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PDBsum entry 1h3g

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protein metals Protein-protein interface(s) links
Hydrolase PDB id
1h3g
Jmol
Contents
Protein chains
598 a.a. *
Metals
_CA ×4
Waters ×693
* Residue conservation analysis
PDB id:
1h3g
Name: Hydrolase
Title: Cyclomaltodextrinase from flavobacterium sp. No. 92: from DNA sequence to protein structure
Structure: Cyclomaltodextrinase. Chain: a, b. Synonym: cdase. Engineered: yes
Source: Flavobacterium sp.. Flavobacterium. Organism_taxid: 239. Strain: no 92. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
2.1Å     R-factor:   0.189     R-free:   0.223
Authors: H.B.Fritzsche,T.Schwede,S.Jelakovic,G.E.Schulz
Key ref:
H.B.Fritzsche et al. (2003). Covalent and three-dimensional structure of the cyclodextrinase from Flavobacterium sp. no. 92. Eur J Biochem, 270, 2332-2341. PubMed id: 12752453 DOI: 10.1046/j.1432-1033.2003.03603.x
Date:
03-Sep-02     Release date:   14-Aug-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8KKG0  (Q8KKG0_9FLAO) -  Cyclomaltodextrinase
Seq:
Struc:
 
Seq:
Struc:
619 a.a.
598 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.54  - Cyclomaltodextrinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Cyclomaltodextrin + H2O = linear maltodextrin
Cyclomaltodextrin
+ H(2)O
= linear maltodextrin
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
    Added reference    
 
 
DOI no: 10.1046/j.1432-1033.2003.03603.x Eur J Biochem 270:2332-2341 (2003)
PubMed id: 12752453  
 
 
Covalent and three-dimensional structure of the cyclodextrinase from Flavobacterium sp. no. 92.
H.B.Fritzsche, T.Schwede, G.E.Schulz.
 
  ABSTRACT  
 
Starting with oligopeptide sequences and using PCR, the gene of the cyclodextrinase from Flavobacterium sp. no. 92 was derived from the genomic DNA. The gene was sequenced and expressed in Escherichia coli; the gene product was purified and crystallized. An X-ray diffraction analysis using seleno-methionines with multiwavelength anomalous diffraction techniques yielded the refined 3D structure at 2.1 A resolution. The enzyme hydrolyzes alpha(1,4)-glycosidic bonds of cyclodextrins and linear malto-oligosaccharides. It belongs to the glycosylhydrolase family no. 13 and has a chain fold similar to that of alpha-amylases, cyclodextrin glycosyltransferases, and other cyclodextrinases. In contrast with most family members but in agreement with other cyclodextrinases, the enzyme contains an additional characteristic N-terminal domain of about 100 residues. This domain participates in the formation of a putative D2-symmetric tetramer but not in cyclodextrin binding at the active center as observed with the other cyclodextrinases. Moreover, the domain is located at a position quite different from that of the other cyclodextrinases. Whether oligomerization facilitates the cyclodextrin deformation required for hydrolysis is discussed.
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. D[2]-symmetric tetramer structure of CDase in the crystal together with the symmetry axes.(A) Front view placing the crystallographic twofold axis horizontally in the paper plane. The crystallographic axis runs through the large interface and the vertical noncrystallographic axis runs through the small interface between the N-terminal domains. One subunit is given in the colors and in an orientation similar to Fig. 2 Go-. A -CD (orange) derived from a superposition with the complex between -CD and the homologous enzyme TVA-II [47] marks the active center. (B) View from the left side of (A), which is along the crystallographic twofold axis, showing a smooth silhouette.
Figure 8.
Fig. 8. Active-center region in a superposition of CDase (blue with light green domain B) with the TVA-II dimer (grey with dark green domain B and pink N-terminal domain). The N-terminal domain of the other subunit of the TVA-II dimer is shown in red including Tyr45'. The bound -CD molecule is from a complex with TVA-II [47]. Active-center residues of CDase are given as ball-and-stick models.
 
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: Eur J Biochem (2003, 270, 2332-2341) copyright 2003.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21063757 M.C.Chi, T.J.Wu, T.T.Chuang, H.L.Chen, H.F.Lo, and L.L.Lin (2010).
Biophysical characterization of a recombinant α-amylase from thermophilic Bacillus sp. strain TS-23.
  Protein J, 29, 572-582.  
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
17238236 M.Ferrer, A.Beloqui, O.V.Golyshina, F.J.Plou, A.Neef, T.N.Chernikova, L.Fernández-Arrojo, I.Ghazi, A.Ballesteros, K.Elborough, K.N.Timmis, and P.N.Golyshin (2007).
Biochemical and structural features of a novel cyclodextrinase from cow rumen metagenome.
  Biotechnol J, 2, 207-213.  
16302977 A.Abe, H.Yoshida, T.Tonozuka, Y.Sakano, and S.Kamitori (2005).
Complexes of Thermoactinomyces vulgaris R-47 alpha-amylase 1 and pullulan model oligossacharides provide new insight into the mechanism for recognizing substrates with alpha-(1,6) glycosidic linkages.
  FEBS J, 272, 6145-6153.
PDB codes: 2d0f 2d0g 2d0h
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
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.