PDBsum entry: 1h3g

Hydrolase

PDB-id: 1h3g

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

598 a.a. *

Metal ions

_CA ×4

Waters ×693

* Residue conservation analysis

Tools

Clefts Calculation

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.

UniProt:

Chains A, B: Q8KKG0 (Q8KKG0_9FLAO)

Seq:

Struc:

Seq:

Struc:

Seq:

619 a.a.

Struc:

598 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Enzyme class:

E.C.3.2.1.54   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Cyclomaltodextrin + H₂O = linear maltodextrin (see diagram below)

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

Quick_links

Procheck

Clefts

Surface

Key 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.