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PDBsum entry 1d3c

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protein ligands metals links
Transferase PDB id
1d3c
Jmol
Contents
Protein chain
686 a.a. *
Ligands
GLC-GLC
GLC-GLC-GLC-GLC-
GLC-GLC-GLC-GLC
×3
MPD
Metals
_CA ×3
Waters ×639
* Residue conservation analysis
PDB id:
1d3c
Name: Transferase
Title: Michaelis complex of bacillus circulans strain 251 cyclodextrin glycosyltransferase with gamma-cyclodextrin
Structure: Cyclodextrin glycosyltransferase. Chain: a. Engineered: yes. Mutation: yes
Source: Bacillus circulans. Organism_taxid: 1397. Strain: 251. Cellular_location: extracellular. Expressed in: bacillus subtilis. Expression_system_taxid: 1423.
Resolution:
1.78Å     R-factor:   0.222     R-free:   0.258
Authors: J.C.M.Uitdehaag,K.H.Kalk,B.A.Van Der Veen,L.Dijkhuizen, B.W.Dijkstra
Key ref:
J.C.Uitdehaag et al. (1999). The cyclization mechanism of cyclodextrin glycosyltransferase (CGTase) as revealed by a gamma-cyclodextrin-CGTase complex at 1.8-A resolution. J Biol Chem, 274, 34868-34876. PubMed id: 10574960 DOI: 10.1074/jbc.274.49.34868
Date:
29-Sep-99     Release date:   22-Dec-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P43379  (CDGT2_BACCI) -  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  

 

 
DOI no: 10.1074/jbc.274.49.34868 J Biol Chem 274:34868-34876 (1999)
PubMed id: 10574960  
 
 
The cyclization mechanism of cyclodextrin glycosyltransferase (CGTase) as revealed by a gamma-cyclodextrin-CGTase complex at 1.8-A resolution.
J.C.Uitdehaag, K.H.Kalk, B.A.van Der Veen, L.Dijkhuizen, B.W.Dijkstra.
 
  ABSTRACT  
 
The enzyme cyclodextrin glycosyltransferase is closely related to alpha-amylases but has the unique ability to produce cyclodextrins (circular alpha(1-->4)-linked glucoses) from starch. To characterize this specificity we determined a 1.8-A structure of an E257Q/D229N mutant cyclodextrin glycosyltransferase in complex with its product gamma-cyclodextrin, which reveals for the first time how cyclodextrin is competently bound. Across subsites -2, -1, and +1, the cyclodextrin ring binds in a twisted mode similar to linear sugars, giving rise to deformation of its circular symmetry. At subsites -3 and +2, the cyclodextrin binds in a manner different from linear sugars. Sequence comparisons and site-directed mutagenesis experiments support the conclusion that subsites -3 and +2 confer the cyclization activity in addition to subsite -6 and Tyr-195. On this basis, a role of the individual residues during the cyclization reaction cycle is proposed.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Stereo picture indicating the maltononaose (7) (gray) and -cyclodextrin (black) conformation in the CGTase active site. The white C backbone has the conformation observed in the -cyclodextrin complex. The backbone conformations of the loops 87-93 144-151, 175-182, and 190-199 in the maltononaose complex are indicated in gray.
Figure 5.
Fig. 5. Overview of the interactions between CGTase and maltononaose (7) (A) or -cyclodextrin (B). The distances associated with the interactions are in Table III. For clarity, not all interactions at subsites 2, 1, and +1 are shown. Symm rel. contacts, contacts made to a symmetry-related CGTase molecule in the crystal.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1999, 274, 34868-34876) copyright 1999.  
  Figures were selected by the author.  

