4UZU

Three-dimensional structure of a variant `Termamyl-like' Geobacillus stearothermophilus alpha-amylase at 1.9 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Three-Dimensional Structure of a Variant `Termamyl-Like' Geobacillus Stearothermophilus Alpha-Amylase at 1.9 A Resolution

Offen, W.A., Viksoe-Nielsen, A., Borchert, T.V., Wilson, K.S., Davies, G.J.

(2015) Acta Crystallogr.,Sect.F 71: 66

  • DOI: 10.1107/S2053230X14026508

  • PubMed Abstract: 

    • The enzyme-catalysed degradation of starch is central to many industrial processes, including sugar manufacture and first-generation biofuels. Classical biotechnological platforms involve steam explosion of starch followed by the action of endo-actin ...

    The enzyme-catalysed degradation of starch is central to many industrial processes, including sugar manufacture and first-generation biofuels. Classical biotechnological platforms involve steam explosion of starch followed by the action of endo-acting glycoside hydrolases termed α-amylases and then exo-acting α-glucosidases (glucoamylases) to yield glucose, which is subsequently processed. A key enzymatic player in this pipeline is the `Termamyl' class of bacterial α-amylases and designed/evolved variants thereof. Here, the three-dimensional structure of one such Termamyl α-amylase variant based upon the parent Geobacillus stearothermophilus α-amylase is presented. The structure has been solved at 1.9 Å resolution, revealing the classical three-domain fold stabilized by Ca2+ and a Ca2+-Na+-Ca2+ triad. As expected, the structure is similar to the G. stearothermophilus α-amylase but with main-chain deviations of up to 3 Å in some regions, reflecting both the mutations and differing crystal-packing environments.

    Organizational Affiliation: 

    York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA-AMYLASE
A
513Geobacillus stearothermophilusMutation(s): 1 
Gene Names: amyS
EC: 3.2.1.1
Find proteins for P06279 (Geobacillus stearothermophilus)
Go to UniProtKB:  P06279
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLY
Query on GLY
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Download CCD File 
A
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA
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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL
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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA
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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.170 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 108.180α = 90.00
b = 108.180β = 90.00
c = 181.490γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
REFMACrefinement
PHASERphasing
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2015-02-04
    Type: Database references