1CK6

BINDING MODE OF SALICYLHYDROXAMIC ACID TO ARTHROMYCES RAMOSUS PEROXIDASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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


  • 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 benzhydro ...

    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: 
    • 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
    • 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
    • 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
    • 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) Protein Sci. 15: 216
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (PEROXIDASE)
A
344Arthromyces ramosusEC: 1.11.1.7
Find proteins for P28313 (Arthromyces ramosus)
Go to UniProtKB:  P28313
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SHA
Query on SHA

Download SDF File 
Download CCD File 
A
SALICYLHYDROXAMIC ACID
C7 H7 N O3
HBROZNQEVUILML-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
HEM
Query on HEM

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.163 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 74.410α = 90.00
b = 74.410β = 90.00
c = 116.950γ = 90.00
Software Package:
Software NamePurpose
PROCESSdata reduction
PROCESSdata scaling
X-PLORphasing
X-PLORrefinement
PROCESSdata collection
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-12-29
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations