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Hydrolase PDB id
2zq0
Jmol
Contents
Protein chains
704 a.a. *
Ligands
ACR ×2
Metals
_CA ×2
Waters ×1523
* Residue conservation analysis
PDB id:
2zq0
Name: Hydrolase
Title: Crystal structure of susb complexed with acarbose
Structure: Alpha-glucosidase (alpha-glucosidase susb). Chain: a, b. Fragment: residues 22-738. Engineered: yes
Source: Bacteroides thetaiotaomicron. Organism_taxid: 818. Strain: vpi-5482. Gene: susb, bt_3703. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.60Å     R-factor:   0.171     R-free:   0.187
Authors: M.Yao,I.Tanaka,M.Kitamura
Key ref:
M.Kitamura et al. (2008). Structural and Functional Analysis of a Glycoside Hydrolase Family 97 Enzyme from Bacteroides thetaiotaomicron. J Biol Chem, 283, 36328-36337. PubMed id: 18981178 DOI: 10.1074/jbc.M806115200
Date:
31-Jul-08     Release date:   28-Oct-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P71094  (P71094_BACTN) -  Alpha-glucosidase
Seq:
Struc: 		 
Seq:
Struc: 		738 a.a.
704 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     metal ion binding     1 term  

 

 
DOI no: 10.1074/jbc.M806115200 J Biol Chem 283:36328-36337 (2008)
PubMed id: 18981178  
 
 
Structural and Functional Analysis of a Glycoside Hydrolase Family 97 Enzyme from Bacteroides thetaiotaomicron.
M.Kitamura, M.Okuyama, F.Tanzawa, H.Mori, Y.Kitago, N.Watanabe, A.Kimura, I.Tanaka, M.Yao.
 
  ABSTRACT  
 
SusB, an 84-kDa alpha-glucoside hydrolase involved in the starch utilization system (sus) of Bacteroides thetaiotaomicron, belongs to glycoside hydrolase (GH) family 97. We have determined the enzymatic characteristics and the crystal structures in free and acarbose-bound form at 1.6A resolution. SusB hydrolyzes the alpha-glucosidic linkage, with inversion of anomeric configuration liberating the beta-anomer of glucose as the reaction product. The substrate specificity of SusB, hydrolyzing not only alpha-1,4-glucosidic linkages but also alpha-1,6-, alpha-1,3-, and alpha-1,2-glucosidic linkages, is clearly different from other well known glucoamylases belonging to GH15. The structure of SusB was solved by the single-wavelength anomalous diffraction method with sulfur atoms as anomalous scatterers using an in-house x-ray source. SusB includes three domains as follows: the N-terminal, catalytic, and C-terminal domains. The structure of the SusB-acarbose complex shows a constellation of carboxyl groups at the catalytic center; Glu(532) is positioned to provide protonic assistance to leaving group departure, with Glu(439) and Glu(508) both positioned to provide base-catalyzed assistance for inverting nucleophilic attack by water. A structural comparison with other glycoside hydrolases revealed significant similarity between the catalytic domain of SusB and those of alpha-retaining glycoside hydrolases belonging to GH27, -36, and -31 despite the differences in catalytic mechanism. SusB and the other retaining enzymes appear to have diverged from a common ancestor and individually acquired the functional carboxyl groups during the process of evolution. Furthermore, sequence comparison of the active site based on the structure of SusB indicated that GH97 included both retaining and inverting enzymes.
 
  Selected figure(s)  
 
Figure 3.
A, composite of the acarbose molecule and a calcium ion, and their omit map. The contour level of the F[o] - F[c] map is 3σ. Domains N and A are shown in yellow and cyan, respectively (the same colors are used in B). B, stereo views of the active pocket with bound acarbose (gray) and a calcium ion (gray). All oxygen and nitrogen atoms are shown in red and blue, respectively. 		Figure 4.
Stereo view of a calcium binding site in native (A) and acarbose complex (B) structures. The calcium ion is shown as a large black sphere, and water molecules are shown as small black spheres. All residues coordinated to the calcium ion are indicated.
 
  The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2008, 283, 36328-36337) copyright 2008.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21082169 M.Gabriško, and S.Janeček (2011).
Characterization of maltase clusters in the genus Drosophila.
  J Mol Evol, 72, 104-118.  
21397496 S.Park, S.Hyun, and J.Yu (2011).
Selective α-glucosidase substrates and inhibitors containing short aromatic peptidyl moieties.
  Bioorg Med Chem Lett, 21, 2441-2444.  
21048085 K.Hashimoto, and A.R.Panchenko (2010).
Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states.
  Proc Natl Acad Sci U S A, 107, 20352-20357.  
20159465 N.M.Koropatkin, and T.J.Smith (2010).
SusG: a unique cell-membrane-associated alpha-amylase from a prominent human gut symbiont targets complex starch molecules.
  Structure, 18, 200-215.
PDB codes: 3k8k 3k8l 3k8m
20066263 T.M.Gloster, and G.J.Davies (2010).
Glycosidase inhibition: assessing mimicry of the transition state.
  Org Biomol Chem, 8, 305-320.  
20552664 T.V.Vuong, and D.B.Wilson (2010).
Glycoside hydrolases: catalytic base/nucleophile diversity.
  Biotechnol Bioeng, 107, 195-205.  
19553672 E.C.Martens, N.M.Koropatkin, T.J.Smith, and J.I.Gordon (2009).
Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm.
  J Biol Chem, 284, 24673-24677.  
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.