteins 15: 216

    Organizational Affiliation

    Department of Microbial Chemistry, Faculty of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan.

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (PEROXIDASE)A344Agaricales sp. 'Arthromyces ramosusMutation(s): 0 
Find proteins for P28313 (Arthromyces ramosus)
Explore P28313 
Go to UniProtKB:  P28313
Protein Feature View
  • Reference Sequence


Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on HEM

Download Ideal Coordinates CCD File 
C34 H32 Fe N4 O4
 Ligand Interaction
Query on BMA

Download Ideal Coordinates CCD File 
C [auth A]beta-D-mannopyranose
C6 H12 O6
 Ligand Interaction
Query on SHA

Download Ideal Coordinates CCD File 
C7 H7 N O3
 Ligand Interaction
Query on CA

Download Ideal Coordinates CCD File 
D [auth A], E [auth A]CALCIUM ION
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.163 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.41α = 90
b = 74.41β = 90
c = 116.95γ = 90
Software Package:
Software NamePurpose
PROCESSdata collection
PROCESSdata reduction
X-PLORmodel building
PROCESSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-12-29
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations
  • Version 1.4: 2019-11-27
    Changes: Database references, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary