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Glycosyltransferase PDB id
1cgt
Jmol
Contents
Protein chain
684 a.a. *
Metals
_CA ×2
Waters ×588
* Residue conservation analysis
PDB id:
1cgt
Name: Glycosyltransferase
Title: Structure of cyclodextrin glycosyltransferase refined at 2.0 angstroms resolution
Structure: Cyclodextrin glycosyl-transferase. Chain: a. Engineered: yes
Source: Bacillus circulans. Organism_taxid: 1397
Resolution:
2.00Å     R-factor:   0.166    
Authors: C.Klein,G.E.Schulz
Key ref: C.Klein and G.E.Schulz (1991). Structure of cyclodextrin glycosyltransferase refined at 2.0 A resolution. J Mol Biol, 217, 737-750. PubMed id: 1826034 DOI: 10.1016/0022-2836(91)90530-J
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

 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     9 terms  

 

 
DOI no: 10.1016/0022-2836(91)90530-J J Mol Biol 217:737-750 (1991)
PubMed id: 1826034  
 
 
Structure of cyclodextrin glycosyltransferase refined at 2.0 A resolution.
C.Klein, G.E.Schulz.
 
  ABSTRACT  
 
The previously reported structural model of cyclodextrin glycosyltransferase (EC 2.4.1.19) from Bacillus circulans has been improved. For this purpose the known sequence was built into an electron density map established by multiple isomorphous replacement and subsequent solvent-flattening at 2.5 A resolution. The resulting model was refined at 2.0 A resolution using a simulated annealing refinement method. Based on 70,171 independent reflections in the range 7.0 to 2.0 A resolution, a final R-factor of 17.6% was obtained with a model obeying standard geometry within 0.013 A in bond lengths and 2.7 degrees in bond angles. The final model consists of all 684 amino acid residues, two calcium ions and 588 solvent molecules.
 

