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PDBsum entry 1v3m

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
1v3m
Jmol
Contents
Protein chains
686 a.a. *
Ligands
GLC-ACI-GLD-GAL ×2
GLC ×2
GAL ×3
GLC-GLC
Metals
_CA ×4
Waters ×685
* Residue conservation analysis
PDB id:
1v3m
Name: Transferase
Title: Crystal structure of f283y mutant cyclodextrin glycosyltrans complexed with a pseudo-tetraose derived from acarbose
Structure: Cyclomaltodextrin glucanotransferase. Chain: a, b. Synonym: cyclodextrin-glycosyltransferase, cgtase. Engineered: yes. Mutation: yes
Source: Bacillus sp.. Organism_taxid: 1410. Strain: 1011. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.163     R-free:   0.218
Authors: R.Kanai,K.Haga,T.Akiba,K.Yamane,K.Harata
Key ref:
R.Kanai et al. (2004). Role of Phe283 in enzymatic reaction of cyclodextrin glycosyltransferase from alkalophilic Bacillus sp.1011: Substrate binding and arrangement of the catalytic site. Protein Sci, 13, 457-465. PubMed id: 14739329 DOI: 10.1110/ps.03408504
Date:
03-Nov-03     Release date:   03-Aug-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P05618  (CDGT_BACS0) -  Cyclomaltodextrin glucanotransferase
Seq:
Struc:
 
Seq:
Struc:
713 a.a.
686 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.2.4.1.19  - Cyclomaltodextrin glucanotransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Degrades starch to cyclodextrins by formation of a 1,4-alpha-D- glucosidic bond.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     catalytic activity     8 terms  

 

 
DOI no: 10.1110/ps.03408504 Protein Sci 13:457-465 (2004)
PubMed id: 14739329  
 
 
Role of Phe283 in enzymatic reaction of cyclodextrin glycosyltransferase from alkalophilic Bacillus sp.1011: Substrate binding and arrangement of the catalytic site.
R.Kanai, K.Haga, T.Akiba, K.Yamane, K.Harata.
 
  ABSTRACT  
 
Cyclodextrin glycosyltransferase (CGTase) belonging to the alpha-amylase family mainly catalyzes transglycosylation and produces cyclodextrins from starch and related alpha-1,4-glucans. The catalytic site of CGTase specifically conserves four aromatic residues, Phe183, Tyr195, Phe259, and Phe283, which are not found in alpha-amylase. To elucidate the structural role of Phe283, we determined the crystal structures of native and acarbose-complexed mutant CGTases in which Phe283 was replaced with leucine (F283L) or tyrosine (F283Y). The temperature factors of the region 259-269 in native F283L increased >10 A(2) compared with the wild type. The complex formation with acarbose not only increased the temperature factors (>10 A(2)) but also changed the structure of the region 257-267. This region is stabilized by interactions of Phe283 with Phe259 and Leu260 and plays an important role in the cyclodextrin binding. The conformation of the side-chains of Glu257, Phe259, His327, and Asp328 in the catalytic site was altered by the mutation of Phe283 with leucine, and this indicates that Phe283 partly arranges the structure of the catalytic site through contacts with Glu257 and Phe259. The replacement of Phe283 with tyrosine decreased the enzymatic activity in the basic pH range. The hydroxyl group of Tyr283 forms hydrogen bonds with the carboxyl group of Glu257, and the pK(a) of Glu257 in F283Y may be lower than that in the wild type.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Absolute starch degrading activity. pH Profiles for F283L (Nakamura et al. 1994 [solid circles]), F283Y mutant (solid squares), and wild-type CGTase (solid diamonds).
Figure 4.
Figure 4. Comparison of structures and temperature factors. (A) Difference of isotropic temperature factors for equivalent C atoms between F283L and wild-type CGTase. (B) Difference of isotropic temperature factors for equivalent C atoms between F283L_ACA and F283L. (C) Positional difference for equivalent C atoms in domain A (residues 1-138 and 204-406) between F283L_ACA and F283L.
 
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2004, 13, 457-465) copyright 2004.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21344678 G.Hai Tran, T.Desmet, M.R.De Groeve, and W.Soetaert (2011).
Probing the active site of cellodextrin phosphorylase from Clostridium stercorarium: Kinetic characterization, ligand docking, and site-directed mutagenesis.
  Biotechnol Prog, 27, 326-332.  
16172888 H.Bach, and D.L.Gutnick (2006).
Novel polysaccharide-protein-based amphipathic formulations.
  Appl Microbiol Biotechnol, 71, 34-38.  
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