spacer
spacer

PDBsum entry 3cgt

Go to PDB code: 
protein ligands metals links
Glycosyltransferase PDB id
3cgt
Jmol
Contents
Protein chain
684 a.a. *
Ligands
BCD
Metals
_CA ×2
Waters ×205
* Residue conservation analysis
PDB id:
3cgt
Name: Glycosyltransferase
Title: Structure of cyclodextrin glycosyltransferase complexed with its main product beta-cyclodextrin
Structure: Cyclodextrin glycosyltransferase. Chain: a. Synonym: cyclodextrin glucanotransferase, cgtase, 1,4- alpha-d-glucan\:1,4-alpha-d-glucopyranosyltransferase (cyclizing). Engineered: yes. Mutation: yes
Source: Bacillus circulans. Organism_taxid: 1397. Strain: 8. Cellular_location: extracellular. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.40Å     R-factor:   0.177     R-free:   0.228
Authors: A.K.Schmidt,G.E.Schulz
Key ref:
A.K.Schmidt et al. (1998). Structure of cyclodextrin glycosyltransferase complexed with a derivative of its main product beta-cyclodextrin. Biochemistry, 37, 5909-5915. PubMed id: 9558324 DOI: 10.1021/bi9729918
Date:
22-Jan-98     Release date:   27-May-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P30920  (CDGT1_BACCI) -  Cyclomaltodextrin glucanotransferase
Seq:
Struc:
 
Seq:
Struc:
718 a.a.
684 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.2.4.1.19  - 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: 10.1021/bi9729918 Biochemistry 37:5909-5915 (1998)
PubMed id: 9558324  
 
 
Structure of cyclodextrin glycosyltransferase complexed with a derivative of its main product beta-cyclodextrin.
A.K.Schmidt, S.Cottaz, H.Driguez, G.E.Schulz.
 
  ABSTRACT  
 
Crystals of the inactive mutant Glu257-->Ala of cyclodextrin glycosyltransferase were soaked with the cyclodextrin (CD) derivative S-(alpha-D-glucopyranosyl)-6-thio-beta-CD. The structural analysis showed its beta-CD moiety with no density indication for the exocyclic glucosyl unit. For steric reasons, however, the position of this unit is restricted to be at only two of the seven glucosyl groups of beta-CD. The analysis indicated that the enzyme can cyclize branched alpha-glucans. The ligated beta-CD moiety revealed how the enzyme binds its predominant cyclic product. The conformation of the ligated beta-CD was intermediate between the more symmetrical conformation in beta-CD dodecahydrate crystals and the conformation of a bound linear alpha-glucan chain. Its scissile bond was displaced by 2.8 A from the position in linear alpha-glucans. Accordingly, the complex represents the situation after the cyclization reaction but before diffusion into the solvent, where a more symmetrical conformation is assumed, or the equivalent state in the reverse reaction. Furthermore, a unifying nomenclature for oligosaccharide-binding subsites in proteins is proposed.
 