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.  
19682075 C.Christiansen, M.Abou Hachem, S.Janecek, A.Viksø-Nielsen, A.Blennow, and B.Svensson (2009).
The carbohydrate-binding module family 20--diversity, structure, and function.
  FEBS J, 276, 5006-5029.  
19769746 J.Vasur, R.Kawai, E.Andersson, K.Igarashi, M.Sandgren, M.Samejima, and J.Ståhlberg (2009).
X-ray crystal structures of Phanerochaete chrysosporium Laminarinase 16A in complex with products from lichenin and laminarin hydrolysis.
  FEBS J, 276, 3858-3869.
PDB codes: 2w39 2w52
19670211 R.Koike, A.Kidera, and M.Ota (2009).
Alteration of oligomeric state and domain architecture is essential for functional transformation between transferase and hydrolase with the same scaffold.
  Protein Sci, 18, 2060-2066.  
19367403 R.M.Kelly, L.Dijkhuizen, and H.Leemhuis (2009).
The evolution of cyclodextrin glucanotransferase product specificity.
  Appl Microbiol Biotechnol, 84, 119-133.  
19154742 Y.Y.Tseng, J.Dundas, and J.Liang (2009).
Predicting protein function and binding profile via matching of local evolutionary and geometric surface patterns.
  J Mol Biol, 387, 451-464.  
18704190 S.Jemli, E.Ben Messaoud, S.Ben Mabrouk, and S.Bejar (2008).
The cyclodextrin glycosyltransferase of Paenibacillus pabuli US132 strain: molecular characterization and overproduction of the recombinant enzyme.
  J Biomed Biotechnol, 2008, 692573.  
17371546 T.Tonozuka, A.Sogawa, M.Yamada, N.Matsumoto, H.Yoshida, S.Kamitori, K.Ichikawa, M.Mizuno, A.Nishikawa, and Y.Sakano (2007).
Structural basis for cyclodextrin recognition by Thermoactinomyces vulgaris cyclo/maltodextrin-binding protein.
  FEBS J, 274, 2109-2120.
PDB codes: 2dfz 2zyk
17891389 Z.Li, M.Wang, F.Wang, Z.Gu, G.Du, J.Wu, and J.Chen (2007).
gamma-Cyclodextrin: a review on enzymatic production and applications.
  Appl Microbiol Biotechnol, 77, 245-255.  
16926508 H.Watanabe, T.Nishimoto, K.Mukai, M.Kubota, H.Chaen, and S.Fukuda (2006).
A novel glucanotransferase from a Bacillus circulans strain that produces a cyclomaltopentaose cyclized by an alpha-1,6-linkage.
  Biosci Biotechnol Biochem, 70, 1954-1960.  
17090949 H.Watanabe, T.Nishimoto, M.Kubota, H.Chaen, and S.Fukuda (2006).
Cloning, sequencing, and expression of the genes encoding an isocyclomaltooligosaccharide glucanotransferase and an alpha-amylase from a Bacillus circulans strain.
  Biosci Biotechnol Biochem, 70, 2690-2702.  
16012834 K.Hirano, T.Ishihara, S.Ogasawara, H.Maeda, K.Abe, T.Nakajima, and Y.Yamagata (2006).
Molecular cloning and characterization of a novel gamma-CGTase from alkalophilic Bacillus sp.
  Appl Microbiol Biotechnol, 70, 193-201.  
16461650 K.Mukai, H.Watanabe, M.Kubota, H.Chaen, S.Fukuda, and M.Kurimoto (2006).
Purification, characterization, and gene cloning of a novel maltosyltransferase from an Arthrobacter globiformis strain that produces an alternating alpha-1,4- and alpha-1,6-cyclic tetrasaccharide from starch.
  Appl Environ Microbiol, 72, 1065-1071.  
15701681 A.T.Laurie, and R.M.Jackson (2005).
Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites.
  Bioinformatics, 21, 1908-1916.  
15630515 Q.Qi, and W.Zimmermann (2005).
Cyclodextrin glucanotransferase: from gene to applications.
  Appl Microbiol Biotechnol, 66, 475-485.  
14705029 H.Leemhuis, H.J.Rozeboom, B.W.Dijkstra, and L.Dijkhuizen (2004).
Improved thermostability of bacillus circulans cyclodextrin glycosyltransferase by the introduction of a salt bridge.
  Proteins, 54, 128-134.
PDB code: 1pj9
14739329 R.Kanai, K.Haga, T.Akiba, K.Yamane, and K.Harata (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.
PDB codes: 1v3j 1v3k 1v3l 1v3m
12492486 H.Leemhuis, B.W.Dijkstra, and L.Dijkhuizen (2003).
Thermoanaerobacterium thermosulfurigenes cyclodextrin glycosyltransferase.
  Eur J Biochem, 270, 155-162.  
12554949 H.W.Choe, K.S.Park, J.Labahn, J.Granzin, C.J.Kim, and G.Büldt (2003).
Crystallization and preliminary X-ray diffraction studies of alpha-cyclodextrin glucanotransferase isolated from Bacillus macerans.
  Acta Crystallogr D Biol Crystallogr, 59, 348-349.  
11257505 E.A.MacGregor, S.Janecek, and B.Svensson (2001).
Relationship of sequence and structure to specificity in the alpha-amylase family of enzymes.
  Biochim Biophys Acta, 1546, 1.  
11288183 J.C.Uitdehaag, B.A.van der Veen, L.Dijkhuizen, R.Elber, and B.W.Dijkstra (2001).
Enzymatic circularization of a malto-octaose linear chain studied by stochastic reaction path calculations on cyclodextrin glycosyltransferase.
  Proteins, 43, 327-335.  
11282590 Y.Terada, H.Sanbe, T.Takaha, S.Kitahata, K.Koizumi, and S.Okada (2001).
Comparative study of the cyclization reactions of three bacterial cyclomaltodextrin glucanotransferases.
  Appl Environ Microbiol, 67, 1453-1460.  
10651801 B.A.van der Veen, G.J.van Alebeek, J.C.Uitdehaag, B.W.Dijkstra, and L.Dijkhuizen (2000).
The three transglycosylation reactions catalyzed by cyclodextrin glycosyltransferase from Bacillus circulans (strain 251) proceed via different kinetic mechanisms.
  Eur J Biochem, 267, 658-665.  
10848958 B.A.van der Veen, J.C.Uitdehaag, B.W.Dijkstra, and L.Dijkhuizen (2000).
The role of arginine 47 in the cyclization and coupling reactions of cyclodextrin glycosyltransferase from Bacillus circulans strain 251 implications for product inhibition and product specificity.
  Eur J Biochem, 267, 3432-3441.  
11006547 C.S.Rye, and S.G.Withers (2000).
Glycosidase mechanisms.
  Curr Opin Chem Biol, 4, 573-580.  
10869182 J.C.Uitdehaag, G.J.van Alebeek, B.A.van Der Veen, L.Dijkhuizen, and B.W.Dijkstra (2000).
Structures of maltohexaose and maltoheptaose bound at the donor sites of cyclodextrin glycosyltransferase give insight into the mechanisms of transglycosylation activity and cyclodextrin size specificity.
  Biochemistry, 39, 7772-7780.
PDB codes: 1eo5 1eo7
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.