PDBsum entry: 1ud5

Hydrolase

PDB-id: 1ud5

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Description

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Header records

References

PROCHECK

Protein chain

480 a.a. *

Metal ions

_RB ×6

_NA ×2

Waters ×103

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

1ud5

Name:

Hydrolase

Title:

Crystal structure of amyk38 with rubidium ion

Structure:

Amylase. Chain: a. Fragment: residues 1-480. Synonym: alpha-amylase. Engineered: yes

Source:

Bacillus sp. Ksm-k38. Organism_taxid: 129736. Expressed in: bacillus subtilis. Expression_system_taxid: 1423.

UniProt:

Q93I48 (Q93I48_9BACI)

Seq:

Struc:

Seq:

501 a.a.

Struc:

480 a.a.

Key:

PfamA domain

Secondary structure

Resolution:

2.70Å

R-factor:

0.213

R-free:

0.269

Authors:

T.Nonaka,M.Fujihashi,A.Kita,H.Hagihara,K.Ozaki,S.Ito,K.Miki

Key ref:

T.Nonaka et al. (2003). Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) and its sodium ion binding sites.. J Biol Chem, 278, 24818-24824. [PubMed id: 12719434] [DOI: 10.1074/jbc.M212763200]

Date:

28-Apr-03

Release date:

22-Jul-03

Related entries:

1ud2
the structure which sodium ions, instead of calcium ions,
are used to retain the structure and function of amyk38.
1ud3
the structure of the n289h mutant of amyk38.
1ud4
the structure of the calcium-free alpha-amylase, amyk38,
from the crystal grown in the cacl2 containing solution.
1ud6
this structure was determined from the dataset of the
... plus others (see Header records)

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Procheck

Clefts

Surface

Key reference

DOI no: 10.1074/jbc.M212763200

J Biol Chem 278:24818-24824 (2003)

PubMed id: 12719434

Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) and its sodium ion binding sites.

T.Nonaka, M.Fujihashi, A.Kita, H.Hagihara, K.Ozaki, S.Ito, K.Miki.

ABSTRACT

The crystal structure of a calcium-free alpha-amylase (AmyK38) from Bacillus sp. strain KSM-K38, which resists chelating reagents and chemical oxidants, has been determined by the molecular replacement method and refined to a crystallographic R-factor of 19.9% (R-free of 23.2%) at 2.13-A resolution. The main chain folding of AmyK38 is almost homologous to that of Bacillus licheniformis alpha-amylase. However, neither a highly conserved calcium ion, which is located at the interface between domains A and B, nor any other calcium ions appear to exist in the AmyK38 molecule, although three sodium ions were found, one of which is located at the position corresponding to that of a highly conserved calcium ion of other alpha-amylases. The existence of these sodium ions was crystallographically confirmed by the structures of three metal-exchanged and mutated enzymes. This is the first case in which the structure of the calcium-free alpha-amylase has been determined by crystallography, and it was suggested that these sodium ions, instead of calcium ions, are used to retain the structure and function of AmyK38.

Selected figure(s)

Figure 2.
FIG. 2. Stereo view of the ribbon model of the overall structure of AmyK38. Three domains (A, B, and C) are shown in red, blue, and green, respectively. Three sodium ions, Na I, Na II, and Na III, are shown as yellow spheres. The N and C termini of AmyK38 are in the domains A and C, respectively. Domain A is the most well conserved ( / )[8]-barrel domain in -amylases. Domain C, which is composed of -strands with the socalled Greek key motif, is also conserved in amylolytic enzymes, except in barley -amylase. Na I and Na II are located at the sites corresponding to the Ca^2^+ ions (Ca I and Ca III) in the BLA structure. These figures were drawn by MOLSCRIPT and Raster3D (34, 35).

Figure 3.
FIG. 3. Stereo views of three sodium ions binding sites of AmyK38 and BLA (Protein Data Bank accession code 1bli [PDB] (1)). Pentagonal and quadrilateral bipyramidal cages surrounding metal ions are drawn by solid or broken lines. Sodium and calcium ions are drawn as yellow and sky-blue spheres, respectively. These figures were drawn by MOLSCRIPT, Raster3D, and Conscript (34-36). In a, the [A] weighted omit map (lightblue; contoured at 4.0 ) is shown, and refined models of the Na I site of wild-type AmyK38 are shown in the upper section. The model in the lower section is the calcium-sodium-calcium triad containing the Ca I site of BLA corresponding to the Na I site of AmyK38. In b, the [A] weighted omit map (light blue; contoured at 4.0 ) is shown, and refined models of the Na II site of wild-type AmyK38 are shown in the upper section. The model in the lower section is the Ca III site of BLA corresponding to the Na II site of AmyK38. In c, the [A] weighted omit map (light blue; contoured at 4.0 ) is shown, and the refined model of the Na III site of wild-type AmyK38 is shown in the upper section. The model in the lower section is the site of BLA corresponding to the Na III site of AmyK38. d, the superimposition of the refined structure of N289H AmyK38 on BLA around the corresponding site of the Na III site in wild-type AmyK38. The model of BLA is drawn transparently.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 24818-24824) copyright 2003.

Figures were selected by an automated process.