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PDBsum entry 2bz9

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protein ligands Protein-protein interface(s) links
Electron transport PDB id
2bz9
Jmol
Contents
Protein chains
430 a.a. *
Ligands
HEM ×2
Waters ×216
* Residue conservation analysis
PDB id:
2bz9
Name: Electron transport
Title: Ligand-free structure of sterol 14alpha-demethylase from mycobacterium tuberculosis in p2(1) space group
Structure: Sterol 14alpha-demethylase. Chain: a, b. Engineered: yes. Mutation: yes
Source: Mycobacterium tuberculosis. Organism_taxid: 1773. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Monomer (from PDB file)
Resolution:
2.21Å     R-factor:   0.215     R-free:   0.275
Authors: L.V.Yermalitskaya,M.R.Waterman,L.M.Podust
Key ref: L.M.Podust et al. (2007). Small-molecule scaffolds for CYP51 inhibitors identified by high-throughput screening and defined by X-ray crystallography. Antimicrob Agents Chemother, 51, 3915-3923. PubMed id: 17846131
Date:
12-Aug-05     Release date:   07-Dec-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam  
P9WPP9  (CP51_MYCTU) -  Lanosterol 14-alpha demethylase
Seq:
Struc:
451 a.a.
430 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.1.14.13.70  - Sterol 14-alpha-demethylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Sterol ring B, C, D modification
      Reaction: A 14-alpha-methylsteroid + 3 O2 + 3 NADPH = a Delta14-steroid + formate + 3 NADP+ + 4 H2O
14-alpha-methylsteroid
+ 3 × O(2)
+ 3 × NADPH
= Delta(14)-steroid
Bound ligand (Het Group name = HEM)
matches with 62.00% similarity
+ formate
+ 3 × NADP(+)
+ 4 × H(2)O
      Cofactor: Heme-thiolate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     demethylation   6 terms 
  Biochemical function     oxidoreductase activity     7 terms  

 

 
    reference    
 
 
Antimicrob Agents Chemother 51:3915-3923 (2007)
PubMed id: 17846131  
 
 
Small-molecule scaffolds for CYP51 inhibitors identified by high-throughput screening and defined by X-ray crystallography.
L.M.Podust, J.P.von Kries, A.N.Eddine, Y.Kim, L.V.Yermalitskaya, R.Kuehne, H.Ouellet, T.Warrier, M.Alteköster, J.S.Lee, J.Rademann, H.Oschkinat, S.H.Kaufmann, M.R.Waterman.
 
  ABSTRACT  
 
Sterol 14alpha-demethylase (CYP51), a major checkpoint in membrane sterol biosynthesis, is a key target for fungal antibiotic therapy. We sought small organic molecules for lead candidate CYP51 inhibitors. The changes in CYP51 spectral properties following ligand binding make CYP51 a convenient target for high-throughput screening technologies. These changes are characteristic of either substrate binding (type I) or inhibitor binding (type II) in the active site. We screened a library of 20,000 organic molecules against Mycobacterium tuberculosis CYP51 (CYP51(Mt)), examined the top type I and type II binding hits for their inhibitory effects on M. tuberculosis in broth culture, and analyzed them spectrally for their ability to discriminate between CYP51(Mt) and two reference M. tuberculosis CYP proteins, CYP130 and CYP125. We determined the binding mode for one of the top type II hits, alpha-ethyl-N-4-pyridinyl-benzeneacetamide (EPBA), by solving the X-ray structure of the CYP51(Mt)-EPBA complex to a resolution of 1.53 A. EPBA binds coordinately to the heme iron in the CYP51(Mt) active site through a lone pair of nitrogen electrons and also through hydrogen bonds with residues H259 and Y76, which are invariable in the CYP51 family, and hydrophobic interactions in a phylum- and/or substrate-specific cavity of CYP51. We also identified a second compound with structural and binding properties similar to those of EPBA, 2-(benzo[d]-2,1,3-thiadiazole-4-sulfonyl)-2-amino-2-phenyl-N-(pyridinyl-4)-acetamide (BSPPA). The congruence between the geometries of EPBA and BSPPA and the CYP51 binding site singles out EPBA and BSPPA as lead candidate CYP51 inhibitors with optimization potential for efficient discrimination between host and pathogen enzymes.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20625155 A.G.Warrilow, C.M.Martel, J.E.Parker, N.Melo, D.C.Lamb, W.D.Nes, D.E.Kelly, and S.L.Kelly (2010).
Azole binding properties of Candida albicans sterol 14-alpha demethylase (CaCYP51).
  Antimicrob Agents Chemother, 54, 4235-4245.  
19593597 C.Sheng, S.Chen, H.Ji, G.Dong, X.Che, W.Wang, Z.Miao, J.Yao, J.Lü, W.Guo, and W.Zhang (2010).
Evolutionary trace analysis of CYP51 family: implication for site-directed mutagenesis and novel antifungal drug design.
  J Mol Model, 16, 279-284.  
19635450 H.Ouellet, J.B.Johnston, and P.R.Ortiz de Montellano (2010).
The Mycobacterium tuberculosis cytochrome P450 system.
  Arch Biochem Biophys, 493, 82-95.  
20385875 P.S.Doyle, C.K.Chen, J.B.Johnston, S.D.Hopkins, S.S.Leung, M.P.Jacobson, J.C.Engel, J.H.McKerrow, and L.M.Podust (2010).
A nonazole CYP51 inhibitor cures Chagas' disease in a mouse model of acute infection.
  Antimicrob Agents Chemother, 54, 2480-2488.  
20446763 T.C.Pochapsky, S.Kazanis, and M.Dang (2010).
Conformational plasticity and structure/function relationships in cytochromes P450.
  Antioxid Redox Signal, 13, 1273-1296.  
19190730 C.K.Chen, P.S.Doyle, L.V.Yermalitskaya, Z.B.Mackey, K.K.Ang, J.H.McKerrow, and L.M.Podust (2009).
Trypanosoma cruzi CYP51 Inhibitor Derived from a Mycobacterium tuberculosis Screen Hit.
  PLoS Negl Trop Dis, 3, e372.
PDB codes: 2w09 2w0a 2w0b
19470512 C.Sheng, Z.Miao, H.Ji, J.Yao, W.Wang, X.Che, G.Dong, J.Lü, W.Guo, and W.Zhang (2009).
Three-dimensional model of lanosterol 14 alpha-demethylase from Cryptococcus neoformans: active-site characterization and insights into azole binding.
  Antimicrob Agents Chemother, 53, 3487-3495.  
19605350 L.M.Podust, H.Ouellet, J.P.von Kries, and P.R.de Montellano (2009).
Interaction of Mycobacterium tuberculosis CYP130 with heterocyclic arylamines.
  J Biol Chem, 284, 25211-25219.
PDB codes: 2wgy 2wh8 2whf
18367444 A.N.Eddine, J.P.von Kries, M.V.Podust, T.Warrier, S.H.Kaufmann, and L.M.Podust (2008).
X-ray structure of 4,4'-dihydroxybenzophenone mimicking sterol substrate in the active site of sterol 14alpha-demethylase (CYP51).
  J Biol Chem, 283, 15152-15159.
PDB code: 2vku
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.