PDBsum entry 2g8s

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protein ligands metals Protein-protein interface(s) links
Sugar binding protein PDB id
Protein chains
348 a.a. *
EDO ×25
_CA ×2
Waters ×1024
* Residue conservation analysis
PDB id:
Name: Sugar binding protein
Title: Crystal structure of the soluble aldose sugar dehydrogenase (asd) from escherichia coli in the apo-form
Structure: Glucose/sorbosone dehydrogenases. Chain: a, b. Engineered: yes
Source: Escherichia coli k12. Organism_taxid: 83333. Strain: k-12. Gene: ylii. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.50Å     R-factor:   0.148     R-free:   0.183
Authors: S.M.Southall,J.J.Doel,D.J.Richardson,A.Oubrie
Key ref:
S.M.Southall et al. (2006). Soluble aldose sugar dehydrogenase from Escherichia coli: a highly exposed active site conferring broad substrate specificity. J Biol Chem, 281, 30650-30659. PubMed id: 16864586 DOI: 10.1074/jbc.M601783200
03-Mar-06     Release date:   08-Aug-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P75804  (YLII_ECOLI) -  Soluble aldose sugar dehydrogenase YliI
371 a.a.
348 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     outer membrane-bounded periplasmic space   1 term 
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     catalytic activity     7 terms  


DOI no: 10.1074/jbc.M601783200 J Biol Chem 281:30650-30659 (2006)
PubMed id: 16864586  
Soluble aldose sugar dehydrogenase from Escherichia coli: a highly exposed active site conferring broad substrate specificity.
S.M.Southall, J.J.Doel, D.J.Richardson, A.Oubrie.
A water-soluble aldose sugar dehydrogenase (Asd) has been purified for the first time from Escherichia coli. The enzyme is able to act upon a broad range of aldose sugars, encompassing hexoses, pentoses, disaccharides, and trisaccharides, and is able to oxidize glucose to gluconolactone with subsequent hydrolysis to gluconic acid. The enzyme shows the ability to bind pyrroloquinoline quinone (PQQ) in the presence of Ca2+ in a manner that is proportional to its catalytic activity. The x-ray structure has been determined in the apo-form and as the PQQ-bound active holoenzyme. The beta-propeller fold of this protein is conserved between E. coli Asd and Acinetobacter calcoaceticus soluble glucose dehydrogenase (sGdh), with major structural differences lying in loop and surface-exposed regions. Many of the residues involved in binding the cofactor are conserved between the two enzymes, but significant differences exist in residues likely to contact substrates. PQQ is bound in a large cleft in the protein surface and is uniquely solvent-accessible compared with other PQQ enzymes. The exposed and charged nature of the active site and the activity profile of this enzyme indicate possible factors that underlie a low affinity for glucose but generic broad substrate specificity for aldose sugars. These structural and catalytic properties of the enzymes have led us to propose that E. coli Asd provides a prototype structure for a new subgroup of PQQ-dependent soluble dehydrogenases that is distinct from the A. calcoaceticus sGdh subgroup.
  Selected figure(s)  
Figure 4.
FIGURE 4. The overall structure of E. coli YliI (Asd). A, schematic representation of the overall structure of E. coli YliI. "Blades" of the propeller structure are labeled 1–6. B, overlay of the loop region between strands 4C and 4D from E. coli YliI (Asd) (yellow) and A. calcoaceticus sGdh (red), which is involved in dimerization in A. calcoaceticus sGdh. Calcium ions are shown as spheres.
Figure 7.
FIGURE 7. Representation of the surface charges of YliI (Asd) from E. coli (top) and the D-glucose-bound form of A. calcoaceticus sGdh (bottom). PQQ and D-glucose are shown in yellow. Positively charged regions are colored blue, and negatively charged regions are colored red.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 30650-30659) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20936374 L.Tetianec, I.Bratkovskaja, J.Kulys, V.Casaite, and R.Meskys (2011).
Probing reactivity of PQQ-dependent carbohydrate dehydrogenases using artificial electron acceptor.
  Appl Biochem Biotechnol, 163, 404-414.  
20506020 S.M.Chiang, and H.E.Schellhorn (2010).
Evolution of the RpoS regulon: origin of RpoS and the conservation of RpoS-dependent regulation in bacteria.
  J Mol Evol, 70, 557-571.  
19561609 I.Bosanac, H.R.Maun, S.J.Scales, X.Wen, A.Lingel, J.F.Bazan, Sauvage, S.G.Hymowitz, and R.A.Lazarus (2009).
The structure of SHH in complex with HHIP reveals a recognition role for the Shh pseudo active site in signaling.
  Nat Struct Mol Biol, 16, 691-697.
PDB codes: 3ho3 3ho4 3ho5
19184595 R.Nouaille, M.Matulova, V.Pätoprstý, A.M.Delort, and E.Forano (2009).
Production of oligosaccharides and cellobionic acid by Fibrobacter succinogenes S85 growing on sugars, cellulose and wheat straw.
  Appl Microbiol Biotechnol, 83, 425-433.  
  17565193 S.P.Kanaujia, C.V.Ranjani, J.Jeyakanthan, M.Nishida, Y.Kitamura, S.Baba, A.Ebihara, N.Shimizu, N.Nakagawa, A.Shinkai, M.Yamamoto, S.Kuramitsu, Y.Shiro, K.Sekar, and S.Yokoyama (2007).
Preliminary X-ray crystallographic study of glucose dehydrogenase from Thermus thermophilus HB8.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 446-448.  
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