Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 62.94 kDa 
• Atom Count: 4660 
• Modelled Residue Count: 518 
• Deposited Residue Count: 528 
• Unique protein chains: 1

2B5D

Crystal structure of the novel alpha-amylase AmyC from Thermotoga maritima

• PDB DOI: 10.2210/pdb2B5D/pdb

• Classification: HYDROLASE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-09-28 Released: 2006-03-07 
• Deposition Author(s): Dickmanns, A., Ballschmiter, M., Liebl, W., Ficner, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.257 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 

Literature

Structure of the novel alpha-amylase AmyC from Thermotoga maritima.

Dickmanns, A., Ballschmiter, M., Liebl, W., Ficner, R.

(2006) Acta Crystallogr D Biol Crystallogr 62: 262-270

• PubMed: 16510973 
• DOI: 10.1107/S0907444905041363
• Primary Citation of Related Structures:  
  2B5D


• PubMed Abstract: 
  

alpha-Amylases are essential enzymes in alpha-glucan metabolism and catalyse the hydrolysis of long sugar polymers such as amylose and starch. The crystal structure of a previously unidentified amylase (AmyC) from the hyperthermophilic organism Thermotoga maritima was determined at 2.2 Angstroms resolution by means of MAD. AmyC lacks sequence similarity to canonical alpha-amylases, which belong to glycosyl hydrolase families 13, 70 and 77, but exhibits significant similarity to a group of as yet uncharacterized proteins in COG1543 and is related to glycerol hydrolase family 57 (GH-57). AmyC reveals features that are characteristic of alpha-amylases, such as a distorted TIM-barrel structure formed by seven beta-strands and alpha-helices (domain A), and two additional but less well conserved domains. The latter are domain B, which contains three helices inserted in the TIM-barrel after beta-sheet 2, and domain C, a five-helix region at the C-terminus. Interestingly, despite moderate sequence homology, structure comparison revealed significant similarities to a member of GH-57 with known three-dimensional structure, Thermococcus litoralis 4-glucanotransferase, and an even higher similarity to a structure of an enzyme of unknown function from Thermus thermophilus.

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Organizational Affiliation: 

Abteilung Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Georg-August-Universität, Göttingen, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alpha-Amylase	A [auth X]	528	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: tm1438 EC: 3.2.1.1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.257 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.164	α = 90
b = 112.164	β = 90
c = 335.544	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-09-28 
• Released Date: 2006-03-07 
Deposition Author(s): Dickmanns, A., Ballschmiter, M., Liebl, W., Ficner, R.

Revision History  

• Version 1.0: 2006-03-07
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance