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PDBsum entry 2iuz

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
2iuz
Jmol PyMol
Contents
Protein chains
395 a.a. *
Ligands
SO4 ×11
D1H ×2
Waters ×881
* Residue conservation analysis
PDB id:
2iuz
Name: Hydrolase
Title: Crystal structure of aspergillus fumigatus chitinase b1 in complex with c2-dicaffeine
Structure: Chitinase. Chain: a, b. Fragment: residues 1-433. Synonym: aspergillus fumigatus chitinase b1, class v chitinase chib1. Engineered: yes
Source: Aspergillus fumigatus. Organism_taxid: 5085. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
1.95Å     R-factor:   0.186     R-free:   0.223
Authors: A.W.Schuttelkopf,O.A.Andersen,F.V.Rao,M.Allwood,C.M.Lloyd, I.M.Eggleston,D.M.F.Van Aalten
Key ref:
A.W.Schüttelkopf et al. (2006). Screening-based discovery and structural dissection of a novel family 18 chitinase inhibitor. J Biol Chem, 281, 27278-27285. PubMed id: 16844689 DOI: 10.1074/jbc.M604048200
Date:
08-Jun-06     Release date:   12-Jun-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q873X9  (Q873X9_ASPFM) -  Endochitinase B1
Seq:
Struc:
433 a.a.
395 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.14  - Chitinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of the 1,4-beta-linkages of N-acetyl-D-glucosamine polymers of chitin.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   2 terms 
  Biochemical function     hydrolase activity, hydrolyzing O-glycosyl compounds     2 terms  

 

 
DOI no: 10.1074/jbc.M604048200 J Biol Chem 281:27278-27285 (2006)
PubMed id: 16844689  
 
 
Screening-based discovery and structural dissection of a novel family 18 chitinase inhibitor.
A.W.Schüttelkopf, O.A.Andersen, F.V.Rao, M.Allwood, C.Lloyd, I.M.Eggleston, D.M.van Aalten.
 
  ABSTRACT  
 
Family 18 chitinases play key roles in the life cycles of a variety of organisms ranging from bacteria to man. Very recently it has been shown that one of the mammalian chitinases is highly overexpressed in the asthmatic lung and contributes to the pathogenic process through recruitment of inflammatory cells. Although several potent natural product chitinase inhibitors have been identified, their chemotherapeutic potential or their use as cell biological tools is limited due to their size, complex chemistry, and limited availability. We describe a virtual screening-based approach to identification of a novel, purine-based, chitinase inhibitor. This inhibitor acts in the low micromolar (Ki=2.8+/-0.2 microM) range in a competitive mode. Dissection of the binding mode by x-ray crystallography reveals that the compound, which consists of two linked caffeine moieties, binds in the active site through extensive and not previously observed stacking interactions with conserved, solvent exposed tryptophans. Such exposed aromatics are also present in the structures of many other carbohydrate processing enzymes. The compound exhibits favorable chemical properties and is likely to be useful as a general scaffold for development of pan-family 18 chitinase inhibitors.
 
  Selected figure(s)  
 
