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PDBsum entry 2jkp

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
2jkp
Jmol
Contents
Protein chains
687 a.a. *
Ligands
CTS ×2
EDO ×4
Metals
_CA ×2
Waters ×1255
* Residue conservation analysis
PDB id:
2jkp
Name: Hydrolase
Title: Structure of a family 97 alpha-glucosidase from bacteroides thetaiotaomicron in complex with castanospermine
Structure: Alpha-glucosidase (alpha-glucosidase susb). Chain: a, b. Fragment: residues 22-738. Synonym: alpha-glucosidase. Engineered: yes
Source: Bacteroides thetaiotaomicron. Organism_taxid: 226186. Strain: vpi-5482. Expressed in: escherichia coli. Expression_system_taxid: 511693.
Resolution:
1.99Å     R-factor:   0.176     R-free:   0.227
Authors: T.M.Gloster,J.P.Turkenburg,J.R.Potts,B.Henrissat,G.J.Davies
Key ref:
T.M.Gloster et al. (2008). Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora. Chem Biol, 15, 1058-1067. PubMed id: 18848471 DOI: 10.1016/j.chembiol.2008.09.005
Date:
29-Aug-08     Release date:   30-Sep-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
G8JZS4  (G8JZS4_BACTN) -  Glucan 1,4-alpha-glucosidase SusB
Seq:
Struc:
 
Seq:
Struc:
738 a.a.
687 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.3  - Glucan 1,4-alpha-glucosidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of terminal 1,4-linked alpha-D-glucose residues successively from non-reducing ends of the chains with release of beta-D-glucose.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     periplasmic space   2 terms 
  Biological process     metabolic process   4 terms 
  Biochemical function     hydrolase activity     6 terms  

 

 
DOI no: 10.1016/j.chembiol.2008.09.005 Chem Biol 15:1058-1067 (2008)
PubMed id: 18848471  
 
 
Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora.
T.M.Gloster, J.P.Turkenburg, J.R.Potts, B.Henrissat, G.J.Davies.
 
  ABSTRACT  
 
Enzymatic cleavage of the glycosidic bond yields products in which the anomeric configuration is either retained or inverted. Each mechanism reflects the dispositions of the enzyme functional groups; a facet of which is essentially conserved in 113 glycoside hydrolase (GH) families. We show that family GH97 has diverged significantly, as it contains both inverting and retaining alpha-glycosidases. This reflects evolution of the active center; a glutamate acts as a general base in inverting members, exemplified by Bacteroides thetaiotaomicron alpha-glucosidase BtGH97a, whereas an aspartate likely acts as a nucleophile in retaining members. The structure of BtGH97a and its complexes with inhibitors, coupled to kinetic analysis of active-site variants, reveals an unusual calcium ion dependence. 1H NMR analysis shows an inversion mechanism for BtGH97a, whereas another GH97 enzyme from B. thetaiotaomicron, BtGH97b, functions as a retaining alpha-galactosidase.
 
  Selected figure(s)  
 
Figure 1.
GH Mechanisms and [alpha]-Glucosidase Inhibitors (A and B) Hydrolysis with (A) inversion and (B) retention of anomeric configuration. (C) Inhibitors deoxynojirimycin (1), castanospermine (2), and acarbose (3). Chem Biol. 2008 October 20; 15(10-3): 1058–1067. doi: 10.1016/j.chembiol.2008.09.005. Copyright [copyright] 2008 Elsevier Ltd.
Figure 2.
Structural Insights into BtGH97a (A) Divergent stereo ribbon representation of BtGH97a; the N-terminal domain is in red, the core ([beta]/[alpha])[8] domain in yellow, and the C-terminal domain in blue. (B and C) Ball-and-stick representation of BtGH97a in complex with (B) 1 and (C) 2; observed electron density for the maximum likelihood weighted 2F[obs] [minus sign] F[calc] map is contoured at 1[sigma]. The purple spheres represent calcium ions. (D) Ball-and-stick representation of the active-site overlap between BtGH97a and a GH27 enzyme (PDB ID code 1UAS). Figures were drawn using BOBSCRIPT (Esnouf, 1997). (E) Interactions between BtGH97 and 1. Chem Biol. 2008 October 20; 15(10-3): 1058–1067. doi: 10.1016/j.chembiol.2008.09.005. Copyright [copyright] 2008 Elsevier Ltd.
 
  The above figures are reprinted from an Open Access publication published by Cell Press: Chem Biol (2008, 15, 1058-1067) copyright 2008.  
  Figures were selected by an automated process.  

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.  
21431156 M.N.Gandy, A.W.Debowski, and K.A.Stubbs (2011).
A general method for affinity-based proteomic profiling of exo-α-glycosidases.
  Chem Commun (Camb), 47, 5037-5039.  
20665773 A.Lammerts van Bueren, S.D.Popat, C.H.Lin, and G.J.Davies (2010).
Structural and thermodynamic analyses of α-L-fucosidase inhibitors.
  Chembiochem, 11, 1971-1974.
PDB codes: 2xib 2xii
  20944224 A.P.Yeh, P.Abdubek, T.Astakhova, H.L.Axelrod, C.Bakolitsa, X.Cai, D.Carlton, C.Chen, H.J.Chiu, M.Chiu, T.Clayton, D.Das, M.C.Deller, L.Duan, K.Ellrott, C.L.Farr, J.Feuerhelm, J.C.Grant, A.Grzechnik, G.W.Han, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, P.Kozbial, S.S.Krishna, A.Kumar, W.W.Lam, D.Marciano, D.McMullan, M.D.Miller, A.T.Morse, E.Nigoghossian, A.Nopakun, L.Okach, C.Puckett, R.Reyes, H.J.Tien, C.B.Trame, H.van den Bedem, D.Weekes, T.Wooten, Q.Xu, K.O.Hodgson, J.Wooley, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2010).
Structure of Bacteroides thetaiotaomicron BT2081 at 2.05 Å resolution: the first structural representative of a new protein family that may play a role in carbohydrate metabolism.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1287-1296.
PDB code: 3hbz
  20944220 P.J.Turnbaugh, B.Henrissat, and J.I.Gordon (2010).
Viewing the human microbiome through three-dimensional glasses: integrating structural and functional studies to better define the properties of myriad carbohydrate-active enzymes.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1261-1264.  
20066263 T.M.Gloster, and G.J.Davies (2010).
Glycosidase inhibition: assessing mimicry of the transition state.
  Org Biomol Chem, 8, 305-320.  
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.