5WQU

Crystal structure of Sweet Potato Beta-Amylase complexed with Maltotetraose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.170 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Structural insights on starch hydrolysis by plant beta-amylase and its evolutionary relationship with bacterial enzymes

Vajravijayan, S.Pletnev, S.Mani, N.Pletneva, N.Nandhagopal, N.Gunasekaran, K.

(2018) Int J Biol Macromol 113: 329-337

  • DOI: https://doi.org/10.1016/j.ijbiomac.2018.02.138
  • Primary Citation of Related Structures:  
    5WQS, 5WQU

  • PubMed Abstract: 

    The conversion of starch to maltose is catalysed in plants by β-amylase. The enzymatic mechanism has been well-characterized for the soybean and barley enzymes, which utilise a glutamic acid-glutamate pair. In the present study, we present a surprise observation of maltotetraose at the active site, the presence of which elucidates the clear role of Thr344 as a conformational "switch" between substrate binding and product release during hydrolysis. This observation is confirmed by the selection of maltotetraose by the crystallized enzyme although that carbohydrate was present in only trace amounts. The conformation of the residues in the substrate-binding site changed upon substrate binding, leading to the movement of threonine, glutamic acid, and the loop conformation, elucidating a missing link in the existing mechanism. By aligning our substrate-free and maltotetraose-bound structures with other existing structures, the sequence of events from substrate binding to hydrolysis can be visualized. Apart from this, the evolutionary relationship among β-amylases of bacterial and amyloplastic origin could be established. The presence of a sugar-binding domain in the bacterial enzyme and its absence in the plant counterpart could be attributed to a carbohydrate-rich environment. Interestingly, cladogram analysis indicates the presence of N-terminal additions in some plant β-amylases. Based on sequence similarity, we postulate that the role of such additions is important for the regulation of enzymatic activity, particularly under stress conditions.


  • Organizational Affiliation

    Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-amylase498Ipomoea batatasMutation(s): 0 
EC: 3.2.1.2
UniProt
Find proteins for P10537 (Ipomoea batatas)
Explore P10537 
Go to UniProtKB:  P10537
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10537
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B
4N/A
Glycosylation Resources
GlyTouCan:  G87171PZ
GlyCosmos:  G87171PZ
GlyGen:  G87171PZ
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.170 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.547α = 90
b = 128.547β = 90
c = 66.207γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKLdata reduction
HKLdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2018-06-06
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary