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PDBsum entry 1h5v

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protein ligands metals links
Hydrolase PDB id
1h5v
Jmol
Contents
Protein chain
301 a.a. *
Ligands
GLC-SSG-SGC-SGC-
MA3
Metals
_CA ×10
_NA ×2
Waters ×537
* Residue conservation analysis
PDB id:
1h5v
Name: Hydrolase
Title: Thiopentasaccharide complex of the endoglucanase cel5a from bacillus agaradharens at 1.1 a resolution in the tetragonal crystal form
Structure: Endoglucanase 5a. Chain: a. Fragment: catalytic core domain residues 27-331. Synonym: endo-1,4-beta-glucanase, cellulase. Engineered: yes
Source: Bacillus agaradhaerens. Organism_taxid: 76935. Strain: pl2306. Expressed in: bacillus subtilis. Expression_system_taxid: 1423.
Resolution:
1.10Å     R-factor:   0.120     R-free:   0.138
Authors: A.Varrot,G.Sulzenbacher,M.Schulein,H.Driguez,G.J.Davies
Key ref:
A.Varrot et al. (2001). Atomic resolution structure of endoglucanase Cel5A in complex with methyl 4,4II,4III,4IV-tetrathio-alpha-cellopentoside highlights the alternative binding modes targeted by substrate mimics. Acta Crystallogr D Biol Crystallogr, 57, 1739-1742. PubMed id: 11679762 DOI: 10.1107/S0907444901013993
Date:
28-May-01     Release date:   23-May-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O85465  (GUN5_BACAG) -  Endoglucanase 5A
Seq:
Struc:
400 a.a.
301 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.4  - 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     carbohydrate metabolic process   1 term 
  Biochemical function     hydrolase activity, hydrolyzing O-glycosyl compounds     1 term  

 

 
DOI no: 10.1107/S0907444901013993 Acta Crystallogr D Biol Crystallogr 57:1739-1742 (2001)
PubMed id: 11679762  
 
 
Atomic resolution structure of endoglucanase Cel5A in complex with methyl 4,4II,4III,4IV-tetrathio-alpha-cellopentoside highlights the alternative binding modes targeted by substrate mimics.
A.Varrot, M.Schülein, S.Fruchard, H.Driguez, G.J.Davies.
 
  ABSTRACT  
 
Many three-dimensional structures of retaining beta-D-glycoside hydrolases have been determined, yet oligosaccharide complexes in which the ligand spans the catalytic centre are rare. Those that have been reported so far have revealed two modes of binding: those in which the substrate adopts a distorted skew-boat or envelope conformation in the -1 subsite, reflecting the distortion observed during the catalytic cycle, and those which bypass the true catalytic centre and thus lie in a non-productive manner across the -1 subsite. The three-dimensional structure of a retaining endocellulase, Bacillus agaradhaerens Cel5A, in complex with methyl 4,4(II),4(III),4(IV)-tetrathio-alpha-cellopentoside falls into this latter category. The 1.1 A structure reveals the binding of five pyranosides, all in the (4)C(1) chair conformation, occupying the -3, -2, +1 and +2 subsites whilst evading the catalytic machinery located in the true -1 subsite. Such binding is in marked contrast to the structure of another retaining endocellulase, the Fusarium oxysporum Cel7B, the identical ligand in which displayed a distorted skew-boat conformation at the active centre. These two binding modes may reflect different steps in the binding and catalytic process.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 (a) Observations of distorted pyranoside rings in the active centre of retaining -D glycoside hydrolases. (1) 4E conformation of an unhydrolysed chiotobiose in the centre of S. marcesens chitobiase (Tews et al., 1996[Tews, I., Perrakis, A., Oppenheim, A., Dauter, Z., Wilson, K. S. & Vorgias, C. E. (1996). Nature Struct. Biol. 3, 638-648.]); (2) 1S[3] skew-boat conformation of 2,4-dinitrophenyl 2-deoxy-2-fluoro- -D-cellobioside bound to Cel5A (Davies, Dauter et al., 1998[Davies, G. J., Dauter, M., Brzozowski, A. M., Bjornvad, M. E., Anderson, K. V. & Schülein, M. (1998). Biochemistry, 37, 1926-1932.]); (3) 1S[3] skew-boat conformation for methyl 4^II,4^III,4^IV-tetrathio- -cellopentoside bound to H. insolens Cel7B (Sulzenbacher et al., 1996[Sulzenbacher, G., Driguez, H., Henrissat, B., Schülein, M. & Davies, G. J. (1996). Biochemistry, 35, 15280-15287.]). (b) Compound 4 is the same methyl 4^II,4^III,4^IV-tetrathio- -cellopentoside observed as a string of 4C[1] chair conformed sugars, as observed in Cel5A (this work).
Figure 4.
Figure 4 A schematic representation of the interactions of Cel5A with the SDP5 inhibitor. Only the displaced -1, +1 and +2 subsites are shown for clarity.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 1739-1742) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19543714 H.Schagerlöf, C.Nilsson, L.Gorton, F.Tjerneld, H.Stålbrand, and A.Cohen (2009).
Use of 18O water and ESI-MS detection in subsite characterisation and investigation of the hydrolytic action of an endoglucanase.
  Anal Bioanal Chem, 394, 1977-1984.  
19053460 P.Peralta-Yahya, B.T.Carter, H.Lin, H.Tao, and V.W.Cornish (2008).
High-throughput selection for cellulase catalysts using chemical complementation.
  J Am Chem Soc, 130, 17446-17452.  
15853815 J.Jänis, J.Hakanpää, N.Hakulinen, F.M.Ibatullin, A.Hoxha, P.J.Derrick, J.Rouvinen, and P.Vainiotalo (2005).
Determination of thioxylo-oligosaccharide binding to family 11 xylanases using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and X-ray crystallography.
  FEBS J, 272, 2317-2333.
PDB code: 1xnk
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