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PDBsum entry 1ciu

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protein metals links
Glycosidase PDB id
1ciu
Jmol
Contents
Protein chain
683 a.a. *
Metals
_CA ×2
Waters ×343
* Residue conservation analysis
PDB id:
1ciu
Name: Glycosidase
Title: Thermostable cgtase from thermoanaerobacterium thermosulfurigenes em1 at ph 8.0.
Structure: Cyclodextrin glycosyltransferase. Chain: a. Synonym: cgtase. Ec: 2.4.1.19
Source: Thermoanaerobacterium thermosulfurigenes. Organism_taxid: 33950
Resolution:
2.30Å     R-factor:   0.179     R-free:   0.200
Authors: R.M.A.Knegtel,B.W.Dijkstra
Key ref:
R.M.Knegtel et al. (1996). Crystal structure at 2.3 A resolution and revised nucleotide sequence of the thermostable cyclodextrin glycosyltransferase from Thermonanaerobacterium thermosulfurigenes EM1. J Mol Biol, 256, 611-622. PubMed id: 8604143 DOI: 10.1006/jmbi.1996.0113
Date:
23-Oct-95     Release date:   08-Mar-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P26827  (CDGT_THETU) -  Cyclomaltodextrin glucanotransferase
Seq:
Struc:
 
Seq:
Struc:
710 a.a.
683 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: 10.1006/jmbi.1996.0113 J Mol Biol 256:611-622 (1996)
PubMed id: 8604143  
 
 
Crystal structure at 2.3 A resolution and revised nucleotide sequence of the thermostable cyclodextrin glycosyltransferase from Thermonanaerobacterium thermosulfurigenes EM1.
R.M.Knegtel, R.D.Wind, H.J.Rozeboom, K.H.Kalk, R.M.Buitelaar, L.Dijkhuizen, B.W.Dijkstra.
 
  ABSTRACT  
 
The crystal structure of the cyclodextrin glycosyltransferase (CGTase) from the thermophilic microorganism Thermoanaerobacterium thermosulfurigenes EM1 has been elucidated at 2.3 A resolution. The final model consists of all 683 amino acid residues, two calcium ions and 343 water molecules, and has a crystallographic R-factor of 17.9% (Rfree 24.9%) with excellent stereochemistry. The overall fold of the enzyme is highly similar to that reported for mesophilic CGTases and differences are observed only at surface loop regions. Closer inspection of these loop regions and comparison with other CGTase structures reveals that especially loops 88-95, 335-339 and 534-539 possibly contribute with novel hydrogen bonds and apolar contacts to the stabilization of the enzyme. Other structural features that might confer thermostability to the T. thermosulfurigenes EM1 CGTase are the introduction of five new salt-bridges and three Gly to Ala/Pro substitutions. The abundance of Ser, Thr and Tyr residues near the active site and oligosaccharide binding sites might explain the increased thermostability of CGTase in the presence of starch, by allowing amylose chains to bind non-specifically to the protein. Additional stabilization of the A/E domain interface through apolar contacts involves residues Phe273 and Tyr187. No additional or improved calcium binding is observed in the structure, suggesting that the observed stabilization in the presence of calcium ions is caused by the reduced exchange of calcium from the protein to the solvent, rendering it less susceptible to unfolding. The 50% decrease in cyclization activity of the T. thermosulfurigenes EM1 CGTase compared with that of B. circulans strain 251 appears to be caused by the changes in the conformation and amino acid composition of the 88-95 loop. In the T. thermosulfurigenes EM1 CGTase there is no residue homologous to Tyr89, which was observed to take part in stacking interactions with bound substrate in the case of the B. circulans strain 251 CGTase. The lack of this interaction in the enzyme-substrate complex is expected to destabilize bound substrates prior to cyclization. Apparently, some catalytic functionality of CGTase has been sacrificed for the sake of structural stability by modifying loop regions near the active site.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Stereo views of the corrected portion of the amino acid sequence of the T. thermosulfurigenes EM1 CGTase as present in the refined model with corresponding electron density contoured at 1s in sa-weighted 2Fo - Fc maps. Residues Tyr101, Lys107 to Pro111 and Glu363 to Asp371 are indicated.
Figure 4.
Figure 4. Stereo view of the rearrangement of aromatic residues at the A/E domain interface. The T. thermosulfurigenes EM1 structure is drawn in bold, the B. circulans strain 251 CGTase structure with thin lines. Aromatic residues of the thermostable protein are labelled. The side-chain of Phe237 is rotated such that it contacts Tyr272 and Phe273, while Tyr187 contacts Phe623 and Tyr635 from the E domain.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 256, 611-622) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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.  
  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.  
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
14993702 M.Akita, Y.Hatada, Y.Hidaka, Y.Ohta, M.Takada, Y.Nakagawa, K.Ogawa, T.Nakakuki, S.Ito, and K.Horikoshi (2004).
Crystallization and preliminary X-ray study of gamma-type cyclodextrin glycosyltransferase from Bacillus clarkii.
  Acta Crystallogr D Biol Crystallogr, 60, 586-587.  
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.  
12540849 M.Machius, N.Declerck, R.Huber, and G.Wiegand (2003).
Kinetic stabilization of Bacillus licheniformis alpha-amylase through introduction of hydrophobic residues at the surface.
  J Biol Chem, 278, 11546-11553.
PDB code: 1ob0
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.  
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.  
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.  
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.  
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
11087953 N.Panasik, J.E.Brenchley, and G.K.Farber (2000).
Distributions of structural features contributing to thermostability in mesophilic and thermophilic alpha/beta barrel glycosyl hydrolases.
  Biochim Biophys Acta, 1543, 189-201.  
10409823 L.Lo Leggio, S.Kalogiannis, M.K.Bhat, and R.W.Pickersgill (1999).
High resolution structure and sequence of T. aurantiacus xylanase I: implications for the evolution of thermostability in family 10 xylanases and enzymes with (beta)alpha-barrel architecture.
  Proteins, 36, 295-306.
PDB codes: 1tax 1tix
  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
9849940 J.Sanz-Aparicio, J.A.Hermoso, M.Martínez-Ripoll, B.González, C.López-Camacho, and J.Polaina (1998).
Structural basis of increased resistance to thermal denaturation induced by single amino acid substitution in the sequence of beta-glucosidase A from Bacillus polymyxa.
  Proteins, 33, 567-576.
PDB code: 1e4i
9753433 K.Gruber, G.Klintschar, M.Hayn, A.Schlacher, W.Steiner, and C.Kratky (1998).
Thermophilic xylanase from Thermomyces lanuginosus: high-resolution X-ray structure and modeling studies.
  Biochemistry, 37, 13475-13485.
PDB code: 1yna
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
9265720 B.Lee, and G.Vasmatzis (1997).
Stabilization of protein structures.
  Curr Opin Biotechnol, 8, 423-428.  
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
  9165087 L.Prade, P.Hof, and B.Bieseler (1997).
Dimer interface of glutathione S-transferase from Arabidopsis thaliana: influence of the G-site architecture on the dimer interface and implications for classification.
  Biol Chem, 378, 317-320.  
9166771 M.Hennig, R.Sterner, K.Kirschner, and J.N.Jansonius (1997).
Crystal structure at 2.0 A resolution of phosphoribosyl anthranilate isomerase from the hyperthermophile Thermotoga maritima: possible determinants of protein stability.
  Biochemistry, 36, 6009-6016.
PDB code: 1nsj
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.