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PDBsum entry 1r7a

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1r7a
Jmol
Contents
Protein chains
504 a.a. *
Ligands
TRS ×2
Waters ×1421
* Residue conservation analysis
PDB id:
1r7a
Name: Transferase
Title: Sucrose phosphorylase from bifidobacterium adolescentis
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:
1.77Å     R-factor:   0.164     R-free:   0.195
Authors: D.Sprogoe,L.A.M.Van Den Broek,O.Mirza,J.S.Kastrup, A.G.J.Voragen,M.Gajhede,L.K.Skov
Key ref:
D.Sprogøe et al. (2004). Crystal structure of sucrose phosphorylase from Bifidobacterium adolescentis. Biochemistry, 43, 1156-1162. PubMed id: 14756551 DOI: 10.1021/bi0356395
Date:
21-Oct-03     Release date:   10-Feb-04    
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
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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
+ 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: 10.1021/bi0356395 Biochemistry 43:1156-1162 (2004)
PubMed id: 14756551  
 
 
Crystal structure of sucrose phosphorylase from Bifidobacterium adolescentis.
D.Sprogøe, L.A.van den Broek, O.Mirza, J.S.Kastrup, A.G.Voragen, M.Gajhede, L.K.Skov.
 
  ABSTRACT  
 
Around 80 enzymes are implicated in the generic starch and sucrose pathways. One of these enzymes is sucrose phosphorylase, which reversibly catalyzes the conversion of sucrose and orthophosphate to d-Fructose and alpha-d-glucose 1-phosphate. Here, we present the crystal structure of sucrose phosphorylase from Bifidobacterium adolescentis (BiSP) refined at 1.77 A resolution. It represents the first 3D structure of a sucrose phosphorylase and is the first structure of a phosphate-dependent enzyme from the glycoside hydrolase family 13. The structure of BiSP is composed of the four domains A, B, B', and C. Domain A comprises the (beta/alpha)(8)-barrel common to family 13. The catalytic active-site residues (Asp192 and Glu232) are located at the tips of beta-sheets 4 and 5 in the (beta/alpha)(8)-barrel, as required for family 13 members. The topology of the B' domain disfavors oligosaccharide binding and reduces the size of the substrate access channel compared to other family 13 members, underlining the role of this domain in modulating the function of these enzymes. It is remarkable that the fold of the C domain is not observed in any other known hydrolases of family 13. BiSP was found as a homodimer in the crystal, and a dimer contact surface area of 960 A(2) per monomer was calculated. The majority of the interactions are confined to the two B domains, but interactions between the loop 8 regions of the two barrels are also observed. This results in a large cavity in the dimer, including the entrance to the two active sites.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20872729 A.Cerdobbel, K.De Winter, T.Desmet, and W.Soetaert (2010).
Sucrose phosphorylase as cross-linked enzyme aggregate: improved thermal stability for industrial applications.
  Biotechnol J, 5, 1192-1197.  
20812985 K.Yamamoto, H.Miyake, M.Kusunoki, and S.Osaki (2010).
Crystal structures of isomaltase from Saccharomyces cerevisiae and in complex with its competitive inhibitor maltose.
  FEBS J, 277, 4205-4214.
PDB codes: 3a4a 3aj7
19966417 E.Champion, M.Remaud-Simeon, L.K.Skov, J.S.Kastrup, M.Gajhede, and O.Mirza (2009).
The apo structure of sucrose hydrolase from Xanthomonas campestris pv. campestris shows an open active-site groove.
  Acta Crystallogr D Biol Crystallogr, 65, 1309-1314.
PDB code: 2wpg
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.  
16523284 B.Kullin, V.R.Abratt, and S.J.Reid (2006).
A functional analysis of the Bifidobacterium longum cscA and scrP genes in sucrose utilization.
  Appl Microbiol Biotechnol, 72, 975-981.  
16990265 O.Mirza, L.K.Skov, D.Sprogøe, L.A.van den Broek, G.Beldman, J.S.Kastrup, and M.Gajhede (2006).
Structural rearrangements of sucrose phosphorylase from Bifidobacterium adolescentis during sucrose conversion.
  J Biol Chem, 281, 35576-35584.
PDB codes: 2gdu 2gdv
16214343 A.Gutteridge, and J.M.Thornton (2005).
Understanding nature's catalytic toolkit.
  Trends Biochem Sci, 30, 622-629.  
15660210 S.J.Reid, and V.R.Abratt (2005).
Sucrose utilisation in bacteria: genetic organisation and regulation.
  Appl Microbiol Biotechnol, 67, 312-321.  
15375133 C.I.Caescu, O.Vidal, F.Krzewinski, V.Artenie, and S.Bouquelet (2004).
Bifidobacterium longum requires a fructokinase (Frk; ATP:D-fructose 6-phosphotransferase, EC 2.7.1.4) for fructose catabolism.
  J Bacteriol, 186, 6515-6525.  
15274915 M.Hidaka, Y.Honda, M.Kitaoka, S.Nirasawa, K.Hayashi, T.Wakagi, H.Shoun, and S.Fushinobu (2004).
Chitobiose phosphorylase from Vibrio proteolyticus, a member of glycosyl transferase family 36, has a clan GH-L-like (alpha/alpha)(6) barrel fold.
  Structure, 12, 937-947.
PDB codes: 1v7v 1v7w 1v7x
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.