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PDBsum entry 2cxg

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protein ligands metals links
Glycosyltransferase PDB id
2cxg
Jmol
Contents
Protein chain
686 a.a. *
Ligands
GLC-GLC ×2
GLC-G6D-ACI-GLC
GLC-GLC-GLC-GLC
Metals
_CA ×2
Waters ×92
* Residue conservation analysis
PDB id:
2cxg
Name: Glycosyltransferase
Title: Cyclodextrin glycosyltransferase complexed to the inhibitor acarbose
Structure: Cyclodextrin glycosyltransferase. Chain: a. Synonym: cgtase. Other_details: complexed to an acarbose-derived maltotetraose inhibitor
Source: Bacillus circulans. Organism_taxid: 1397. Strain: 251
Resolution:
2.50Å     R-factor:   0.187     R-free:   0.230
Authors: B.V.Strokopytov,J.C.M.Uitdehaag,R.Ruiterkamp,B.W.Dijkstra
Key ref:
B.Strokopytov et al. (1995). X-ray structure of cyclodextrin glycosyltransferase complexed with acarbose. Implications for the catalytic mechanism of glycosidases. Biochemistry, 34, 2234-2240. PubMed id: 7857935 DOI: 10.1021/bi00007a018
Date:
08-May-98     Release date:   14-Oct-98    
Supersedes: 1cxg
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

 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/bi00007a018 Biochemistry 34:2234-2240 (1995)
PubMed id: 7857935  
 
 
X-ray structure of cyclodextrin glycosyltransferase complexed with acarbose. Implications for the catalytic mechanism of glycosidases.
B.Strokopytov, D.Penninga, H.J.Rozeboom, K.H.Kalk, L.Dijkhuizen, B.W.Dijkstra.
 
