4AEF

THE CRYSTAL STRUCTURE OF THERMOSTABLE AMYLASE FROM THE PYROCOCCUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A Novel Domain Arrangement in a Monomeric Cyclodextrin-Hydrolyzing Enzyme from the Hyperthermophile Pyrococcus Furiosus.

Park, J.-T.Song, H.-N.Jung, T.-Y.Lee, M.H.Park, S.G.Woo, E.-J.Park, K.-H.

(2013) Biochim Biophys Acta 1834: 380

  • DOI: https://doi.org/10.1016/j.bbapap.2012.08.001
  • Primary Citation of Related Structures:  
    4AEF

  • PubMed Abstract: 

    PFTA (Pyrococcus furiosus thermostable amylase) is a hyperthermophilic amylase isolated from the archaeon Pyrococcus furiosus. This enzyme possesses characteristics of both α-amylase- and cyclodextrin (CD)-hydrolyzing enzymes, allowing it to degrade pullulan, CD and acarbose-activities that are absent in most α-amylases-without the transferring activity that is common in CD-hydrolyzing enzymes. The crystal structure of PFTA revealed a unique monomeric subunit with an extended N-terminal region and an N'-domain folded into its own active site-a significantly altered domain configuration relative to that of the conventional dimeric CD-hydrolyzing amylases in glycoside hydrolase family 13. The active site is formed by the interface of the N'-domain and the catalytic domain and exhibits a broad and wide-open geometry without the concave pocket that is commonly found in the active sites of maltogenic amylases. The mutation of a residue (Gly415 to Glu) located at the domain interface between the N'- and catalytic domains yielded an enzyme that produced a significantly higher purity maltoheptaose (G7) from β-CD, supporting the involvement of this interface in substrate recognition and indicating that this mutant enzyme is a suitable candidate for the production of pure G7. The unique configuration of the active site distinguishes this archaic monomeric enzyme from classical bacterial CD-hydrolyzing amylases and provides a molecular basis for its enzymatic characteristics and for its potential use in industrial applications.


  • Organizational Affiliation

    Department of Food Science and Technology, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 305-764, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NEOPULLULANASE (ALPHA-AMYLASE II)
A, B
645Pyrococcus furiosusMutation(s): 0 
EC: 3.2.1.135
UniProt
Find proteins for Q8TZP8 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8TZP8 
Go to UniProtKB:  Q8TZP8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TZP8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.065α = 90
b = 150.065β = 90
c = 67.856γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2013-01-16
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Other, Refinement description