5WQS

Crystal structure of Apo Beta-Amylase from Sweet potato


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1016/j.ijbiomac.2018.02.138
  • Structures With Same Primary Citation

  • 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 ...

    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. Electronic address: gunaunom@gmail.com.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-amylaseA498Ipomoea batatasMutation(s): 0 
Gene Names: BMY1AMYB
EC: 3.2.1.2
Find proteins for P10537 (Ipomoea batatas)
Explore P10537 
Go to UniProtKB:  P10537
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IPA
Query on IPA

Download CCD File 
A
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.347α = 90
b = 128.347β = 90
c = 66.701γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2018-06-06
    Changes: Data collection, Database references
  • Version 1.2: 2018-07-11
    Changes: Data collection, Database references, Structure summary