  ABSTRACT  
 
Crystals of cyclodextrin glycosyltransferase (CGTase) from Bacillus circulans strain 251 were soaked in buffer solutions containing the pseudotetrasaccharide acarbose, a strong amylase- and CGTase inhibitor. The X-ray structure of the complex was elucidated at 2.5-A resolution with a final crystallographic R value of 15.8% for all data between 8.0 and 2.5 A. Acarbose is bound near the catalytic residues Asp229, Glu257, and Asp328. The carboxylic group of Glu257 is at hydrogen bonding distance from the glycosidic oxygen in the scissile bond between the B and C sugars (residue A is at the nonreducing end of the inhibitor). Asp328 makes hydrogen bonds with the 4-amino-4,6-dideoxyglucose (residue B), and Asp229 is in a close van der Waals contact with the C1 atom of this sugar. From this we conclude that in CGTase Glu257 acts as the proton donor and Asp229 serves as the general base or nucleophile, while Asp328 is involved in substrate binding and may be important for elevating the pKa of Glu257. On the basis of these results it appears that the absence of the C6-hydroxyl group in the B sugar is responsible for the inhibitory properties of acarbose on CGTase. This suggests that the C6-hydroxyl group of this sugar plays an essential role in the catalytic mechanism of CGTase.(ABSTRACT TRUNCATED AT 250 WORDS)
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20159465 N.M.Koropatkin, and T.J.Smith (2010).
SusG: a unique cell-membrane-associated alpha-amylase from a prominent human gut symbiont targets complex starch molecules.
  Structure, 18, 200-215.
PDB codes: 3k8k 3k8l 3k8m
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.  
17630303 S.J.Yang, B.C.Min, Y.W.Kim, S.M.Jang, B.H.Lee, and K.H.Park (2007).
Changes in the catalytic properties of Pyrococcus furiosus thermostable amylase by mutagenesis of the substrate binding sites.
  Appl Environ Microbiol, 73, 5607-5612.  
16926507 T.Yamamoto, K.Terasawa, Y.M.Kim, A.Kimura, Y.Kitamura, M.Kobayashi, and K.Funane (2006).
Identification of catalytic amino acids of cyclodextran glucanotransferase from Bacillus circulans T-3040.
  Biosci Biotechnol Biochem, 70, 1947-1953.  
16517633 Z.Wang, Q.Qi, and P.G.Wang (2006).
Engineering of cyclodextrin glucanotransferase on the cell surface of Saccharomyces cerevisiae for improved cyclodextrin production.
  Appl Environ Microbiol, 72, 1873-1877.  
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
12492486 H.Leemhuis, B.W.Dijkstra, and L.Dijkhuizen (2003).
Thermoanaerobacterium thermosulfurigenes cyclodextrin glycosyltransferase.
  Eur J Biochem, 270, 155-162.  
12930989 J.E.Nielsen, and J.A.McCammon (2003).
Calculating pKa values in enzyme active sites.
  Protein Sci, 12, 1894-1901.  
14617662 M.Kagawa, Z.Fujimoto, M.Momma, K.Takase, and H.Mizuno (2003).
Crystal structure of Bacillus subtilis alpha-amylase in complex with acarbose.
  J Bacteriol, 185, 6981-6984.
PDB code: 1ua7
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
12119024 M.J.Kim, H.S.Lee, J.S.Cho, T.J.Kim, T.W.Moon, S.T.Oh, J.W.Kim, B.H.Oh, and K.H.Park (2002).
Preparation and characterization of alpha-D-glucopyranosyl-alpha-acarviosinyl-D-glucopyranose, a novel inhibitor specific for maltose-producing amylase.
  Biochemistry, 41, 9099-9108.  
12021442 N.Aghajari, G.Feller, C.Gerday, and R.Haser (2002).
Structural basis of alpha-amylase activation by chloride.
  Protein Sci, 11, 1435-1441.
PDB codes: 1jd7 1jd9 1l0p
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.  
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.  
11443082 M.Hemker, A.Stratmann, K.Goeke, W.Schröder, J.Lenz, W.Piepersberg, and H.Pape (2001).
Identification, cloning, expression, and characterization of the extracellular acarbose-modifying glycosyltransferase, AcbD, from Actinoplanes sp. strain SE50.
  J Bacteriol, 183, 4484-4492.  
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
  11082203 I.Przylas, Y.Terada, K.Fujii, T.Takaha, W.Saenger, and N.Sträter (2000).
X-ray structure of acarbose bound to amylomaltase from Thermus aquaticus. Implications for the synthesis of large cyclic glucans.
  Eur J Biochem, 267, 6903-6913.
PDB code: 1esw
10944350 J.Burke, A.Roujeinikova, P.J.Baker, S.Sedelnikova, C.Raasch, W.Liebl, and D.W.Rice (2000).
Crystallization and preliminary X-ray crystallographic studies on maltosyltransferase from Thermotoga maritima.
  Acta Crystallogr D Biol Crystallogr, 56, 1049-1050.  
