4GKL

Crystal structure of a noncanonic maltogenic alpha-amylase AmyB from Thermotoga neapolitana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of a novel alpha-amylase AmyB from Thermotoga neapolitana that produces maltose from the nonreducing end of polysaccharides

Jun, S.Y.Kim, J.S.Choi, K.H.Cha, J.Ha, N.C.

(2013) Acta Crystallogr.,Sect.D 69: 442-450

  • DOI: 10.1107/S0907444912049219

  • PubMed Abstract: 
  • An intracellular α-amylase, AmyB, has been cloned from the hyperthermophilic bacterium Thermotoga neapolitana. AmyB belongs to glycoside hydrolase family 13 and liberates maltose from diverse substrates, including starch, amylose, amylopectin and gly ...

    An intracellular α-amylase, AmyB, has been cloned from the hyperthermophilic bacterium Thermotoga neapolitana. AmyB belongs to glycoside hydrolase family 13 and liberates maltose from diverse substrates, including starch, amylose, amylopectin and glycogen. The final product of AmyB is similar to that of typical maltogenic amylases, but AmyB cleaves maltose units from the nonreducing end, which is a unique property of this α-amylase. In this study, the crystal structure of AmyB from T. neapolitana has been determined at 2.4 Å resolution, revealing that the monomeric AmyB comprises domains A, B and C like other α-amylases, but with structural variations. In the structure, a wider active site and a putative extra sugar-binding site at the top of the active site were found. Subsequent biochemical results suggest that the extra sugar-binding site is suitable for recognizing the nonreducing end of the substrates, explaining the unique activity of this enzyme. These findings provide a structural basis for the ability of an α-amylase that has the common α-amylase structure to show a diverse substrate specificity.


    Organizational Affiliation

    Department of Manufacturing Pharmacy and Research Institute for Drug Development, Pusan National University, Busan 609-735, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-amylase
A, B
422Thermotoga neapolitanaGene Names: amyB
Find proteins for B5ARZ9 (Thermotoga neapolitana)
Go to UniProtKB:  B5ARZ9
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 66.880α = 90.00
b = 74.449β = 107.77
c = 108.900γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CCP4phasing
HKL-2000data collection
PHENIXrefinement
DENZOdata reduction
CCP4model building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2015-02-25
    Type: Database references