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PDBsum entry 1hsr
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Oxidoreductase PDB id
1hsr

 

 

 

 

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Contents
Protein chain
336 a.a. *
Ligands
NAG-NAG
HEM
BHO
Metals
_CA ×2
Waters ×241
* Residue conservation analysis
PDB id:
1hsr
Name: Oxidoreductase
Title: Binding mode of benzhydroxamic acid to arthromyces ramosus peroxidase
Structure: Peroxidase. Chain: a. Ec: 1.11.1.7
Source: 'Arthromyces ramosus'. Organism_taxid: 5451
Resolution:
1.60Å     R-factor:   0.187    
Authors: K.Fukuyama,H.Itakura
Key ref:
H.Itakura et al. (1997). Binding mode of benzhydroxamic acid to Arthromyces ramosus peroxidase shown by X-ray crystallographic analysis of the complex at 1.6 A resolution. Febs Lett, 412, 107-110. PubMed id: 9257700 DOI: 10.1016/S0014-5793(97)00751-5
Date:
01-Jul-97     Release date:   01-Jul-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P28313  (PER_ARTRA) -  Peroxidase from Arthromyces ramosus
Seq:
Struc: 		364 a.a.
336 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.11.1.7  - peroxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 a phenolic donor + H2O2 = 2 a phenolic radical donor + 2 H2O
2 × a phenolic donor
 + H2O2
 = 2 × a phenolic radical donor
 + 2 × H2O
      Cofactor: Heme
Heme
Bound ligand (Het Group name = HEM) matches with 95.45% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1016/S0014-5793(97)00751-5 Febs Lett 412:107-110 (1997)
PubMed id: 9257700  
 
 
Binding mode of benzhydroxamic acid to Arthromyces ramosus peroxidase shown by X-ray crystallographic analysis of the complex at 1.6 A resolution.
H.Itakura, Y.Oda, K.Fukuyama.
 
  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 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.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. The BHA and SHA structures with the atom numberings used in the text. 		Figure 3.
Fig. 3. Environment of the BHA molecule shown by a stereo-pair. Possible hydrogen bonds involving BHA are shown by broken lines. The lower side of the figure is the surface of the ARP molecule. The hydrogen bond distances for BHA are O(7)…Arg^52N[ε], 3.3 Å; N(7)…Pro^154O, 2.8 Å; O(8)…His^56N[ε], 2.6 Å; and O(8)…415, 2.7 Å. The respective distances of Fe…415 and Fe…O(8) are 2.7 Å and 4.4 Å. The distance between C(1) in BHA and the methyl carbon bonded to C(18) in the heme is 3.9 Å. The torsion angle about C(1)−C(7) bond of BHA is 14°. The dihedral angle between the benzene ring of BHA and the pyrrole D ring of the heme is 9°.
 
