1HSR

BINDING MODE OF BENZHYDROXAMIC ACID TO ARTHROMYCES RAMOSUS PEROXIDASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 107-110


  • PubMed Abstract: 
  • The crystal structure of Arthromyces ramosus peroxidase (ARP) in complex with benzhydroxamic acid (BHA) as determined by X-ray analysis at 1.6 A shows unambiguously how BHA binds to ARP. BHA is located in the distal heme pocket. Its functional groups ...

    The crystal structure of Arthromyces ramosus peroxidase (ARP) in complex with benzhydroxamic acid (BHA) as determined by X-ray analysis at 1.6 A shows unambiguously how BHA binds to ARP. BHA is located in the distal heme pocket. Its functional groups are held by three hydrogen bonds to His56N(epsilon), Arg52N(epsilon), and Pro(154)O, but are too far away to interact with the heme iron. The aromatic ring of BHA is positioned at the entrance of the channel to the heme pocket, approximately parallel to the heme group. Most water molecules at the active site of the native enzyme are replaced by BHA, leaving a ligand, probably a water molecule, at the sixth position of the heme. Results are compared with spectroscopic data.


    Related Citations: 
    • 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
    • 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
    • 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
    • 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


    Organizational Affiliation

    Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PEROXIDASE
A
344Arthromyces ramosusEC: 1.11.1.7
Find proteins for P28313 (Arthromyces ramosus)
Go to UniProtKB:  P28313
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-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

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BHO
Query on BHO

Download SDF File 
Download CCD File 
A
BENZHYDROXAMIC ACID
C7 H7 N O2
VDEUYMSGMPQMIK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Work: 0.187 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 74.500α = 90.00
b = 74.500β = 90.00
c = 118.010γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-07-01
    Type: Initial release
  • Version 1.1: 2008-03-24
    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, Other