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.  
19367403 R.M.Kelly, L.Dijkhuizen, and H.Leemhuis (2009).
The evolution of cyclodextrin glucanotransferase product specificity.
  Appl Microbiol Biotechnol, 84, 119-133.  
18552192 J.Y.Damián-Almazo, A.Moreno, A.López-Munguía, X.Soberón, F.González-Muñoz, and G.Saab-Rincón (2008).
Enhancement of the alcoholytic activity of alpha-amylase AmyA from Thermotoga maritima MSB8 (DSM 3109) by site-directed mutagenesis.
  Appl Environ Microbiol, 74, 5168-5177.  
  16508106 K.Imamura, T.Matsuura, Z.Ye, T.Takaha, K.Fujii, M.Kusunoki, and Y.Nitta (2005).
Crystallization and preliminary X-ray crystallographic study of disproportionating enzyme from potato.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 109-111.  
16262690 M.Machovic, B.Svensson, E.A.MacGregor, and S.Janecek (2005).
A new clan of CBM families based on bioinformatics of starch-binding domains from families CBM20 and CBM21.
  FEBS J, 272, 5497-5513.  
15630515 Q.Qi, and W.Zimmermann (2005).
Cyclodextrin glucanotransferase: from gene to applications.
  Appl Microbiol Biotechnol, 66, 475-485.  
15939348 R.Rodríguez-Sanoja, N.Oviedo, and S.Sánchez (2005).
Microbial starch-binding domain.
  Curr Opin Microbiol, 8, 260-267.  
14763853 D.H.Kweon, D.H.Lee, N.S.Han, and J.H.Seo (2004).
Solid-phase refolding of cyclodextrin glycosyltransferase adsorbed on cation-exchange resin.
  Biotechnol Prog, 20, 277-283.  
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
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
12618437 H.Imamura, S.Fushinobu, M.Yamamoto, T.Kumasaka, B.S.Jeon, T.Wakagi, and H.Matsuzawa (2003).
Crystal structures of 4-alpha-glucanotransferase from Thermococcus litoralis and its complex with an inhibitor.
  J Biol Chem, 278, 19378-19386.
PDB codes: 1k1w 1k1x 1k1y
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.  
12581203 S.Janecek, B.Svensson, and E.A.MacGregor (2003).
Relation between domain evolution, specificity, and taxonomy of the alpha-amylase family members containing a C-terminal starch-binding domain.
  Eur J Biochem, 270, 635-645.  
12196524 M.C.Abad, K.Binderup, J.Rios-Steiner, R.K.Arni, J.Preiss, and J.H.Geiger (2002).
The X-ray crystallographic structure of Escherichia coli branching enzyme.
  J Biol Chem, 277, 42164-42170.
PDB code: 1m7x
11737209 H.Mori, K.S.Bak-Jensen, T.E.Gottschalk, M.S.Motawia, I.Damager, B.L.Møller, and B.Svensson (2001).
Modulation of activity and substrate binding modes by mutation of single and double subsites +1/+2 and -5/-6 of barley alpha-amylase 1.
  Eur J Biochem, 268, 6545-6558.  
11553913 T.Wakayama, K.Ohashi, K.Mizuno, and S.Iseki (2001).
Cloning and characterization of a novel mouse immunoglobulin superfamily gene expressed in early spermatogenic cells.
  Mol Reprod Dev, 60, 158-164.  
11302176 T.Yokota, T.Tonozuka, S.Kamitori, and Y.Sakano (2001).
The deletion of amino-terminal domain in Thermoactinomyces vulgaris R-47 alpha-amylases: effects of domain N on activity, specificity, stability and dimerization.
  Biosci Biotechnol Biochem, 65, 401-408.  
11272837 Y.Mezaki, Y.Katsuya, M.Kubota, and Y.Matsuura (2001).
Crystallization and structural analysis of intact maltotetraose-forming exo-amylase from Pseudomonas stutzeri.
  Biosci Biotechnol Biochem, 65, 222-225.
PDB code: 1gcy
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.  
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.  
10869188 D.J.Nichols, P.L.Keeling, M.Spalding, and H.Guan (2000).
Involvement of conserved aspartate and glutamate residues in the catalysis and substrate binding of maize starch synthase.
  Biochemistry, 39, 7820-7825.  
10877806 K.Ohdan, T.Kuriki, H.Takata, H.Kaneko, and S.Okada (2000).
Introduction of raw starch-binding domains into Bacillus subtilis alpha-amylase by fusion with the starch-binding domain of Bacillus cyclomaltodextrin glucanotransferase.
  Appl Environ Microbiol, 66, 3058-3064.  
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
  11080642 T.Kajander, P.C.Kahn, S.H.Passila, D.C.Cohen, L.Lehtiö, W.Adolfsen, J.Warwicker, U.Schell, and A.Goldman (2000).
Buried charged surface in proteins.
  Structure, 8, 1203-1214.
PDB code: 1f9c
10966577 X.Zhou, F.Alber, G.Folkers, G.H.Gonnet, and G.Chelvanayagam (2000).
An analysis of the helix-to-strand transition between peptides with identical sequence.
  Proteins, 41, 248-256.  
10353816 B.Mikami, M.Adachi, T.Kage, E.Sarikaya, T.Nanmori, R.Shinke, and S.Utsumi (1999).
Structure of raw starch-digesting Bacillus cereus beta-amylase complexed with maltose.
  Biochemistry, 38, 7050-7061.
PDB codes: 1b90 1b9z
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
  10508102 K.Ohdan, T.Kuriki, H.Kaneko, J.Shimada, T.Takada, Z.Fujimoto, H.Mizuno, and S.Okada (1999).
Characteristics of two forms of alpha-amylases and structural implication.
  Appl Environ Microbiol, 65, 4652-4658.  
  10548053 N.Nagano, E.G.Hutchinson, and J.M.Thornton (1999).
Barrel structures in proteins: automatic identification and classification including a sequence analysis of TIM barrels.
  Protein Sci, 8, 2072-2084.  
  10049841 Y.Terada, K.Fujii, T.Takaha, and S.Okada (1999).
Thermus aquaticus ATCC 33923 amylomaltase gene cloning and expression and enzyme characterization: production of cycloamylose.
  Appl Environ Microbiol, 65, 910-915.  
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
9636047 K.Binderup, and J.Preiss (1998).
Glutamate-459 is important for Escherichia coli branching enzyme activity.
  Biochemistry, 37, 9033-9037.  
9853672 K.Funane, N.Libessart, D.Stewart, T.Michishita, and J.Preiss (1998).
Analysis of essential histidine residues of maize branching enzymes by chemical modification and site-directed mutagenesis.