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: Febs Lett (1997, 412, 107-110) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19907057 A.K.Singh, R.P.Kumar, N.Pandey, N.Singh, M.Sinha, A.Bhushan, P.Kaur, S.Sharma, and T.P.Singh (2010).
Mode of binding of the tuberculosis prodrug isoniazid to heme peroxidases: binding studies and crystal structure of bovine lactoperoxidase with isoniazid at 2.7 A resolution.
  J Biol Chem, 285, 1569-1576.
PDB codes: 3gc1 3i6n
19465478 A.K.Singh, N.Singh, M.Sinha, A.Bhushan, P.Kaur, A.Srinivasan, S.Sharma, and T.P.Singh (2009).
Binding modes of aromatic ligands to mammalian heme peroxidases with associated functional implications: crystal structures of lactoperoxidase complexes with acetylsalicylic acid, salicylhydroxamic acid, and benzylhydroxamic acid.
  J Biol Chem, 284, 20311-20318.
PDB code: 3gcl
19015819 J.Kulys, Z.Dapkunas, and R.Stupak (2009).
Intensification of biocatalytical processes by synergistic substrate conversion. Fungal peroxidase catalyzed N-hydroxy derivative oxidation in presence of 10-propyl sulfonic acid phenoxazine.
  Appl Biochem Biotechnol, 158, 445-456.  
18056997 C.Metcalfe, I.K.Macdonald, E.J.Murphy, K.A.Brown, E.L.Raven, and P.C.Moody (2008).
The tuberculosis prodrug isoniazid bound to activating peroxidases.
  J Biol Chem, 283, 6193-6200.
PDB codes: 2v23 2v2e 2vcf 2vcn 2vcs
16443605 R.Pogni, M.C.Baratto, C.Teutloff, S.Giansanti, F.J.Ruiz-Dueñas, T.Choinowski, K.Piontek, A.T.Martínez, F.Lendzian, and R.Basosi (2006).
A tryptophan neutral radical in the oxidized state of versatile peroxidase from Pleurotus eryngii: a combined multifrequency EPR and density functional theory study.
  J Biol Chem, 281, 9517-9526.  
16211102 J.Lee, A.J.Chubb, E.Moman, B.M.McLoughlin, C.T.Sharkey, J.G.Kelly, K.B.Nolan, M.Devocelle, and D.J.Fitzgerald (2005).
Parallel synthesis and in vitro activity of novel anthranilic hydroxamate-based inhibitors of the prostaglandin H2 synthase peroxidase activity.
  Org Biomol Chem, 3, 3678-3685.  
15651036 S.B.Kirton, C.W.Murray, M.L.Verdonk, and R.D.Taylor (2005).
Prediction of binding modes for ligands in the cytochromes P450 and other heme-containing proteins.
  Proteins, 58, 836-844.  
15231844 R.Pierattelli, L.Banci, N.A.Eady, J.Bodiguel, J.N.Jones, P.C.Moody, E.L.Raven, B.Jamart-Grégoire, and K.A.Brown (2004).
Enzyme-catalyzed mechanism of isoniazid activation in class I and class III peroxidases.
  J Biol Chem, 279, 39000-39009.  
12777760 K.Houborg, P.Harris, J.Petersen, P.Rowland, J.C.Poulsen, P.Schneider, J.Vind, and S.Larsen (2003).
Impact of the physical and chemical environment on the molecular structure of Coprinus cinereus peroxidase.
  Acta Crystallogr D Biol Crystallogr, 59, 989-996.
PDB codes: 1h3j 1ly9 1lyc 1lyk
12506108 S.Chouchane, S.Girotto, S.Kapetanaki, J.P.Schelvis, S.Yu, and R.S.Magliozzo (2003).
Analysis of heme structural heterogeneity in Mycobacterium tuberculosis catalase-peroxidase (KatG).
  J Biol Chem, 278, 8154-8162.  
11745121 B.D.Howes, H.A.Heering, T.O.Roberts, F.Schneider-Belhadadd, A.T.Smith, and G.Smulevich (2001).
Mutation of residues critical for benzohydroxamic acid binding to horseradish peroxidase isoenzyme C.
  Biopolymers, 62, 261-267.  
11545682 J.Kulys, and A.Ziemys (2001).
A role of proton transfer in peroxidase-catalyzed process elucidated by substrates docking calculations.
  BMC Struct Biol, 1, 3.  
10981701 N.L.Gil-ad, N.Bar-Nun, T.Noy, and A.M.Mayer (2000).
Enzymes of Botrytis cinerea capable of breaking down hydrogen peroxide.
  FEMS Microbiol Lett, 190, 121-126.  
9609699 A.Henriksen, D.J.Schuller, K.Meno, K.G.Welinder, A.T.Smith, and M.Gajhede (1998).
Structural interactions between horseradish peroxidase C and the substrate benzhydroxamic acid determined by X-ray crystallography.
  Biochemistry, 37, 8054-8060.
PDB code: 2atj
9667928 A.T.Smith, and N.C.Veitch (1998).
Substrate binding and catalysis in heme peroxidases.
  Curr Opin Chem Biol, 2, 269-278.  
9790672 W.A.Doyle, W.Blodig, N.C.Veitch, K.Piontek, and A.T.Smith (1998).
Two substrate interaction sites in lignin peroxidase revealed by site-directed mutagenesis.
  Biochemistry, 37, 15097-15105.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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