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PDBsum entry 1cgu

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protein ligands metals links
Glycosyltransferase PDB id
1cgu
Jmol
Contents
Protein chain
684 a.a. *
Ligands
GLC-GLC
Metals
_CA ×2
Waters ×478
* Residue conservation analysis
PDB id:
1cgu
Name: Glycosyltransferase
Title: Catalytic center of cyclodextrin glycosyltransferase derived from x-ray structure analysis combined with site- directed mutagenesis
Structure: Cyclodextrin glycosyl-transferase. Chain: a. Engineered: yes
Source: Bacillus circulans. Organism_taxid: 1397
Resolution:
2.50Å     R-factor:   0.187    
Authors: C.Klein,J.Hollender,H.Bender,G.E.Schulz
Key ref:
C.Klein et al. (1992). Catalytic center of cyclodextrin glycosyltransferase derived from X-ray structure analysis combined with site-directed mutagenesis. Biochemistry, 31, 8740-8746. PubMed id: 1390660 DOI: 10.1021/bi00152a009
Date:
10-Jun-92     Release date:   31-Jan-94    
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/bi00152a009 Biochemistry 31:8740-8746 (1992)
PubMed id: 1390660  
 
 
Catalytic center of cyclodextrin glycosyltransferase derived from X-ray structure analysis combined with site-directed mutagenesis.
C.Klein, J.Hollender, H.Bender, G.E.Schulz.
 
  ABSTRACT  
 
An X-ray structure analysis of a crystal of mutant Asp229----Ala of cyclodextrin glycosyltransferase from Bacillus circulans (Ec 2.4.1.19) that had been shortly exposed to beta-cyclodextrin showed density corresponding to a maltose bound at the catalytic center. The crystal structure was refined to an R-factor of 18.7% at 2.5-A resolution. The catalytic center is defined by homology with the structurally known alpha-amylases and by the observation that mutants Asp229----Ala and Asp328----Ala are almost inactive. By model building, the density-defined maltose was extended to a full beta-cyclodextrin, which then indicated the general locations of seven subsites for glucosyl units. The catalytically competent residues Asp229, Glu257, and Asp328 are at the reducing end of the density-defined maltose. In the unligated wild-type structure, Glu257 and Asp328 form a 2.6-A hydrogen bond between their carboxylates in an arrangement that resembles those of the catalytically competent carboxylates in acid proteases. Presumably, the first catalytic step is an attack of the proton between Glu257 and Asp328 on the oxygen of the glycosidic bond.
 