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
10841756 T.J.Kim, C.S.Park, H.Y.Cho, S.S.Cha, J.S.Kim, S.B.Lee, T.W.Moon, J.W.Kim, B.H.Oh, and K.H.Park (2000).
Role of the glutamate 332 residue in the transglycosylation activity of ThermusMaltogenic amylase.
  Biochemistry, 39, 6773-6780.  
10866815 V.Monchois, M.Vignon, P.C.Escalier, B.Svensson, and R.R.Russell (2000).
Involvement of Gln937 of Streptococcus downei GTF-I glucansucrase in transition-state stabilization.
  Eur J Biochem, 267, 4127-4136.  
  10198028 C.Brunkhorst, C.Andersen, and E.Schneider (1999).
Acarbose, a pseudooligosaccharide, is transported but not metabolized by the maltose-maltodextrin system of Escherichia coli.
  J Bacteriol, 181, 2612-2619.  
10872458 H.D.Ly, and S.G.Withers (1999).
Mutagenesis of glycosidases.
  Annu Rev Biochem, 68, 487-522.  
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
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.  
10220320 M.O'Reilly, K.A.Watson, and L.N.Johnson (1999).
The crystal structure of the Escherichia coli maltodextrin phosphorylase-acarbose complex.
  Biochemistry, 38, 5337-5345.
PDB code: 2ecp
  10103262 T.J.Kim, M.J.Kim, B.C.Kim, J.C.Kim, T.K.Cheong, J.W.Kim, and K.H.Park (1999).
Modes of action of acarbose hydrolysis and transglycosylation catalyzed by a thermostable maltogenic amylase, the gene for which was cloned from a Thermus strain.
  Appl Environ Microbiol, 65, 1644-1651.  
10387084 Z.Dauter, M.Dauter, A.M.Brzozowski, S.Christensen, T.V.Borchert, L.Beier, K.S.Wilson, and G.J.Davies (1999).
X-ray structure of Novamyl, the five-domain "maltogenic" alpha-amylase from Bacillus stearothermophilus: maltose and acarbose complexes at 1.7A resolution.
  Biochemistry, 38, 8385-8392.
PDB codes: 1qho 1qhp
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
10209866 K.H.Park, M.J.Kim, H.S.Lee, N.S.Han, D.Kim, and J.F.Robyt (1998).
Transglycosylation reactions of Bacillus stearothermophilus maltogenic amylase with acarbose and various acceptors.
  Carbohydr Res, 313, 235-246.  
  9541387 N.Aghajari, G.Feller, C.Gerday, and R.Haser (1998).
Crystal structures of the psychrophilic alpha-amylase from Alteromonas haloplanctis in its native form and complexed with an inhibitor.
  Protein Sci, 7, 564-572.
PDB codes: 1aqh 1aqm
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
9860832 R.Mosi, H.Sham, J.C.Uitdehaag, R.Ruiterkamp, B.W.Dijkstra, and S.G.Withers (1998).
Reassessment of acarbose as a transition state analogue inhibitor of cyclodextrin glycosyltransferase.
  Biochemistry, 37, 17192-17198.  
9721603 S.Janecek (1998).
Sequence of archaeal Methanococcus jannaschii alpha-amylase contains features of families 13 and 57 of glycosyl hydrolases: a trace of their common ancestor?
  Folia Microbiol (Praha), 43, 123-128.  
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
9283074 A.M.Brzozowski, and G.J.Davies (1997).
Structure of the Aspergillus oryzae alpha-amylase complexed with the inhibitor acarbose at 2.0 A resolution.
  Biochemistry, 36, 10837-10845.
PDB code: 7taa
  9171379 H.Tsumori, T.Minami, and H.K.Kuramitsu (1997).
Identification of essential amino acids in the Streptococcus mutans glucosyltransferases.
  J Bacteriol, 179, 3391-3396.  
  9385631 M.Qian, S.Spinelli, H.Driguez, and F.Payan (1997).
Structure of a pancreatic alpha-amylase bound to a substrate analogue at 2.03 A resolution.
  Protein Sci, 6, 2285-2296.
PDB code: 1jfh
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.  
9019410 Y.P.Yuan, J.Schultz, M.Mlodzik, and P.Bork (1997).
Secreted fringe-like signaling molecules may be glycosyltransferases.
  Cell, 88, 9.  
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
8798613 G.Feller, O.Bussy, C.Houssier, and C.Gerday (1996).
Structural and functional aspects of chloride binding to Alteromonas haloplanctis alpha-amylase.
  J Biol Chem, 271, 23836-23841.  
8617773 S.A.Short, S.R.Armstrong, S.E.Ealick, and D.J.Porter (1996).
Active site amino acids that participate in the catalytic mechanism of nucleoside 2'-deoxyribosyltransferase.
  J Biol Chem, 271, 4978-4987.  
7556163 F.Casset, A.Imberty, R.Haser, F.Payan, and S.Perez (1995).
Molecular modelling of the interaction between the catalytic site of pig pancreatic alpha-amylase and amylose fragments.
  Eur J Biochem, 232, 284-293.  
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
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.