PDBsum entry 1ks5

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protein links
Hydrolase PDB id
Protein chain
223 a.a. *
Waters ×125
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Structure of aspergillus niger endoglucanase
Structure: Endoglucanase a. Chain: a. Fragment: catalytic domain. Ec:
Source: Aspergillus niger. Organism_taxid: 5061. Strain: cbs 554.65
2.10Å     R-factor:   0.175     R-free:   0.191
Authors: S.Khademi,D.Zhang,S. M.Swanson,A.Wartenberg,C.Witte,E. F.Meyer
Key ref:
S.Khademi et al. (2002). Determination of the structure of an endoglucanase from Aspergillus niger and its mode of inhibition by palladium chloride. Acta Crystallogr D Biol Crystallogr, 58, 660-667. PubMed id: 11914491 DOI: 10.1107/S0907444902003360
10-Jan-02     Release date:   21-Jan-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
O74705  (O74705_ASPNG) -  Endoglucanase A
239 a.a.
223 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Cellulase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endohydrolysis of 1,4-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     hydrolase activity     4 terms  


DOI no: 10.1107/S0907444902003360 Acta Crystallogr D Biol Crystallogr 58:660-667 (2002)
PubMed id: 11914491  
Determination of the structure of an endoglucanase from Aspergillus niger and its mode of inhibition by palladium chloride.
S.Khademi, D.Zhang, S.M.Swanson, A.Wartenberg, K.Witte, E.F.Meyer.
The fungus Aspergillus niger is a main source of industrial cellulase. beta-1,4-Endoglucanase is the major component of cellulase from A. niger. In spite of widespread applications, little is known about the structure of this enzyme. Here, the structure of beta-1,4-endoglucanase from A. niger (EglA) was determined at 2.1 A resolution. Although there is a low sequence identity between EglA and CelB2, another member of family 12, the three-dimensional structures of their core regions are quite similar. The structural differences are mostly found in the loop regions, where CelB2 has an extra beta-sheet (beta-sheet C) at the non-reducing end of the binding cleft of the native enzyme. Incubation of EglA with PdCl(2) irreversibly inhibits the EglA activity. Structural studies of the enzyme-palladium complex show that three Pd(2+) ions bind to each EglA molecule. One of the Pd(2+) ions forms a coordinate covalent bond with Met118 S(delta) and the nucleophilic Glu116 O(epsilon1) at the active site of the enzyme. The other two Pd(2+) ions bind on the surface of the protein. Binding of Pd(2+) ions to EglA does not change the general conformation of the backbone of the protein significantly. Based on this structural study, one can conclude that the palladium ion directly binds to and blocks the active site of EglA and thus inactivates the enzyme.
  Selected figure(s)  
Figure 2.
Figure 2 Ribbon stereo diagram of EglA. -sheet A is in blue, -sheet B is in green and helices are in red.
Figure 6.
Figure 6 (a) The structure of EglA complexed with three Pd^2+ ions, B, C and D. (b), (c) and (d) The binding site for Pd^2+ ions B, C and D, respectively. The electron-density maps (F[o] - F[c]) for the three Pd^2+ ions are contoured at 7.0 . The Pd^2+ ions are in green.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2002, 58, 660-667) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19205687 H.Nakazawa, K.Okada, T.Onodera, W.Ogasawara, H.Okada, and Y.Morikawa (2009).
Directed evolution of endoglucanase III (Cel12A) from Trichoderma reesei.
  Appl Microbiol Biotechnol, 83, 649-657.  
15604820 L.Hildén, and G.Johansson (2004).
Recent developments on cellulases and carbohydrate-binding modules with cellulose affinity.
  Biotechnol Lett, 26, 1683-1693.  
14627738 M.Sandgren, P.J.Gualfetti, C.Paech, S.Paech, A.Shaw, L.S.Gross, M.Saldajeno, G.I.Berglund, T.A.Jones, and C.Mitchinson (2003).
The Humicola grisea Cel12A enzyme structure at 1.2 A resolution and the impact of its free cysteine residues on thermal stability.
  Protein Sci, 12, 2782-2793.
PDB codes: 1olq 1olr
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