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

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.201 

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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 D Biol Crystallogr 69: 442-450

  • DOI: https://doi.org/10.1107/S0907444912049219
  • Primary Citation of Related Structures:  

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
422Thermotoga neapolitanaMutation(s): 0 
Gene Names: amyB
Find proteins for B5ARZ9 (Thermotoga neapolitana)
Explore B5ARZ9 
Go to UniProtKB:  B5ARZ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5ARZ9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.88α = 90
b = 74.449β = 107.77
c = 108.9γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CCP4model building
DENZOdata reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2015-02-25
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-03-20
    Changes: Source and taxonomy