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PDBsum entry 2ecp

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protein ligands Protein-protein interface(s) links
Acarbose PDB id
2ecp
Jmol
Contents
Protein chains
796 a.a. *
Ligands
ACR ×2
PLP ×2
GOL ×2
Waters ×93
* Residue conservation analysis
PDB id:
2ecp
Name: Acarbose
Title: The crystal structure of the e. Coli maltodextrin phosphoryl complex
Structure: Maltodextrin phosphorylase. Chain: a, b. Synonym: ecp, malp. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Cell_line: delta mala518. Tissue: muscle. Cellular_location: cytoplasm. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: delta mala518.
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
2.95Å     R-factor:   0.241     R-free:   0.293
Authors: M.O'Reilly,K.A.Watson,L.N.Johnson
Key ref:
M.O'Reilly et al. (1999). The crystal structure of the Escherichia coli maltodextrin phosphorylase-acarbose complex. Biochemistry, 38, 5337-5345. PubMed id: 10220320 DOI: 10.1021/bi9828573
Date:
27-Oct-98     Release date:   15-Jun-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00490  (PHSM_ECOLI) -  Maltodextrin phosphorylase
Seq:
Struc:
 
Seq:
Struc:
797 a.a.
796 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 11 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.2.4.1.1  - Glycogen phosphorylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Glycogen
      Reaction: ((1->4)-alpha-D-glucosyl)(n) + phosphate = ((1->4)-alpha-D-glucosyl)(n-1) + alpha-D-glucose 1-phosphate
((1->4)-alpha-D-glucosyl)(n)
+ phosphate
= ((1->4)-alpha-D-glucosyl)(n-1)
+
alpha-D-glucose 1-phosphate
Bound ligand (Het Group name = PLP)
matches with 63.16% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi9828573 Biochemistry 38:5337-5345 (1999)
PubMed id: 10220320  
 
 
The crystal structure of the Escherichia coli maltodextrin phosphorylase-acarbose complex.
M.O'Reilly, K.A.Watson, L.N.Johnson.
 
  ABSTRACT  
 
Acarbose is a naturally occurring pseudo-tetrasaccharide. It has been used in conjunction with other drugs in the treatment of diabetes where it acts as an inhibitor of intestinal glucosidases. To probe the interactions of acarbose with other carbohydrate recognition enzymes, the crystal structure of E. coli maltodextrin phosphorylase (MalP) complexed with acarbose has been determined at 2.95 A resolution and refined to crystallographic R-values of R (Rfree) = 0.241 (0.293), respectively. Acarbose adopts a conformation that is close to its major minimum free energy conformation in the MalP-acarbose structure. The acarviosine moiety of acarbose occupies sub-sites +1 and +2 and the disaccharide sub-sites +3 and +4. (The site of phosphorolysis is between sub-sites -1 and +1.) This is the first identification of sub-sites +3 and +4 of MalP. Interactions of the glucosyl residues in sub-sites +2 and +4 are dominated by carbohydrate stacking interactions with tyrosine residues. These tyrosines (Tyr280 and Tyr613, respectively, in the rabbit muscle phosphorylase numbering scheme) are conserved in all species of phosphorylase. A glycerol molecule from the cryoprotectant occupies sub-site -1. The identification of four oligosaccharide sub-sites, that extend from the interior of the phosphorylase close to the catalytic site to the exterior surface of MalP, provides a structural rationalization of the substrate selectivity of MalP for a pentasaccharide substrate. Crystallographic binding studies of acarbose with amylases, glucoamylases, and glycosyltranferases and NMR studies of acarbose in solution have shown that acarbose can adopt two different conformations. This flexibility allows acarbose to target a number of different enzymes. The two alternative conformations of acarbose when bound to different carbohydrate enzymes are discussed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18518825 L.L.Lairson, B.Henrissat, G.J.Davies, and S.G.Withers (2008).
Glycosyltransferases: structures, functions, and mechanisms.
  Annu Rev Biochem, 77, 521-555.  
17803683 A.Schwarz, L.Brecker, and B.Nidetzky (2007).
Probing the active site of Corynebacterium callunae starch phosphorylase through the characterization of wild-type and His334-->Gly mutant enzymes.
  FEBS J, 274, 5105-5115.  
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
  11082203 I.Przylas, Y.Terada, K.Fujii, T.Takaha, W.Saenger, and N.Sträter (2000).
X-ray structure of acarbose bound to amylomaltase from Thermus aquaticus. Implications for the synthesis of large cyclic glucans.
  Eur J Biochem, 267, 6903-6913.
PDB code: 1esw
  10892808 R.Griessler, S.D'Auria, F.Tanfani, and B.Nidetzky (2000).
Thermal denaturation pathway of starch phosphorylase from Corynebacterium callunae: oxyanion binding provides the glue that efficiently stabilizes the dimer structure of the protein.
  Protein Sci, 9, 1149-1161.  
10469642 K.A.Watson, C.McCleverty, S.Geremia, S.Cottaz, H.Driguez, and L.N.Johnson (1999).
Phosphorylase recognition and phosphorolysis of its oligosaccharide substrate: answers to a long outstanding question.
  EMBO J, 18, 4619-4632.
PDB codes: 1e4o 1qm5
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.