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PDBsum entry 1pam

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protein metals Protein-protein interface(s) links
Glycosyltransferase PDB id
1pam
Jmol
Contents
Protein chains
686 a.a. *
Metals
_CA ×4
Waters ×805
* Residue conservation analysis
PDB id:
1pam
Name: Glycosyltransferase
Title: Cyclodextrin glucanotransferase
Structure: Cyclodextrin glucanotransferase. Chain: a, b. Engineered: yes
Source: Bacillus sp.. Organism_taxid: 1410. Strain: 1011. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: alkalophilic bacillus sp. 1011
Resolution:
1.80Å     R-factor:   0.161     R-free:   0.211
Authors: K.Harata,K.Haga,A.Nakamura,M.Aoyagi,K.Yamane
Key ref:
K.Harata et al. (1996). X-ray structure of cyclodextrin glucanotransferase from alkalophilic Bacillus sp. 1011. Comparison of two independent molecules at 1.8 A resolution. Acta Crystallogr D Biol Crystallogr, 52, 1136-1145. PubMed id: 15299574 DOI: 10.1107/S0907444996008438
Date:
08-Jul-96     Release date:   11-Jan-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P05618  (CDGT_BACS0) -  Cyclomaltodextrin glucanotransferase
Seq:
Struc:
 
Seq:
Struc:
713 a.a.
686 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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: 10.1107/S0907444996008438 Acta Crystallogr D Biol Crystallogr 52:1136-1145 (1996)
PubMed id: 15299574  
 
 
X-ray structure of cyclodextrin glucanotransferase from alkalophilic Bacillus sp. 1011. Comparison of two independent molecules at 1.8 A resolution.
K.Harata, K.Haga, A.Nakamura, M.Aoyagi, K.Yamane.
 
  ABSTRACT  
 
Cyclodextrin glucanotransferase (CGTase) is an enzyme which produces cyclodextrins by the degradation of starch. The enzyme from alkalophilic Bacillus sp. 1011, consisting of 686 amino acid residues, was crystallized from the solution containing 20% PEG 3000 and 20% 2-propanol at pH 5.6 adjusted with citrate buffer. The space group was P1 and the unit cell contained two molecules (V(m) = 2.41 A(3) Da(-1)). The structure was solved by the molecular replacement method and refined to a conventional R value of 0.161 (R(free) = 0.211) for the reflections in the resolution range 1.8-10 A by energy minimization combined with simulated annealing. The molecule consists of five domains, designated A-E, and its backbone structure is similar to the structure of other bacterial CGTases. The molecule has two calcium binding sites where calcium ions are coordinated by seven ligands, forming a distorted pentagonal bipyramid. The two independent molecules are related by a pseudotwofold symmetry and are superimposed with an r.m.s. deviation value of 0.32 A for equivalent C(alpha) atoms. Comparison of these molecules indicated the relatively large mobility of domains C and E with respect to domain A. The active site is filled with water molecules forming a hydrogen-bond network with polar side-chain groups. Two water molecules commonly found in the active center of both molecules link to several catalytically important residues by hydrogen bonds and participate in maintaining a similar orientation of side chains in the two independent molecules.
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. The backbone structure of CGTase drwn using the program (Kraulis, 1991). The five domains are shown with colrs, blu (domain A), yellow (domain B), green (domain C), red (domain D) and light blue (domain E). Calcim ions are denoted by pink­colored circles.
Figure 5.
Fig. 5. Suprposition of the backbone structure of CGTase from B. spp. 1011 (wite), B. stearothermophilus (red), B. circulans strain 8 (bue) and B. circulans strain 251 (green).
Figure 13.
Fig. 13. Schematic dra\ving of the geometry of active center. Inter­ atomic distances in molecule (2) are given in parenthe~,es.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1996, 52, 1136-1145) 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.  
17891389 Z.Li, M.Wang, F.Wang, Z.Gu, G.Du, J.Wu, and J.Chen (2007).
gamma-Cyclodextrin: a review on enzymatic production and applications.
  Appl Microbiol Biotechnol, 77, 245-255.  
16012834 K.Hirano, T.Ishihara, S.Ogasawara, H.Maeda, K.Abe, T.Nakajima, and Y.Yamagata (2006).
Molecular cloning and characterization of a novel gamma-CGTase from alkalophilic Bacillus sp.
  Appl Microbiol Biotechnol, 70, 193-201.  
  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.  
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
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
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.  
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.