PDBsum entry: 1ea9

Hydrolase

PDB-id: 1ea9

Biological unit = asymmetric unit,
as shown
(as defined in PDB file)

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

583 a.a. *

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1ea9

Name:

Hydrolase

Title:

Cyclomaltodextrinase

Structure:

Cyclomaltodextrinase. Chain: c, d. Ec: 3.2.1.54

Source:

Bacillus sp.. Organism_taxid: 1409

Biological unit:

Dimer (from PDB file)

UniProt:

Chains C, D: Q59226 (Q59226_BACSP)

Seq:

Struc:

Seq:

Struc:

Seq:

558 a.a.

Struc:

583 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 19 residue positions (black crosses)

Enzyme class:

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

Reaction:

Cyclomaltodextrin + H₂O = linear maltodextrin (see diagram below)

Resolution:

3.20Å

R-factor:

0.214

Authors:

H.-S.Cho,M.-S.Kim,B.-H.Oh

Key ref:

H.S.Lee et al. (2002). Cyclomaltodextrinase, neopullulanase, and maltogenic amylase are nearly indistinguishable from each other.. J Biol Chem, 277, 21891-21897. [PubMed id: 11923309] [DOI: 10.1074/jbc.M201623200]

Date:

12-Jul-01

Release date:

06-Jun-02

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1074/jbc.M201623200

J Biol Chem 277:21891-21897 (2002)

PubMed id: 11923309

Cyclomaltodextrinase, neopullulanase, and maltogenic amylase are nearly indistinguishable from each other.

H.S.Lee, M.S.Kim, H.S.Cho, J.I.Kim, T.J.Kim, J.H.Choi, C.Park, H.S.Lee, B.H.Oh, K.H.Park.

ABSTRACT

Over 20 enzymes denoted as cyclomaltodextrinase, maltogenic amylase, or neopullulanase that share 40-86% sequence identity with each other are found in public data bases. These enzymes are distinguished from typical alpha-amylases by containing a novel N-terminal domain and exhibiting preferential substrate specificities for cyclomaltodextrins (CDs) over starch. In this research field, a great deal of confusion exists regarding the features distinguishing the three groups of enzymes from one another. Although a different enzyme code has been assigned to each of the three different enzyme names, even a single differentiating enzymatic property has not been documented in the literature. On the other hand, an outstanding question related to this issue concerns the structural basis for the preference of these enzymes for CDs. To clarify the confusion and to address this question, we have determined the structures of two enzymes, one from alkalophilic Bacillus sp. I-5 and named cyclomaltodextrinase and the other from a Thermus species and named maltogenic amylase. The structure of the Bacillus enzyme reveals a dodecameric assembly composed of six copies of the dimer, which is the structural and functional unit of the Thermus enzyme and an enzyme named neopullulanase. The structure of the Thermus enzyme in complex with beta-CD led to the conclusion that Trp47, a well conserved N-terminal domain residue, contributes greatly to the preference for beta-CD. The common dimer formation through the novel N-terminal domain, which contributes to the preference for CDs by lining the active-site cavity, convincingly indicates that the three groups of enzymes are not different enough to preserve the different names and enzyme codes.

Selected figure(s)

Figure 3.
Fig. 3. Clustered active sites of CDase on the dodecameric assembly. a, dodecameric structure of CDase shown along a crystallographic 3-fold axis. The arrows indicate the three active sites close to each other. There are four sets of these active sites on the assembly. b, schematic drawing of the three active sites of CDase facing each other. A product released from one active site would have easy access to the other two active sites during the course of hydrolysis of CDs to maltose.

Figure 4.
Fig. 4. Stereo view of the binding of -CD to the active site of ThMA. Active-site residues that are within 4 Å of the bound -CD are shown. The critical catalytic residue Glu357 is replaced with leucine in this mutant. Asp328 and Asp424 are the catalytic residues invariant throughout -amylase family members. Residues belonging to the N-terminal and ( / )[8]-barrel domains are shown in blue and green, respectively. All of these residues in ThMA are identical to the corresponding residues in CDase, except for Asp110 which is not a conserved residue (see Fig. 5).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 21891-21897) copyright 2002.

Figures were selected by an automated process.