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.  
18626642 Y.H.Liu, F.P.Lu, Y.Li, J.L.Wang, and C.Gao (2008).
Acid stabilization of Bacillus licheniformis alpha amylase through introduction of mutations.
  Appl Microbiol Biotechnol, 80, 795-803.  
18157528 Y.H.Liu, F.P.Lu, Y.Li, X.B.Yin, Y.Wang, and C.Gao (2008).
Characterisation of mutagenised acid-resistant alpha-amylase expressed in Bacillus subtilis WB600.
  Appl Microbiol Biotechnol, 78, 85-94.  
15630515 Q.Qi, and W.Zimmermann (2005).
Cyclodextrin glucanotransferase: from gene to applications.
  Appl Microbiol Biotechnol, 66, 475-485.  
12930989 J.E.Nielsen, and J.A.McCammon (2003).
Calculating pKa values in enzyme active sites.
  Protein Sci, 12, 1894-1901.  
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.  
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.  
11150610 J.E.Nielsen, and T.V.Borchert (2000).
Protein engineering of bacterial alpha-amylases.
  Biochim Biophys Acta, 1543, 253-274.  
10679895 N.Ishii, K.Haga, K.Yamane, and K.Harata (2000).
Crystal structure of asparagine 233-replaced cyclodextrin glucanotransferase from alkalophilic Bacillus sp. 1011 determined at 1.9 A resolution.
  J Mol Recognit, 13, 35-43.
PDB code: 1d7f
  10091666 E.H.Rydberg, G.Sidhu, H.C.Vo, J.Hewitt, H.C.Côte, Y.Wang, S.Numao, R.T.MacGillivray, C.M.Overall, G.D.Brayer, and S.G.Withers (1999).
Cloning, mutagenesis, and structural analysis of human pancreatic alpha-amylase expressed in Pichia pastoris.
  Protein Sci, 8, 635-643.
PDB code: 1bsi
  9882648 G.P.De Montalk, M.Remaud-Simeon, R.M.Willemot, V.Planchot, and P.Monsan (1999).
Sequence analysis of the gene encoding amylosucrase from Neisseria polysaccharea and characterization of the recombinant enzyme.
  J Bacteriol, 181, 375-381.  
10872458 H.D.Ly, and S.G.Withers (1999).
Mutagenesis of glycosidases.
  Annu Rev Biochem, 68, 487-522.  
  10473430 J.Abe, C.Ushijima, and S.Hizukuri (1999).
Expression of the isoamylase gene of Flavobacterium odoratum KU in Escherichia coli and identification of essential residues of the enzyme by site-directed mutagenesis.
  Appl Environ Microbiol, 65, 4163-4170.  
10491128 J.E.Nielsen, L.Beier, D.Otzen, T.V.Borchert, H.B.Frantzen, K.V.Andersen, and A.Svendsen (1999).
Electrostatics in the active site of an alpha-amylase.
  Eur J Biochem, 264, 816-824.  
9558324 A.K.Schmidt, S.Cottaz, H.Driguez, and G.E.Schulz (1998).
Structure of cyclodextrin glycosyltransferase complexed with a derivative of its main product beta-cyclodextrin.
  Biochemistry, 37, 5909-5915.
PDB code: 3cgt
9488711 R.D.Wind, J.C.Uitdehaag, R.M.Buitelaar, B.W.Dijkstra, and L.Dijkhuizen (1998).
Engineering of cyclodextrin product specificity and pH optima of the thermostable cyclodextrin glycosyltransferase from Thermoanaerobacterium thermosulfurigenes EM1.
  J Biol Chem, 273, 5771-5779.
PDB code: 1a47
  9416598 K.S.Devulapalle, S.D.Goodman, Q.Gao, A.Hemsley, and G.Mooser (1997).
Knowledge-based model of a glucosyltransferase from the oral bacterial group of mutans streptococci.
  Protein Sci, 6, 2489-2493.  
9245426 R.Mosi, S.He, J.Uitdehaag, B.W.Dijkstra, and S.G.Withers (1997).
Trapping and characterization of the reaction intermediate in cyclodextrin glycosyltransferase by use of activated substrates and a mutant enzyme.
  Biochemistry, 36, 9927-9934.  
9288901 S.Arming, B.Strobl, C.Wechselberger, and G.Kreil (1997).
In vitro mutagenesis of PH-20 hyaluronidase from human sperm.
  Eur J Biochem, 247, 810-814.  
8672460 B.Strokopytov, R.M.Knegtel, D.Penninga, H.J.Rozeboom, K.H.Kalk, L.Dijkhuizen, and B.W.Dijkstra (1996).
Structure of cyclodextrin glycosyltransferase complexed with a maltononaose inhibitor at 2.6 angstrom resolution. Implications for product specificity.
  Biochemistry, 35, 4241-4249.
PDB codes: 1dij 2dij
8663322 T.Kuriki, H.Kaneko, M.Yanase, H.Takata, J.Shimada, S.Handa, T.Takada, H.Umeyama, and S.Okada (1996).
Controlling substrate preference and transglycosylation activity of neopullulanase by manipulating steric constraint and hydrophobicity in active center.
  J Biol Chem, 271, 17321-17329.  
7588803 A.J.Jacks, K.Sorimachi, M.F.Le Gal-Coëffet, G.Williamson, D.B.Archer, and M.P.Williamson (1995).
1H and 15N assignments and secondary structure of the starch-binding domain of glucoamylase from Aspergillus niger.
  Eur J Biochem, 233, 568-578.  
8535789 C.Wiesmann, G.Beste, W.Hengstenberg, and G.E.Schulz (1995).
The three-dimensional structure of 6-phospho-beta-galactosidase from Lactococcus lactis.
  Structure, 3, 961-968.
PDB code: 1pbg
7873597 P.Mattsson, N.Battchikova, K.Sippola, and T.Korpela (1995).
The role of histidine residues in the catalytic act of cyclomaltodextrin glucanotransferase from Bacillus circulans var. alkalophilus.
  Biochim Biophys Acta, 1247, 97.  
  7747949 R.D.Wind, W.Liebl, R.M.Buitelaar, D.Penninga, A.Spreinat, L.Dijkhuizen, and H.Bahl (1995).
Cyclodextrin formation by the thermostable alpha-amylase of Thermoanaerobacterium thermosulfurigenes EM1 and reclassification of the enzyme as a cyclodextrin glycosyltransferase.
  Appl Environ Microbiol, 61, 1257-1265.  
7493956 R.M.Knegtel, B.Strokopytov, D.Penninga, O.G.Faber, H.J.Rozeboom, K.H.Kalk, L.Dijkhuizen, and B.W.Dijkstra (1995).
Crystallographic studies of the interaction of cyclodextrin glycosyltransferase from Bacillus circulans strain 251 with natural substrates and products.
  J Biol Chem, 270, 29256-29264.
PDB codes: 1cxe 1cxf 1cxh 1cxi
  7795519 S.G.Withers, and R.Aebersold (1995).
Approaches to labeling and identification of active site residues in glycosidases.
  Protein Sci, 4, 361-372.  
8018865 B.Svensson (1994).
Protein engineering in the alpha-amylase family: catalytic mechanism, substrate specificity, and stability.
  Plant Mol Biol, 25, 141-157.  
7712292 J.D.McCarter, and S.G.Withers (1994).
Mechanisms of enzymatic glycoside hydrolysis.
  Curr Opin Struct Biol, 4, 885-892.  
8168517 K.W.Rodenburg, N.Juge, X.J.Guo, M.Søgaard, J.C.Chaix, and B.Svensson (1994).
Domain B protruding at the third beta strand of the alpha/beta barrel in barley alpha-amylase confers distinct isozyme-specific properties.
  Eur J Biochem, 221, 277-284.  
8136030 H.M.Jespersen, E.A.MacGregor, B.Henrissat, M.R.Sierks, and B.Svensson (1993).
Starch- and glycogen-debranching and branching enzymes: prediction of structural features of the catalytic (beta/alpha)8-barrel domain and evolutionary relationship to other amylolytic enzymes.
  J Protein Chem, 12, 791-805.  
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.