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PDBsum entry 1ukq

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
1ukq
Jmol
Contents
Protein chains
686 a.a. *
Ligands
GLC-ACI-G6D-BGC
GLC-ACI-G6D-GLC
Metals
_CA ×4
Waters ×638
* Residue conservation analysis
PDB id:
1ukq
Name: Transferase
Title: Crystal structure of cyclodextrin glucanotransferase complex pseudo-maltotetraose derived from acarbose
Structure: Cyclomaltodextrin glucanotransferase. Chain: a, b. Synonym: cyclodextrin-glycosyltransferase, cgtase, cyclodex glucanotransferase. Engineered: yes
Source: Bacillus sp.. Organism_taxid: 1410. Strain: 1011. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.184     R-free:   0.246
Authors: K.Haga,R.Kanai,O.Sakamoto,K.Harata,K.Yamane
Key ref: K.Haga et al. (2003). Effects of essential carbohydrate/aromatic stacking interaction with Tyr100 and Phe259 on substrate binding of cyclodextrin glycosyltransferase from alkalophilic Bacillus sp. 1011. J Biochem, 134, 881-891. PubMed id: 14769878
Date:
01-Sep-03     Release date:   24-Feb-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 2 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  

 

 
J Biochem 134:881-891 (2003)
PubMed id: 14769878  
 
 
Effects of essential carbohydrate/aromatic stacking interaction with Tyr100 and Phe259 on substrate binding of cyclodextrin glycosyltransferase from alkalophilic Bacillus sp. 1011.
K.Haga, R.Kanai, O.Sakamoto, M.Aoyagi, K.Harata, K.Yamane.
 
  ABSTRACT  
 
The stacking interaction between a tyrosine residue and the sugar ring at the catalytic subsite -1 is strictly conserved in the glycoside hydrolase family 13 enzymes. Replacing Tyr100 with leucine in cyclodextrin glycosyltransferase (CGTase) from Bacillus sp. 1011 to prevent stacking significantly decreased all CGTase activities. The adjacent stacking interaction with both Phe183 and Phe259 onto the sugar ring at subsite +2 is essentially conserved among CGTases. F183L/F259L mutant CGTase affects donor substrate binding and/or acceptor binding during transglycosylation [Nakamura et al. (1994) Biochemistry 33, 9929-9936]. To elucidate the precise role of carbohydrate/aromatic stacking interaction at subsites -1 and +2 on the substrate binding of CGTases, we analyzed the X-ray structures of wild-type (2.0 A resolution), and Y100L (2.2 A resolution) and F183L/F259L mutant (1.9 A resolution) CGTases complexed with the inhibitor, acarbose. The refined structures revealed that acarbose molecules bound to the Y100L mutant moved from the active center toward the side chain of Tyr195, and the hydrogen bonding and hydrophobic interaction between acarbose and subsites significantly diminished. The position of pseudo-tetrasaccharide binding in the F183L/F259L mutant was closer to the non-reducing end, and the torsion angles of glycosidic linkages at subsites -1 to +1 on molecule 1 and subsites -2 to -1 on molecule 2 significantly changed compared with that of each molecule of wild-type-acarbose complex to adopt the structural change of subsite +2. These structural and biochemical data suggest that substrate binding in the active site of CGTase is critically affected by the carbohydrate/aromatic stacking interaction with Tyr100 at the catalytic subsite -1 and that this effect is likely a result of cooperation between Tyr100 and Phe259 through stacking interaction with substrate at subsite +2.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19763564 H.Leemhuis, R.M.Kelly, and L.Dijkhuizen (2010).
Engineering of cyclodextrin glucanotransferases and the impact for biotechnological applications.
  Appl Microbiol Biotechnol, 85, 823-835.  
19897654 T.Kashimoto, S.Ueno, T.Koga, S.Fukudome, H.Ehara, M.Komai, H.Sugiyama, and N.Susa (2010).
The aromatic ring of phenylalanine 334 is essential for oligomerization of Vibrio vulnificus hemolysin.
  J Bacteriol, 192, 568-574.  
17705310 J.Kondo, M.Hainrichson, I.Nudelman, D.Shallom-Shezifi, C.M.Barbieri, D.S.Pilch, E.Westhof, and T.Baasov (2007).
Differential selectivity of natural and synthetic aminoglycosides towards the eukaryotic and prokaryotic decoding A sites.
  Chembiochem, 8, 1700-1709.
PDB codes: 2o3v 2o3w 2o3x 2o3y
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.