PDBsum entry 1j0h

Hydrolase

PDB id: 1j0h

Contents

Protein chains

588 a.a. *

Metals

_CA ×2

_CL

Waters ×1601

* Residue conservation analysis

PDB id:

1j0h

Name:

Hydrolase

Title:

Crystal structure of bacillus stearothermophilus neopullulanase

Structure:

Neopullulanase. Chain: a, b. Engineered: yes

Source:

Geobacillus stearothermophilus. Organism_taxid: 1422. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.90Å R-factor: 0.163 R-free: 0.203

Authors:

H.Hondoh,T.Kuriki,Y.Matsuura

Key ref:

H.Hondoh et al. (2003). Three-dimensional structure and substrate binding of Bacillus stearothermophilus neopullulanase. J Mol Biol, 326, 177-188. PubMed id: 12547200 DOI: 10.1016/S0022-2836(02)01402-X

Date:

14-Nov-02 Release date: 28-Jan-03

Protein chains

P38940  (NEPU_GEOSE) -  Neopullulanase from Geobacillus stearothermophilus

Seq: 588 a.a.

Struc: 588 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.2.1.135 - neopullulanase.
• Reaction: Hydrolysis of pullulan to panose (6-alpha-D-glucosylmaltose).

DOI no: 10.1016/S0022-2836(02)01402-X

J Mol Biol 326:177-188 (2003)

PubMed id: 12547200

Three-dimensional structure and substrate binding of Bacillus stearothermophilus neopullulanase.

H.Hondoh, T.Kuriki, Y.Matsuura.

ABSTRACT

Crystal structures of Bacillus stearothermophilus TRS40 neopullulanase and its complexes with panose, maltotetraose and isopanose were determined at resolutions of 1.9, 2.4, 2.8 and 3.2A, respectively. Since the latter two carbohydrates are substrates of this enzyme, a deactivated mutant at the catalytic residue Glu357-->Gln was used for complex crystallization. The structures were refined at accuracies with r.m.s. deviations of bond lengths and bond angles ranging from 0.005A to 0.008A and 1.3 degrees to 1.4 degrees, respectively. The active enzyme forms a dimer in the crystalline state and in solution. The monomer enzyme is composed of four domains, N, A, B and C, and has a (beta/alpha)(8)-barrel in domain A. The active site lies between domain A and domain N from the other monomer. The results show that dimer formation makes the active-site cleft narrower than those of ordinary alpha-amylases, which may contribute to the unique substrate specificity of this enzyme toward both alpha-1,4 and alpha-1,6-glucosidic linkages. This specificity may be influenced by the subsite structure. Only subsites -1 and -2 are commonly occupied by the product and substrates, suggesting that equivocal recognition occurs at the other subsites, which contributes to the wide substrate specificity of this enzyme.

Selected figure(s)

Figure 1.
Figure 1. (a) Monomer structure of neopullulanase with domain names. Three catalytic residues, Asp328, Glu357 and Asp424, are shown as ball-and-stick models and a bound calcium ion is shown as an orange sphere. (b) Dimer structure of neopullulanase. Mol-1 and Mol-2 are colored green and red, respectively. Bound panose molecules at the active cleft are shown to indicate the location of the active site. The Figure was produced with MOLSCRIPT 34 and RENDER from the Raster3D package. 35

Figure 6.
Figure 6. Stereo views of the active cleft of the enzyme with bound substrates: panose (green), maltotetraose (blue) and isopanose (red). Hydrophobic residues are shown in yellow.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 326, 177-188) copyright 2003.

Figures were selected by an automated process.