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PDBsum entry 2gdv

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protein ligands Protein-protein interface(s) links
Transferase PDB id
2gdv
Jmol
Contents
Protein chains
504 a.a. *
Ligands
BGC ×2
Waters ×1006
* Residue conservation analysis
PDB id:
2gdv
Name: Transferase
Title: Sucrose phosphorylase from bifidobacterium adolescentis reacted with sucrose
Structure: Sucrose phosphorylase. Chain: a, b. Engineered: yes
Source: Bifidobacterium adolescentis. Organism_taxid: 1680. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.198     R-free:   0.237
Authors: L.K.Skov,O.Mirza,M.Gajhede,J.S.Katsrup
Key ref:
O.Mirza et al. (2006). Structural rearrangements of sucrose phosphorylase from Bifidobacterium adolescentis during sucrose conversion. J Biol Chem, 281, 35576-35584. PubMed id: 16990265 DOI: 10.1074/jbc.M605611200
Date:
17-Mar-06     Release date:   26-Sep-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q84HQ2  (Q84HQ2_BIFAD) -  Sucrose phosphorylase
Seq:
Struc:
504 a.a.
504 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.4.1.7  - Sucrose phosphorylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Sucrose + phosphate = D-fructose + alpha-D-glucose 1-phosphate
Sucrose
+ phosphate
=
D-fructose
Bound ligand (Het Group name = BGC)
matches with 91.00% similarity
+ alpha-D-glucose 1-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   2 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M605611200 J Biol Chem 281:35576-35584 (2006)
PubMed id: 16990265  
 
 
Structural rearrangements of sucrose phosphorylase from Bifidobacterium adolescentis during sucrose conversion.
O.Mirza, L.K.Skov, D.Sprogøe, L.A.van den Broek, G.Beldman, J.S.Kastrup, M.Gajhede.
 
  ABSTRACT  
 
The reaction mechanism of sucrose phosphorylase from Bifidobacterium adolescentis (BiSP) was studied by site-directed mutagenesis and x-ray crystallography. An inactive mutant of BiSP (E232Q) was co-crystallized with sucrose. The structure revealed a substrate-binding mode comparable with that seen in other related sucrose-acting enzymes. Wild-type BiSP was also crystallized in the presence of sucrose. In the dimeric structure, a covalent glucosyl intermediate was formed in one molecule of the BiSP dimer, and after hydrolysis of the glucosyl intermediate, a beta-D-glucose product complex was formed in the other molecule. Although the overall structure of the BiSP-glucosyl intermediate complex is similar to that of the BiSP(E232Q)-sucrose complex, the glucose complex discloses major differences in loop conformations. Two loops (residues 336-344 and 132-137) in the proximity of the active site move up to 16 and 4 A, respectively. On the basis of these findings, we have suggested a reaction cycle that takes into account the large movements in the active-site entrance loops.
 
  Selected figure(s)  
 
Figure 1.
FIGURE 1. Schematic representation of the domain organization of the mixed dimer of BiSP. The glucosyl intermediate (molecule A; left) and the glucose hydrolysis product (molecule B; right) are shown as red spheres. domains A, B, B', and C are colored green, yellow, blue, and orange, respectively. N and C correspond to the N and C termini, respectively, whereas A and B indicate the positions of loops A and B.
Figure 4.
FIGURE 4. Structural changes occurring during the enzyme reaction. A, close-up view of loops A and B of the wild-type BiSP covalent intermediate (molecule A; cyan) superimposed on the glucose product-bound form (molecule B; yellow). The bound glucose of molecule B is shown for clarity. B, close-up view of loops A and B and the noncovalently bound glucose molecule of the wild-type BiSP-glucose complex. Glucose 1-phosphate (yellow) has been modeled based on the position of the glucose interacting with Arg^135 and Tyr^344. C, proposed intermolecular phosphate-binding site created by two Arg^135 residues. The distances indicated by dashed lines are 3.9 Å. The bound sucrose molecules are shown as red van der Waals spheres.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 35576-35584) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19691080 C.Goedl, and B.Nidetzky (2009).
Sucrose phosphorylase harbouring a redesigned, glycosyltransferase-like active site exhibits retaining glucosyl transfer in the absence of a covalent intermediate.
  Chembiochem, 10, 2333-2337.  
18175927 K.Nomura, K.Sugimoto, H.Nishiura, K.Ohdan, T.Nishimura, H.Hayashi, and T.Kuriki (2008).
Glucosylation of acetic acid by sucrose phosphorylase.
  Biosci Biotechnol Biochem, 72, 82-87.  
18040988 L.A.van den Broek, S.W.Hinz, G.Beldman, J.P.Vincken, and A.G.Voragen (2008).
Bifidobacterium carbohydrases-their role in breakdown and synthesis of (potential) prebiotics.
  Mol Nutr Food Res, 52, 146-163.  
18539800 S.Guglielmetti, I.Tamagnini, D.Mora, M.Minuzzo, A.Scarafoni, S.Arioli, J.Hellman, M.Karp, and C.Parini (2008).
Implication of an outer surface lipoprotein in adhesion of Bifidobacterium bifidum to Caco-2 cells.
  Appl Environ Microbiol, 74, 4695-4702.  
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.