Figure 1.
FIGURE 1. The active site of AfChiB1 in complex with xanthine derivatives. Active site residues are shown as gray stick models, possible hydrogen bonds are indicated by dotted black lines, crystallographic waters interacting with ligands are shown as orange spheres. A, the crystallographic complex with pentoxifylline (purple) (19), which provided the starting point for virtual screening. The 3-methylxanthine moiety used as the rigid fragment is shown dark, whereas the 7-methyl group and the oxohexyl tail are lighter. B, the docked conformations (pale green) of the compounds are listed in Table 2. Possible hydrogen bonds have been omitted. C, crystal structure of the AfChiB1-C[2]-dicaffeine complex (stereo). The major conformation of the ligand is shown in purple, the minor (q = 0.25) conformation is shown semitransparently in orange. The unbiased |F[o]| - |F[c]|, [c] electron density map is shown contoured at 2.5 . The label color indicates conservation of the corresponding residue among bacterial-like family 18 chitinases using a color gradient from red (not conserved) to green (completely conserved): to evaluate sequence conservation, a list of family 18 glycoside hydrolases was obtained from CAZy. After removing entries not marked as chitinases (EC 3.2.1.14) and entries lacking a full-length UniProt entry, sequences were downloaded from UniProt and aligned with ClustalW (1). Elimination of sequences lacking the active site motif DXXDXDXE yielded 165 putative chitinase sequences, which were separated by sequence length into 129 bacterial-like chitinases (proteins longer than 370 amino acids) and 36 plant-like chitinases (proteins shorter than 370 amino acids).
Figure 2.
FIGURE 2. A, the chemical structures of the compounds discussed. Standard purine/xanthine atom numbering is shown for compound 1. B, enrichment of particular fragment structure modifications after docking. The bars show the size distributions for groups attached to N-1, N-3, N-7, and C-8 of the xanthine fragment structure for the set of 50,193 fragment search matches (labeled db) and the set of 263 docked compounds selected as possible ligands (labeled docked), distinguishing no attachment (light color; not for N-3), a single non-hydrogen atom (medium color), and more than one non-hydrogen atoms (dark color). C, Lineweaver-Burk plot of C[2]-dicaffeine inhibition of AfChiB1 at different concentrations. The data are compatible with a competitive inhibition model, giving a K[i] of 2.8 ± 0.2 µM.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 27278-27285) copyright 2006.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21044846 A.W.Schüttelkopf, L.Gros, D.E.Blair, J.A.Frearson, D.M.van Aalten, and I.H.Gilbert (2010).
Acetazolamide-based fungal chitinase inhibitors.
  Bioorg Med Chem, 18, 8334-8340.
PDB code: 2xtk
21168763 C.L.Rush, A.W.Schüttelkopf, R.Hurtado-Guerrero, D.E.Blair, A.F.Ibrahim, S.Desvergnes, I.M.Eggleston, and D.M.van Aalten (2010).
Natural product-guided discovery of a fungal chitinase inhibitor.
  Chem Biol, 17, 1275-1281.
PDB codes: 2xuc 2xvn 2xvp
20026047 H.C.Dorfmueller, and D.M.van Aalten (2010).
Screening-based discovery of drug-like O-GlcNAcase inhibitor scaffolds.
  FEBS Lett, 584, 694-700.
PDB code: 2x0y
20829286 J.Yang, Z.Gan, Z.Lou, N.Tao, Q.Mi, L.Liang, Y.Sun, Y.Guo, X.Huang, C.Zou, Z.Rao, Z.Meng, and K.Q.Zhang (2010).
Crystal structure and mutagenesis analysis of chitinase CrChi1 from the nematophagous fungus Clonostachys rosea in complex with the inhibitor caffeine.
  Microbiology, 156, 3566-3574.
PDB codes: 3g6l 3g6m
18285371 I.M.Overton, G.Padovani, M.A.Girolami, and G.J.Barton (2008).
ParCrys: a Parzen window density estimation approach to protein crystallization propensity prediction.
  Bioinformatics, 24, 901-907.  
18355729 O.A.Andersen, A.Nathubhai, M.J.Dixon, I.M.Eggleston, and D.M.van Aalten (2008).
Structure-based dissection of the natural product cyclopentapeptide chitinase inhibitor argifin.
  Chem Biol, 15, 295-301.
PDB codes: 3ch9 3chc 3chd 3che 3chf
17854405 J.P.Latgé (2007).
The cell wall: a carbohydrate armour for the fungal cell.
  Mol Microbiol, 66, 279-290.  
17524989 R.Hurtado-Guerrero, and D.M.van Aalten (2007).
Structure of Saccharomyces cerevisiae chitinase 1 and screening-based discovery of potent inhibitors.
  Chem Biol, 14, 589-599.
PDB codes: 2uy2 2uy3 2uy4 2uy5
17148602 S.DebRoy, J.Dao, M.Söderberg, O.Rossier, and N.P.Cianciotto (2006).
Legionella pneumophila type II secretome reveals unique exoproteins and a chitinase that promotes bacterial persistence in the lung.
  Proc Natl Acad Sci U S A, 103, 19146-19151.  
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 code is shown on the right.

 

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