PDBsum entry 1qi2

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Hydrolase PDB id
Protein chain
302 a.a. *
_CA ×5
Waters ×381
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Endoglucanase cel5a from bacillus agaradhaerens in the tetra crystal form in complex with 2',4'-dinitrophenyl 2-deoxy-2- d-cellotrioside
Structure: Endoglucanase b. Chain: a. Fragment: catalytic core domain. Synonym: cellulase, endo-1,4-beta-glucanase. Engineered: yes
Source: Bacillus agaradhaerens. Organism_taxid: 76935. Strain: ac13. Expressed in: bacillus subtilis. Expression_system_taxid: 1423.
1.75Å     R-factor:   0.170     R-free:   0.210
Authors: A.Varrot,M.Schulein,G.J.Davies
Key ref:
A.Varrot et al. (2000). Insights into ligand-induced conformational change in Cel5A from Bacillus agaradhaerens revealed by a catalytically active crystal form. J Mol Biol, 297, 819-828. PubMed id: 10731432 DOI: 10.1006/jmbi.2000.3567
02-Jun-99     Release date:   07-Jun-00    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
O85465  (GUN5_BACAG) -  Endoglucanase 5A
400 a.a.
302 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     carbohydrate metabolic process   1 term 
  Biochemical function     hydrolase activity, hydrolyzing O-glycosyl compounds     1 term  


DOI no: 10.1006/jmbi.2000.3567 J Mol Biol 297:819-828 (2000)
PubMed id: 10731432  
Insights into ligand-induced conformational change in Cel5A from Bacillus agaradhaerens revealed by a catalytically active crystal form.
A.Varrot, M.Schülein, G.J.Davies.
Glycoside hydrolases are ubiquitous enzymes involved in a diverse array of biological processes, from the breakdown of biomass, through to viral invasion and cellular signalling. Endoglucanase Cel5A from Bacillus agaradhaerens, classified into glycoside hydrolase family 5, has been studied in a catalytically inactive crystal form at low pH conditions, in which native and complex structures revealed the importance of ring distortion during catalysis. Here, we present the structure of Cel5A in a new crystal form obtained at higher pH values in which the enzyme is active "in-crystal". Native, cellotriosyl-enzyme intermediate and beta-d-cellobiose structures were solved at 1.95, 1.75 and 2.1 A resolution, respectively. These structures reveal two classes of conformational change: those caused by crystal-packing and pH, with others induced upon substrate binding. At pH 7 a histidine residue, His206, implicated in substrate-binding and catalysis, but previously far removed from the substrate-binding cleft, moves over 10 A into the active site cleft in order to interact with the substrate in the +2 subsite. Occupation of the -1 subsite by substrate induces a loop closure to optimise protein-ligand interactions. Cel5A, along with the unrelated family 45 and family 6 cellulases, provides further evidence of substantial conformational change in response to ligand binding for this class of hydrolytic enzyme.
  Selected figure(s)  
Figure 6.
Figure 6. Ball and stick representation of the overlay of the b-VI to a-VI loop in the orthorhombic native (grey), tetragonal covalent-intermediate (black) Cel5A structures from B. agaradhaerens, in divergent stereo.
Figure 7.
Figure 7. Schematic of the enzyme-oligosaccharide hydrogen bond network in the covalent intermediate complex. Water molecules are shaded spheres.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 297, 819-828) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20803139 C.Liang, Y.Xue, M.Fioroni, F.Rodríguez-Ropero, C.Zhou, U.Schwaneberg, and Y.Ma (2011).
Cloning and characterization of a thermostable and halo-tolerant endoglucanase from Thermoanaerobacter tengcongensis MB4.
  Appl Microbiol Biotechnol, 89, 315-326.  
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.  
19269961 R.Carapito, A.Imberty, J.M.Jeltsch, S.C.Byrns, P.H.Tam, T.L.Lowary, A.Varrot, and V.Phalip (2009).
Molecular Basis of Arabinobio-hydrolase Activity in Phytopathogenic Fungi: CRYSTAL STRUCTURE AND CATALYTIC MECHANISM OF FUSARIUM GRAMINEARUM GH93 EXO-{alpha}-L-ARABINANASE.
  J Biol Chem, 284, 12285-12296.
PDB codes: 2w5n 2w5o
19279191 R.Suzuki, Z.Fujimoto, S.Ito, S.Kawahara, S.Kaneko, K.Taira, T.Hasegawa, and A.Kuno (2009).
Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86.
  J Biochem, 146, 61-70.
PDB codes: 2d1z 2d20 2d22 2d23 2d24
14715651 G.Sulzenbacher, C.Bignon, T.Nishimura, C.A.Tarling, S.G.Withers, B.Henrissat, and Y.Bourne (2004).
Crystal structure of Thermotoga maritima alpha-L-fucosidase. Insights into the catalytic mechanism and the molecular basis for fucosidosis.
  J Biol Chem, 279, 13119-13128.
PDB codes: 1hl8 1hl9 1odu
14997539 M.S.Sujatha, and P.V.Balaji (2004).
Identification of common structural features of binding sites in galactose-specific proteins.
  Proteins, 55, 44-65.  
12454501 A.Varrot, T.P.Frandsen, H.Driguez, and G.J.Davies (2002).
Structure of the Humicola insolens cellobiohydrolase Cel6A D416A mutant in complex with a non-hydrolysable substrate analogue, methyl cellobiosyl-4-thio-beta-cellobioside, at 1.9 A.
  Acta Crystallogr D Biol Crystallogr, 58, 2201-2204.
PDB code: 1gz1
11980476 M.Abou-Hachem, E.N.Karlsson, P.J.Simpson, S.Linse, P.Sellers, M.P.Williamson, S.J.Jamieson, H.J.Gilbert, D.N.Bolam, and O.Holst (2002).
Calcium binding and thermostability of carbohydrate binding module CBM4-2 of Xyn10A from Rhodothermus marinus.
  Biochemistry, 41, 5720-5729.  
11679762 A.Varrot, M.Schülein, S.Fruchard, H.Driguez, and G.J.Davies (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.
PDB code: 1h5v
11481469 D.M.van Aalten, D.Komander, B.Synstad, S.Gåseidnes, M.G.Peter, and V.G.Eijsink (2001).
Structural insights into the catalytic mechanism of a family 18 exo-chitinase.
  Proc Natl Acad Sci U S A, 98, 8979-8984.
PDB codes: 1e6n 1e6p 1e6r 1e6z
11828460 S.Fort, A.Varrot, M.Schülein, S.Cottaz, H.Driguez, and G.J.Davies (2001).
Mixed-linkage cellooligosaccharides: a new class of glycoside hydrolase inhibitors.
  Chembiochem, 2, 319-325.
PDB code: 1e5j
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.