PDBsum entry 1ug9

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Hydrolase PDB id
Protein chain
1019 a.a. *
_CA ×6
Waters ×551
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of glucodextranase from arthrobacter globi
Structure: Glucodextranase. Chain: a. Ec:
Source: Arthrobacter globiformis. Organism_taxid: 1665. Strain: i42
2.50Å     R-factor:   0.189     R-free:   0.239
Authors: M.Mizuno,T.Tonozuka,S.Suzuki,R.Uotsu-Tomita,A.Ohtaki,S.Kamit A.Nishikawa,Y.Sakano
Key ref:
M.Mizuno et al. (2004). Structural insights into substrate specificity and function of glucodextranase. J Biol Chem, 279, 10575-10583. PubMed id: 14660574 DOI: 10.1074/jbc.M310771200
16-Jun-03     Release date:   09-Dec-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9LBQ9  (Q9LBQ9_ARTGO) -  Glucodextranase
1048 a.a.
1019 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   3 terms 
  Biochemical function     catalytic activity     5 terms  


DOI no: 10.1074/jbc.M310771200 J Biol Chem 279:10575-10583 (2004)
PubMed id: 14660574  
Structural insights into substrate specificity and function of glucodextranase.
M.Mizuno, T.Tonozuka, S.Suzuki, R.Uotsu-Tomita, S.Kamitori, A.Nishikawa, Y.Sakano.
A glucodextranase (iGDase) from Arthrobacter globiformis I42 hydrolyzes alpha-1,6-glucosidic linkages of dextran from the non-reducing end to produce beta-D-glucose via an inverting reaction mechanism and classified into the glycoside hydrolase family 15 (GH15). Here we cloned the iGDase gene and determined the crystal structures of iGDase of the unliganded form and the complex with acarbose at 2.42-A resolution. The structure of iGDase is composed of four domains N, A, B, and C. Domain A forms an (alpha/alpha)(6)-barrel structure and domain N consists of 17 antiparallel beta-strands, and both domains are conserved in bacterial glucoamylases (GAs) and appear to be mainly concerned with catalytic activity. The structure of iGDase complexed with acarbose revealed that the positions and orientations of the residues at subsites -1 and +1 are nearly identical between iGDase and GA; however, the residues corresponding to subsite 3, which form the entrance of the substrate binding pocket, and the position of the open space and constriction of iGDase are different from those of GAs. On the other hand, domains B and C are not found in the bacterial GAs. The primary structure of domain C is homologous with a surface layer homology domain of pullulanases, and the three-dimensional structure of domain C resembles the carbohydrate-binding domain of some glycohydrolases.
  Selected figure(s)  
Figure 4.
FIG. 4. Structural model of acarbose bound to the active site of iGDase. a, schematic topology of acarbose. The saccharide units are labeled as A, B, C, and D from the non-reducing end. The numbers -1 to +3 are subsite numbers corresponding to each unit of acarbose. b, stereo view of 2F[o] - F[c] electron density map of acarbose bound in the active site of iGDase. The map of the acarbose and a water molecule is contoured at the 1.0 . c, schematic drawing of the interactions of acarbose bound to the active site. Hydrogen bonds of less than 3.5 Å are shown as dashed lines. Water molecules are shown as spheres. Two catalytic residues are boxed.
Figure 6.
FIG. 6. The solvent-accessible surface model of iGDase and GAs around the substrate binding pocket. a, iGDase (PDB ID: 1ULV [PDB] ). Gln-380 does not directly interact with acarbose, and constriction of Trp-582 is observed. b, T. thermosaccharolyticum GA (1LF9 [PDB] ). Trp-390 is stacked with acarbose, and the constriction of Tyr-590 is not seen. c, A. awamori var. X-100 (1AGM [PDB] ). An extended loop consisting of five amino acid residues (TGSWG), which are not conserved in iGDase and T. thermosaccharolyticum GA, interacts with acarbose.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 10575-10583) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
15944458 E.Khalikova, P.Susi, and T.Korpela (2005).
Microbial dextran-hydrolyzing enzymes: fundamentals and applications.
  Microbiol Mol Biol Rev, 69, 306-325.  
  16511025 K.Ichikawa, T.Tonozuka, M.Mizuno, Y.Tanabe, S.Kamitori, A.Nishikawa, and Y.Sakano (2005).
Crystallization and preliminary X-ray analysis of Thermoactinomyces vulgaris R-47 maltooligosaccharide-metabolizing enzyme homologous to glucoamylase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 302-304.  
15233783 R.Zona, F.Chang-Pi-Hin, M.J.O'Donohue, and S.Janecek (2004).
Bioinformatics of the glycoside hydrolase family 57 and identification of catalytic residues in amylopullulanase from Thermococcus hydrothermalis.
  Eur J Biochem, 271, 2863-2872.  
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