  J Protein Chem, 17, 579-590.  
9761914 M.J.Cho, S.S.Cha, J.H.Park, H.J.Cha, H.S.Lee, K.H.Park, and B.H.Oh (1998).
Preliminary X-ray crystallographic analysis of a novel maltogenic amylase from Bacillus stearothermophilus ET1.
  Acta Crystallogr D Biol Crystallogr, 54, 416-418.  
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
  9739087 Y.Modis, S.A.Filppula, D.K.Novikov, B.Norledge, J.K.Hiltunen, and R.K.Wierenga (1998).
The crystal structure of dienoyl-CoA isomerase at 1.5 A resolution reveals the importance of aspartate and glutamate sidechains for catalysis.
  Structure, 6, 957-970.
PDB code: 1dci
9188741 A.V.Efimov (1997).
Structural trees for protein superfamilies.
  Proteins, 28, 241-260.  
9013553 B.X.Yan, and Y.Q.Sun (1997).
Glycine residues provide flexibility for enzyme active sites.
  J Biol Chem, 272, 3190-3194.  
  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.  
  9195884 K.Sorimachi, M.F.Le Gal-Coëffet, G.Williamson, D.B.Archer, and M.P.Williamson (1997).
Solution structure of the granular starch binding domain of Aspergillus niger glucoamylase bound to beta-cyclodextrin.
  Structure, 5, 647-661.
PDB codes: 1ac0 1acz
18576090 M.E.Himmel, P.A.Karplus, J.Sakon, W.S.Adney, J.O.Baker, and S.R.Thomas (1997).
Polysaccharide hydrolase folds diversity of structure and convergence of function.
  Appl Biochem Biotechnol, 63, 315-325.  
9200704 M.P.Williamson, M.F.Le Gal-Coëffet, K.Sorimachi, C.S.Furniss, D.B.Archer, and G.Williamson (1997).
Function of conserved tryptophans in the Aspergillus niger glucoamylase 1 starch binding domain.
  Biochemistry, 36, 7535-7539.  
9360973 T.Kuriki, D.C.Stewart, and J.Preiss (1997).
Construction of chimeric enzymes out of maize endosperm branching enzymes I and II: activity and properties.
  J Biol Chem, 272, 28999-29004.  
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
8955113 D.Penninga, B.A.van der Veen, R.M.Knegtel, S.A.van Hijum, H.J.Rozeboom, K.H.Kalk, B.W.Dijkstra, and L.Dijkhuizen (1996).
The raw starch binding domain of cyclodextrin glycosyltransferase from Bacillus circulans strain 251.
  J Biol Chem, 271, 32777-32784.
PDB code: 1tcm
8605217 K.Maruta, K.Hattori, T.Nakada, M.Kubota, T.Sugimoto, and M.Kurimoto (1996).
Cloning and sequencing of trehalose biosynthesis genes from Arthrobacter sp. Q36.
  Biochim Biophys Acta, 1289, 10-13.  
8836102 N.S.Blom, S.Tétreault, R.Coulombe, and J.Sygusch (1996).
Novel active site in Escherichia coli fructose 1,6-bisphosphate aldolase.
  Nat Struct Biol, 3, 856-862.
PDB code: 1dos
8608145 S.Natarajan, and M.R.Sierks (1996).
Functional and structural roles of the highly conserved Trp120 loop region of glucoamylase from Aspergillus awamori.
  Biochemistry, 35, 3050-3058.  
8804578 T.Kuriki, H.Guan, M.Sivak, and J.Preiss (1996).
Analysis of the active center of branching enzyme II from maize endosperm.
  J Protein Chem, 15, 305-313.  
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.  
18623437 B.K.Dalmia, K.Schütte, and Z.L.Nikolov (1995).
Domain E of Bacillus macerans cyclodextrin glucanotransferase: An independent starch-binding domain.
  Biotechnol Bioeng, 47, 575-584.  
  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.  
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
8592705 T.Sandalova, and Y.Lindqvist (1995).
Three-dimensional model of the alpha-subunit of bacterial luciferase.
  Proteins, 23, 241-255.  
8125253 A.P.Kelly, B.Diderichsen, S.Jorgensen, and D.J.McConnell (1994).
Molecular genetic analysis of the pullulanase B gene of Bacillus acidopullulyticus.
  FEMS Microbiol Lett, 115, 97.  
8018865 B.Svensson (1994).
Protein engineering in the alpha-amylase family: catalytic mechanism, substrate specificity, and stability.
  Plant Mol Biol, 25, 141-157.  
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.  
8033904 L.M.Firsov, K.N.Neustroev, A.E.Aleshin, C.M.Metzler, D.E.Metzler, R.D.Scott, B.Stoffer, T.Christensen, and B.Svensson (1994).
NMR spectroscopy of exchangeable protons of glucoamylase and of complexes with inhibitors in the 9-15-ppm range.
  Eur J Biochem, 223, 293-302.  
  8117096 M.V.Ramesh, S.M.Podkovyrov, S.E.Lowe, and J.G.Zeikus (1994).
Cloning and sequencing of the Thermoanaerobacterium saccharolyticum B6A-RI apu gene and purification and characterization of the amylopullulanase from Escherichia coli.
  Appl Environ Microbiol, 60, 94.  
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.  
8141995 S.Janecek, and S.Baláz (1993).
Evolution of parallel beta/alpha-barrel enzyme family lightened by structural data on starch-processing enzymes.
  J Protein Chem, 12, 509-514.  
1499029 B.Svensson, and M.R.Sierks (1992).
Roles of the aromatic side chains in the binding of substrates, inhibitors, and cyclomalto-oligosaccharides to the glucoamylase from Aspergillus niger probed by perturbation difference spectroscopy, chemical modification, and mutagenesis.
  Carbohydr Res, 227, 29-44.  
  1476442 S.Fujiwara, H.Kakihara, K.B.Woo, A.Lejeune, M.Kanemoto, K.Sakaguchi, and T.Imanaka (1992).
Cyclization characteristics of cyclodextrin glucanotransferase are conferred by the NH2-terminal region of the enzyme.
  Appl Environ Microbiol, 58, 4016-4025.  
  1429471 S.Fujiwara, H.Kakihara, K.Sakaguchi, and T.Imanaka (1992).
Analysis of mutations in cyclodextrin glucanotransferase from Bacillus stearothermophilus which affect cyclization characteristics and thermostability.
  J Bacteriol, 174, 7478-7481.  
  1618293 S.Janecek, and S.Baláz (1992).
alpha-Amylases and approaches leading to their enhanced stability.
  FEBS Lett, 304, 1-3.  
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 code is shown on the right.