PDBsum entry: 1jae

Glycosidase

PDB-id: 1jae

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

471 a.a. *

Metal ions

_CL

_CA

Waters ×261

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1jae

Name:

Glycosidase

Title:

Structure of tenebrio molitor larval alpha-amylase

Structure:

Alpha-amylase. Chain: a. Fragment: residues 1 - 471. Ec: 3.2.1.1

Source:

Tenebrio molitor. Yellow mealworm. Organism_taxid: 7067

UniProt:

P56634 (AMY_TENMO)

Seq:

Struc:

Seq:

471 a.a.

Struc:

471 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

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

Enzyme class:

E.C.3.2.1.1   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Endohydrolysis of 1,4-alpha-glucosidic linkages in oligosaccharides and polysaccharides.

Resolution:

1.65Å

R-factor:

0.177

R-free:

0.206

Authors:

S.Strobl,K.Maskos,M.Betz,G.Wiegand,R.Huber,F.X.Gomis-Rueth, G.Frank,R.Glockshuber

Key ref:

S.Strobl et al. (1998). Crystal structure of yellow meal worm alpha-amylase at 1.64 A resolution.. J Mol Biol, 278, 617-628. [PubMed id: 9600843] [DOI: 10.1006/jmbi.1998.1667]

Date:

30-Sep-97

Release date:

04-Nov-98

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1006/jmbi.1998.1667

J Mol Biol 278:617-628 (1998)

PubMed id: 9600843

Crystal structure of yellow meal worm alpha-amylase at 1.64 A resolution.

S.Strobl, K.Maskos, M.Betz, G.Wiegand, R.Huber, F.X.Gomis-Rüth, R.Glockshuber.

ABSTRACT

The three-dimensional structure of the alpha-amylase from Tenebrio molitor larvae (TMA) has been determined by molecular replacement techniques using diffraction data of a crystal of space group P212121 (a=51.24 A; b=93.46 A; c=96.95 A). The structure has been refined to a crystallographic R-factor of 17.7% for 58,219 independent reflections in the 7.0 to 1.64 A resolution range, with root-mean-square deviations of 0.008 A for bond lengths and 1.482 degrees for bond angles. The final model comprises all 471 residues of TMA, 261 water molecules, one calcium cation and one chloride anion. The electron density confirms that the N-terminal glutamine residue has undergone a post-transitional modification resulting in a stable 5-oxo-proline residue. The X-ray structure of TMA provides the first three-dimensional model of an insect alpha-amylase.The monomeric enzyme exhibits an elongated shape approximately 75 Ax46 Ax40 A and consists of three distinct domains, in line with models for alpha-amylases from microbial, plant and mammalian origin. However, the structure of TMA reflects in the substrate and inhibitor binding region a remarkable difference from mammalian alpha-amylases: the lack of a highly flexible, glycine-rich loop, which has been proposed to be involved in a "trap-release" mechanism of substrate hydrolysis by mammalian alpha-amylases. The structural differences between alpha-amylases of various origins might explain the specificity of inhibitors directed exclusively against insect alpha-amylases.

Selected figure(s)

Figure 3.
Figure 3. Superposition of the domain A/domain C interface of TMA (green) and barley α-amylase (BAA) (red). Only the trace of the TMA residues 251 to 326 and 359 to 471 and of the BAA residues 251 to 403 are shown. TMA residues 263 to 266, 304 to 315, 366 to 377, 390 to 406 and 460 to 467 were superimposed on BAA residues 262 to 265, 303 to 314, 333 to 344, 359 to 375 and 395 to 402.

Figure 5.
Figure 5. Coordination of the calcium ion in the TMA structure. The calcium ion is represented by a yellow sphere and water molecules by blue spheres. B domain residues are depicted in red and the A domain residue in green. Coordinating interactions are shown as blue lines.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 278, 617-628) copyright 1998.

Figures were selected by an automated process.