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Hydrolase PDB id
1up7
Jmol
Contents
Protein chains
(+ 2 more) 414 a.a. *
Ligands
NAD ×8
G6P ×8
SO4 ×2
Waters ×759
* Residue conservation analysis
PDB id:
1up7
Name: Hydrolase
Title: Structure of the 6-phospho-beta glucosidase from thermotoga maritima at 2.4 anstrom resolution in the tetragonal form with NAD and glucose-6-phosphate
Structure: 6-phospho-beta-glucosidase. Chain: a, b, c, d, e, f, g, h. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 243274. Strain: msb8. Atcc: 43589. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: synthetic gene
Biol. unit: Tetramer (from PDB file)
Resolution:
2.40Å     R-factor:   0.201     R-free:   0.240
Authors: A.Varrot,V.L.Yip,S.G.Withers,G.J.Davies
Key ref:
A.Varrot et al. (2005). NAD+ and metal-ion dependent hydrolysis by family 4 glycosidases: structural insight into specificity for phospho-beta-D-glucosides. J Mol Biol, 346, 423-435. PubMed id: 15670594 DOI: 10.1016/j.jmb.2004.11.058
Date:
29-Sep-03     Release date:   18-Nov-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9X108  (BGLT_THEMA) -  6-phospho-beta-glucosidase BglT
Seq:
Struc: 		415 a.a.
414 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.86  - 6-phospho-beta-glucosidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 6-phospho-beta-D-glucosyl-(1,4)-D-glucose + H2O = D-glucose + D-glucose 6-phosphate
6-phospho-beta-D-glucosyl-(1,4)-D-glucose
 + H(2)O
 = D-glucose
 +
D-glucose 6-phosphate
Bound ligand (Het Group name = G6P)
corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     8 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2004.11.058 J Mol Biol 346:423-435 (2005)
PubMed id: 15670594  
 
 
NAD+ and metal-ion dependent hydrolysis by family 4 glycosidases: structural insight into specificity for phospho-beta-D-glucosides.
A.Varrot, V.L.Yip, Y.Li, S.S.Rajan, X.Yang, W.F.Anderson, J.Thompson, S.G.Withers, G.J.Davies.
 
  ABSTRACT  
 
The import of disaccharides by many bacteria is achieved through their simultaneous translocation and phosphorylation by the phosphoenolpyruvate-dependent phosphotransferase system (PEP-PTS). The imported phospho-disaccharides are, in some cases, subsequently hydrolyzed by members of the unusual glycoside hydrolase family GH4. The GH4 enzymes, occasionally found also in bacteria such as Thermotoga maritima that do not utilise a PEP-PTS system, require both NAD(+) and Mn(2+) for catalysis. A further curiosity of this family is that closely related enzymes may show specificity for either alpha-d- or beta-d-glycosides. Here, we present, for the first time, the three-dimensional structure (using single-wavelength anomalous dispersion methods, harnessing extensive non-crystallographic symmetry) of the 6-phospho-beta-glycosidase, BglT, from T.maritima in native and complexed (NAD(+) and Glc6P) forms. Comparison of the active-center structure with that of the 6-phospho-alpha-glucosidase GlvA from Bacillus subtilis reveals a striking degree of structural similarity that, in light of previous kinetic isotope effect data, allows the postulation of a common reaction mechanism for both alpha and beta-glycosidases. Given that the "chemistry" occurs primarily on the glycone sugar and features no nucleophilic attack on the intact disaccharide substrate, modulation of anomeric specificity for alpha and beta-linkages is accommodated through comparatively minor structural changes.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Schematic of the proposed BglT catalytic mechanism.
 
  The above figure is reprinted by permission from Elsevier: J Mol Biol (2005, 346, 423-435) copyright 2005.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21369991 D.Kim, S.N.Kim, K.S.Baik, S.C.Park, C.H.Lim, J.O.Kim, T.S.Shin, M.J.Oh, and C.N.Seong (2011).
Screening and characterization of a cellulase gene from the gut microflora of abalone using metagenomic library.
  J Microbiol, 49, 141-145.  
20552664 T.V.Vuong, and D.B.Wilson (2010).
Glycoside hydrolases: catalytic base/nucleophile diversity.
  Biotechnol Bioeng, 107, 195-205.  
19625389 B.G.Hall, A.Pikis, and J.Thompson (2009).
Evolution and biochemistry of family 4 glycosidases: implications for assigning enzyme function in sequence annotations.
  Mol Biol Evol, 26, 2487-2497.  
18558099 D.J.Vocadlo, and G.J.Davies (2008).
Mechanistic insights into glycosidase chemistry.
  Curr Opin Chem Biol, 12, 539-555.  
18310337 J.Thompson, N.Jakubovics, B.Abraham, S.Hess, and A.Pikis (2008).
The sim operon facilitates the transport and metabolism of sucrose isomers in Lactobacillus casei ATCC 334.
  J Bacteriol, 190, 3362-3373.  
18625333 M.E.Tanner (2008).
Transient oxidation as a mechanistic strategy in enzymatic catalysis.
  Curr Opin Chem Biol, 12, 532-538.  
19016847 R.Kluger, and S.Rathgeber (2008).
Catalyzing separation of carbon dioxide in thiamin diphosphate-promoted decarboxylation.
  FEBS J, 275, 6089-6100.  
17401360 Q.P.Liu, G.Sulzenbacher, H.Yuan, E.P.Bennett, G.Pietz, K.Saunders, J.Spence, E.Nudelman, S.B.Levery, T.White, J.M.Neveu, W.S.Lane, Y.Bourne, M.L.Olsson, B.Henrissat, and H.Clausen (2007).
Bacterial glycosidases for the production of universal red blood cells.
  Nat Biotechnol, 25, 454-464.
PDB codes: 2ixa 2ixb
16636060 A.Pikis, S.Hess, I.Arnold, B.Erni, and J.Thompson (2006).
Genetic requirements for growth of Escherichia coli K12 on methyl-alpha-D-glucopyranoside and the five alpha-D-glucosyl-D-fructose isomers of sucrose.
  J Biol Chem, 281, 17900-17908.  
17064285 S.B.Conners, E.F.Mongodin, M.R.Johnson, C.I.Montero, K.E.Nelson, and R.M.Kelly (2006).
Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species.
  FEMS Microbiol Rev, 30, 872-905.  
16917793 V.L.Yip, and S.G.Withers (2006).
Family 4 glycosidases carry out efficient hydrolysis of thioglycosides by an alpha,beta-elimination mechanism.
  Angew Chem Int Ed Engl, 45, 6179-6182.  
16495121 V.L.Yip, and S.G.Withers (2006).
Breakdown of oligosaccharides by the process of elimination.
  Curr Opin Chem Biol, 10, 147-155.  
15983044 T.Jaeger, M.Arsic, and C.Mayer (2005).
Scission of the lactyl ether bond of N-acetylmuramic acid by Escherichia coli "etherase".
  J Biol Chem, 280, 30100-30106.  
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.