5XNE

X-ray Crystal Structure of alpha-acetolactate decarboxylase from Bacillus subtilis strain 168


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


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Literature

Structural and enzymatic characterization of acetolactate decarboxylase from Bacillus subtilis

Ji, F.Li, M.Feng, Y.Wu, S.Wang, T.Pu, Z.Wang, J.Yang, Y.Xue, S.Bao, Y.

(2018) Appl Microbiol Biotechnol 102: 6479-6491

  • DOI: 10.1007/s00253-018-9049-7
  • Primary Citation of Related Structures:  
    5XNE

  • PubMed Abstract: 
  • Acetoin is an important physiological metabolite excreted by microbes. Its functions include avoiding acidification, participating in regulation of the NAD + /NADH ratio, and storing carbon. Acetolactate decarboxylase is a well-characterized anabolic enzyme involved with 3-hydroxy butanone (acetoin) ...

    Acetoin is an important physiological metabolite excreted by microbes. Its functions include avoiding acidification, participating in regulation of the NAD + /NADH ratio, and storing carbon. Acetolactate decarboxylase is a well-characterized anabolic enzyme involved with 3-hydroxy butanone (acetoin). It catalyzes conversion of the (R)- and (S)-enantiomers of acetolactate to generate the single product, (R)-acetoin. In addition to the X-ray crystal structure of acetolactate decarboxylase from Bacillus brevis, although the enzyme is widely present in microorganisms, very few atomic structures of acetolactate decarboxylase are reported. In this paper, we solved and reported a 1.5 Å resolution crystal structure of acetolactate decarboxylase from Bacillus subtilis. Dimeric assembly is observed in the solved structure, which is consistent with the elution profile conducted by molecular filtration. A zinc ion is coordinated by highly conserved histidines (191, 193, and 204) and conserved glutamates (62 and 251). We performed kinetic studies on acetolactate decarboxylase from Bacillus subtilis using circular dichroism, allowing the conversion of acetolactate to chiral acetoin for real-time tracking, yielding a K m value of 21 mM and a k cat value of 2.2 s -1 . Using the two enantiomers of acetolactate as substrates, we further investigated the substrate preference of acetolactate decarboxylase from Bacillus subtilis by means of molecular docking and dynamic simulation in silico. The binding free energy of (S)-acetolactate was found to be ~ 30 kcal/mol greater than that of (R)-acetolactate, indicating a more stable binding for (S)-acetolactate.


    Organizational Affiliation

    School of Food and Environment Science and Engineering, Dalian University of Technology, Panjin, Liaoning, 12422, People's Republic of China. biosci@dlut.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-acetolactate decarboxylaseB [auth A], A [auth B]235Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: alsDBSU36000
EC: 4.1.1.5
UniProt
Find proteins for Q04777 (Bacillus subtilis (strain 168))
Explore Q04777 
Go to UniProtKB:  Q04777
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth B], D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.303α = 90
b = 71.303β = 90
c = 84.134γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-05-22 
  • Released Date: 2018-08-01 
  • Deposition Author(s): Ji, F., Li, M., Feng, Y.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina21506025
Dalian University of TechnologyChinaDUT16RC(4)12

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release