1HSR

BINDING MODE OF BENZHYDROXAMIC ACID TO ARTHROMYCES RAMOSUS PEROXIDASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 

wwPDB Validation 3D Report Full Report



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

  • DOI: 10.1016/s0014-5793(97)00751-5
  • Primary Citation of Related Structures:  
    1HSR

  • 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: 
    • 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 Biology, Graduate School of Science, Osaka University, Toyonaka, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PEROXIDASEA344Agaricales sp. 'Arthromyces ramosusMutation(s): 0 
EC: 1.11.1.7
Find proteins for P28313 (Arthromyces ramosus)
Explore P28313 
Go to UniProtKB:  P28313
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2 N-Glycosylation
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

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

Download CCD File 
A
BENZHYDROXAMIC ACID
C7 H7 N O2
VDEUYMSGMPQMIK-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.5α = 90
b = 74.5β = 90
c = 118.01γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-07-01
    Type: Initial release
  • Version 1.1: 2008-03-24
    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, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary