PDBsum entry: 1bli

Hydrolase

PDB-id: 1bli

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

481 a.a. *

Metal ions

_NA

_CA ×3

Waters ×221

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1bli

Name:

Hydrolase

Title:

Bacillus licheniformis alpha-amylase

Structure:

Alpha-amylase. Chain: a. Synonym: glucanotransferase, alpha-1,4-glucan-4- glucanohydrolase. Engineered: yes. Mutation: yes. Other_details: protein produced by novo nordisk a/s, denmark

Source:

Bacillus licheniformis. Organism_taxid: 1402. Cell_line: 293. Atcc: atcc 6598. Collection: atcc 6598. Gene: amyl. Expressed in: bacillus subtilis. Expression_system_taxid: 1423.

UniProt:

P06278 (AMY_BACLI)

Seq:

Struc:

Seq:

512 a.a.

Struc:

481 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 7 residue positions (black crosses)

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:

1.90Å

R-factor:

0.154

R-free:

0.185

Authors:

M.Machius,N.Declerck,R.Huber,G.Wiegand

Key ref:

M.Machius et al. (1998). Activation of Bacillus licheniformis alpha-amylase through a disorder-->order transition of the substrate-binding site mediated by a calcium-sodium-calcium metal triad.. Structure, 6, 281-292. [PubMed id: 9551551] [DOI: 10.1016/S0969-2126(98)00032-X]

Date:

07-Jan-98

Release date:

23-Mar-99

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1016/S0969-2126(98)00032-X

Structure 6:281-292 (1998)

PubMed id: 9551551

Activation of Bacillus licheniformis alpha-amylase through a disorder-->order transition of the substrate-binding site mediated by a calcium-sodium-calcium metal triad.

M.Machius, N.Declerck, R.Huber, G.Wiegand.

ABSTRACT

BACKGROUND: The structural basis as to how metals regulate the functional state of a protein by altering or stabilizing its conformation has been characterized in relatively few cases because the metal-free form of the protein is often partially disordered and unsuitable for crystallographic analysis. This is not the case, however, for Bacillus licheniformis alpha-amylase (BLA) for which the structure of the metal-free form is available. BLA is a hyperthermostable enzyme which is widely used in biotechnology, for example in the breakdown of starch or as a component of detergents. The determination of the structure of BLA in the metal-containing form, together with comparisons to the apo enzyme, will help us to understand the way in which metal ions can regulate enzyme activity. RESULTS: We report here the crystal structure of native, metal-containing BLA. The structure shows that the calcium-binding site which is conserved in all alpha-amylases forms part of an unprecedented linear triadic metal array, with two calcium ions flanking a central sodium ion. A region around the metal triad comprising 21 residues exhibits a conformational change involving a helix unwinding and a disorder-->order transition compared to the structure of metal-free BLA. Another calcium ion, not previously observed in alpha-amylases, is located at the interface between domains A and C. CONCLUSIONS: We present a structural description of a major conformational rearrangement mediated by metal ions. The metal induced disorder-->order transition observed in BLA leads to the formation of the extended substrate-binding site and explains on a structural level the calcium dependency of alpha-amylases. Sequence comparisons indicate that the unique Ca-Na-Ca metal triad and the additional calcium ion located between domains A and C might be found exclusively in bacterial alpha-amylases which show increased thermostability. The information presented here may help in the rational design of mutants with enhanced performance in biotechnological applications.

Selected figure(s)

Figure 6.
Figure 6. Stereo view CPK representation of BLA with the carbohydrate inhibitor V-1532 from the structure of the PPA-V-1532 complex [23] superimposed. The region which is ordered only in metal-containing BLA is shown in red; calcium ions are in cyan and sodium is in yellow. Residues in domain A of BLA which are homologous to sugar-binding residues in domain A of PPA are shown in green and the pseudo-oligosaccharide inhibitor V-1532 from the PPA-V-1532 complex structure is in blue stick form (see text for details).

The above figure is reprinted by permission from Cell Press: Structure (1998, 6, 281-292) copyright 1998.

Figure was selected by an automated process.