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.  
18703518 E.J.Woo, S.Lee, H.Cha, J.T.Park, S.M.Yoon, H.N.Song, and K.H.Park (2008).
Structural Insight into the Bifunctional Mechanism of the Glycogen-debranching Enzyme TreX from the Archaeon Sulfolobus solfataricus.
  J Biol Chem, 283, 28641-28648.
PDB codes: 2vnc 2vr5 2vuy
18492718 J.Chen, M.K.Ghorai, G.Kenney, and J.Stubbe (2008).
Mechanistic studies on bleomycin-mediated DNA damage: multiple binding modes can result in double-stranded DNA cleavage.
  Nucleic Acids Res, 36, 3781-3790.  
17493580 R.Zidovetzki, and I.Levitan (2007).
Use of cyclodextrins to manipulate plasma membrane cholesterol content: evidence, misconceptions and control strategies.
  Biochim Biophys Acta, 1768, 1311-1324.  
15630515 Q.Qi, and W.Zimmermann (2005).
Cyclodextrin glucanotransferase: from gene to applications.
  Appl Microbiol Biotechnol, 66, 475-485.  
15138257 A.Ohtaki, M.Mizuno, T.Tonozuka, Y.Sakano, and S.Kamitori (2004).
Complex structures of Thermoactinomyces vulgaris R-47 alpha-amylase 2 with acarbose and cyclodextrins demonstrate the multiple substrate recognition mechanism.
  J Biol Chem, 279, 31033-31040.
PDB codes: 1vfk 1vfm 1vfo 1vfu 3a6o
15044473 D.Locke, I.V.Koreen, J.Y.Liu, and A.L.Harris (2004).
Reversible pore block of connexin channels by cyclodextrins.
  J Biol Chem, 279, 22883-22892.  
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
12752453 H.B.Fritzsche, T.Schwede, and G.E.Schulz (2003).
Covalent and three-dimensional structure of the cyclodextrinase from Flavobacterium sp. no. 92.
  Eur J Biochem, 270, 2332-2341.
PDB code: 1h3g
12492486 H.Leemhuis, B.W.Dijkstra, and L.Dijkhuizen (2003).
Thermoanaerobacterium thermosulfurigenes cyclodextrin glycosyltransferase.
  Eur J Biochem, 270, 155-162.  
14661272 L.Greffe, M.T.Jensen, C.Bosso, B.Svensson, and H.Driguez (2003).
Chemoenzymatic synthesis of branched oligo- and polysaccharides as potential substrates for starch active enzymes.
  Chembiochem, 4, 1307-1311.  
12930991 N.Pinotsis, D.D.Leonidas, E.D.Chrysina, N.G.Oikonomakos, and I.M.Mavridis (2003).
The binding of beta- and gamma-cyclodextrins to glycogen phosphorylase b: kinetic and crystallographic studies.
  Protein Sci, 12, 1914-1924.
PDB codes: 1p29 1p2b 1p2d 1p2g
12423336 H.Mori, K.S.Bak-Jensen, and B.Svensson (2002).
Barley alpha-amylase Met53 situated at the high-affinity subsite -2 belongs to a substrate binding motif in the beta-->alpha loop 2 of the catalytic (beta/alpha)8-barrel and is critical for activity and substrate specificity.
  Eur J Biochem, 269, 5377-5390.  
11790748 N.Rashid, J.Cornista, S.Ezaki, T.Fukui, H.Atomi, and T.Imanaka (2002).
Characterization of an archaeal cyclodextrin glucanotransferase with a novel C-terminal domain.
  J Bacteriol, 184, 777-784.  
11679762 A.Varrot, M.Schülein, S.Fruchard, H.Driguez, and G.J.Davies (2001).
Atomic resolution structure of endoglucanase Cel5A in complex with methyl 4,4II,4III,4IV-tetrathio-alpha-cellopentoside highlights the alternative binding modes targeted by substrate mimics.
  Acta Crystallogr D Biol Crystallogr, 57, 1739-1742.
PDB code: 1h5v
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.  
11828459 H.Driguez (2001).
Thiooligosaccharides as tools for structural biology.
  Chembiochem, 2, 311-318.  
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.  
11828460 S.Fort, A.Varrot, M.Schülein, S.Cottaz, H.Driguez, and G.J.Davies (2001).
Mixed-linkage cellooligosaccharides: a new class of glycoside hydrolase inhibitors.
  Chembiochem, 2, 319-325.
PDB code: 1e5j
11330677 T.Yokota, T.Tonozuka, Y.Shimura, K.Ichikawa, S.Kamitori, and Y.Sakano (2001).
Structures of Thermoactinomyces vulgaris R-47 alpha-amylase II complexed with substrate analogues.
  Biosci Biotechnol Biochem, 65, 619-626.
PDB codes: 1jib 1jl8
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.  
10924103 A.M.Brzozowski, D.M.Lawson, J.P.Turkenburg, H.Bisgaard-Frantzen, A.Svendsen, T.V.Borchert, Z.Dauter, K.S.Wilson, and G.J.Davies (2000).
Structural analysis of a chimeric bacterial alpha-amylase. High-resolution analysis of native and ligand complexes.
  Biochemistry, 39, 9099-9107.
PDB codes: 1e3x 1e3z 1e40 1e43
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.  
10574960 J.C.Uitdehaag, K.H.Kalk, B.A.van Der Veen, L.Dijkhuizen, and B.W.Dijkstra (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.
PDB code: 1d3c
10455198 M.Pajatsch, C.Andersen, A.Mathes, A.Böck, R.Benz, and H.Engelhardt (1999).
Properties of a cyclodextrin-specific, unusual porin from Klebsiella oxytoca.
  J Biol Chem, 274, 25159-25166.  
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.