4RJJ | pdb_00004rjj

Acetolactate synthase from Bacillus subtilis bound to ThDP - crystal form II

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 
    0.216 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4RJJ

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 

Literature

Detailed Structure-Function Correlations of Bacillus subtilis Acetolactate Synthase.

Sommer, B., von Moeller, H., Haack, M., Qoura, F., Langner, C., Bourenkov, G., Garbe, D., Loll, B., Bruck, T.

(2015) Chembiochem 16: 110-118

  • DOI: https://doi.org/10.1002/cbic.201402541
  • Primary Citation Related Structures: 
    4RJI, 4RJJ, 4RJK

  • PubMed Abstract: 

    Isobutanol is deemed to be a next-generation biofuel and a renewable platform chemical.1 Non-natural biosynthetic pathways for isobutanol production have been implemented in cell-based and in vitro systems with Bacillus subtilis acetolactate synthase (AlsS) as key biocatalyst.2-6 AlsS catalyzes the condensation of two pyruvate molecules to acetolactate with thiamine diphosphate and Mg(2+) as cofactors. AlsS also catalyzes the conversion of 2-ketoisovalerate into isobutyraldehyde, the immediate precursor of isobutanol. Our phylogenetic analysis suggests that the ALS enzyme family forms a distinct subgroup of ThDP-dependent enzymes. To unravel catalytically relevant structure-function relationships, we solved the AlsS crystal structure at 2.3 Å in the presence of ThDP, Mg(2+) and in a transition state with a 2-lactyl moiety bound to ThDP. We supplemented our structural data by point mutations in the active site to identify catalytically important residues.

    • Organizational Affiliation: 
    • Fachgebiet Industrielle Biokatalyse, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching (Germany).

Macromolecule Content 

  • Total Structure Weight: 507.37 kDa 
  • Atom Count: 36,626 
  • Modeled Residue Count: 4,429 
  • Deposited Residue Count: 4,568 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Acetolactate synthase
A, B, C, D, E
A, B, C, D, E, F, G, H
571Bacillus subtilis PY79Mutation(s): 0 
Gene Names: U712_18080
EC: 4.1.3.18

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TPP

Query on TPP


Download:Ideal Coordinates CCD File
AA [auth D]
AB [auth H]
I [auth A]
IA [auth E]
O [auth B]
AA [auth D],
AB [auth H],
I [auth A],
IA [auth E],
O [auth B],
PA [auth F],
U [auth C],
UA [auth G]
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
PG4

Query on PG4


Download:Ideal Coordinates CCD File
CA [auth D]
CB [auth H]
DA [auth D]
DB [auth H]
EA [auth D]
CA [auth D],
CB [auth H],
DA [auth D],
DB [auth H],
EA [auth D],
EB [auth H],
FA [auth D],
GA [auth D],
K [auth A],
KA [auth E],
L [auth A],
LA [auth E],
M [auth A],
MA [auth E],
N [auth A],
NA [auth E],
OA [auth E],
Q [auth B],
R [auth B],
RA [auth F],
S [auth B],
SA [auth F],
T [auth B],
TA [auth F],
W [auth C],
WA [auth G],
X [auth C],
XA [auth G],
Y [auth C],
YA [auth G],
Z [auth C],
ZA [auth G]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
ACT

Query on ACT


Download:Ideal Coordinates CCD File
HA [auth D]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG

Query on MG


Download:Ideal Coordinates CCD File
BA [auth D]
BB [auth H]
J [auth A]
JA [auth E]
P [auth B]
BA [auth D],
BB [auth H],
J [auth A],
JA [auth E],
P [auth B],
QA [auth F],
V [auth C],
VA [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free:  0.216 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.671α = 90
b = 170.003β = 90
c = 339.812γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2014-11-26
    Changes: Database references
  • Version 1.2: 2015-01-07
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations