4E2O

Crystal structure of alpha-amylase from Geobacillus thermoleovorans, GTA, complexed with acarbose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.103 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Crystal structure of a compact alpha-amylase from Geobacillus thermoleovorans.

Mok, S.C.Teh, A.H.Saito, J.A.Najimudin, N.Alam, M.

(2013) Enzyme.Microb.Technol. 53: 46-54

  • DOI: 10.1016/j.enzmictec.2013.03.009

  • PubMed Abstract: 
  • A truncated form of an α-amylase, GTA, from thermophilic Geobacillus thermoleovorans CCB_US3_UF5 was biochemically and structurally characterized. The recombinant GTA, which lacked both the N- and C-terminal transmembrane regions, functioned optimall ...

    A truncated form of an α-amylase, GTA, from thermophilic Geobacillus thermoleovorans CCB_US3_UF5 was biochemically and structurally characterized. The recombinant GTA, which lacked both the N- and C-terminal transmembrane regions, functioned optimally at 70°C and pH 6.0. While enzyme activity was not enhanced by the addition of CaCl2, GTA's thermostability was significantly improved in the presence of CaCl2. The structure, in complex with an acarbose-derived pseudo-hexasaccharide, consists of the typical three domains and binds one Ca(2+) ion. This Ca(2+) ion was strongly bound and not chelated by EDTA. A predicted second Ca(2+)-binding site, however, was disordered. With limited subsites, two novel substrate-binding residues, Y147 and Y182, may help increase substrate affinity. No distinct starch-binding domain is present, although two regions rich in aromatic residues have been observed. GTA, with a smaller domain B and several shorter loops compared to other α-amylases, has one of the most compact α-amylase folds that may contribute greatly to its tight Ca(2+) binding and thermostability.


    Organizational Affiliation

    Centre for Chemical Biology, Universiti Sains Malaysia, 11800 Penang, Malaysia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-amylase
A
454Geobacillus thermoleovorans CCB_US3_UF5Mutation(s): 0 
Find proteins for G8N704 (Geobacillus thermoleovorans CCB_US3_UF5)
Go to UniProtKB:  G8N704
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BGC
Query on BGC

Download SDF File 
Download CCD File 
A
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
GLC
Query on GLC

Download SDF File 
Download CCD File 
A
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
ACI
Query on ACI

Download SDF File 
Download CCD File 
A
6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL
C7 H13 N O4
XPHOBMULWMGEBA-VZFHVOOUSA-N
 Ligand Interaction
G6D
Query on G6D

Download SDF File 
Download CCD File 
A
6-DEOXY-ALPHA-D-GLUCOSE
D-Quinovose
C6 H12 O5
SHZGCJCMOBCMKK-DVKNGEFBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.103 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.162 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 122.960α = 90.00
b = 122.960β = 90.00
c = 55.660γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
MOLREPphasing
XSCALEdata scaling
XDSdata scaling
CrystalCleardata collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-13
    Type: Initial release
  • Version 1.1: 2013-03-20
    Type: Structure summary
  • Version 1.2: 2014-07-23
    Type: Database references
  • Version 2.0: 2017-10-25
    Type: Atomic model, Derived calculations, Structure summary