6U9D | pdb_00006u9d

Saccharomyces cerevisiae acetohydroxyacid synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 
    0.252 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structures of fungal and plant acetohydroxyacid synthases.

Lonhienne, T.Low, Y.S.Garcia, M.D.Croll, T.Gao, Y.Wang, Q.Brillault, L.Williams, C.M.Fraser, J.A.McGeary, R.P.West, N.P.Landsberg, M.J.Rao, Z.Schenk, G.Guddat, L.W.

(2020) Nature 586: 317-321

  • DOI: https://doi.org/10.1038/s41586-020-2514-3
  • Primary Citation Related Structures: 
    6U9D, 6U9H, 6VZ8, 6WO1

  • PubMed Abstract: 

    Acetohydroxyacid synthase (AHAS), also known as acetolactate synthase, is a flavin adenine dinucleotide-, thiamine diphosphate- and magnesium-dependent enzyme that catalyses the first step in the biosynthesis of branched-chain amino acids 1 . It is the target for more than 50 commercial herbicides 2 . AHAS requires both catalytic and regulatory subunits for maximal activity and functionality. Here we describe structures of the hexadecameric AHAS complexes of Saccharomyces cerevisiae and dodecameric AHAS complexes of Arabidopsis thaliana. We found that the regulatory subunits of these AHAS complexes form a core to which the catalytic subunit dimers are attached, adopting the shape of a Maltese cross. The structures show how the catalytic and regulatory subunits communicate with each other to provide a pathway for activation and for feedback inhibition by branched-chain amino acids. We also show that the AHAS complex of Mycobacterium tuberculosis adopts a similar structure, thus demonstrating that the overall AHAS architecture is conserved across kingdoms.


  • Organizational Affiliation
    • School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia. t.lonhienne@uq.edu.au.

Macromolecule Content 

  • Total Structure Weight: 1,261.93 kDa 
  • Atom Count: 77,705 
  • Modeled Residue Count: 10,004 
  • Deposited Residue Count: 11,292 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Acetolactate synthase catalytic subunit, mitochondrial
A, B, E, F, I
A, B, E, F, I, J, M, N, Q, R, U, V
644Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ILV2SMR1YMR108WYM9718.07
EC: 2.2.1.6
UniProt
Find proteins for P07342 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P07342 
Go to UniProtKB:  P07342
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07342
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Acetolactate synthase small subunit, mitochondrial
C, D, G, H, K
C, D, G, H, K, L, O, P, S, T, W, X
297Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: Ilv2
UniProt
Find proteins for P25605 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25605 
Go to UniProtKB:  P25605
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25605
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
(Subject of Investigation/LOI)

Query on FAD



Download:Ideal Coordinates CCD File
AA [auth A]
AC [auth U]
BB [auth J]
EA [auth B]
EC [auth V]
AA [auth A],
AC [auth U],
BB [auth J],
EA [auth B],
EC [auth V],
IB [auth M],
LB [auth N],
MA [auth E],
QA [auth F],
SB [auth Q],
UB [auth R],
XA [auth I]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
ATP
(Subject of Investigation/LOI)

Query on ATP



Download:Ideal Coordinates CCD File
DB [auth K]
EB [auth L]
GA [auth C]
GC [auth W]
HC [auth W]
DB [auth K],
EB [auth L],
GA [auth C],
GC [auth W],
HC [auth W],
IA [auth D],
OB [auth O],
PB [auth P],
SA [auth G],
TA [auth H],
WB [auth S],
XB [auth T]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
TPP

Query on TPP



Download:Ideal Coordinates CCD File
CA [auth B]
CC [auth V]
GB [auth M]
JB [auth N]
KA [auth E]
CA [auth B],
CC [auth V],
GB [auth M],
JB [auth N],
KA [auth E],
OA [auth F],
QB [auth Q],
VA [auth I],
Y [auth A],
YB [auth U],
ZA [auth J]
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
60G
(Subject of Investigation/LOI)

Query on 60G



Download:Ideal Coordinates CCD File
BA [auth A]
BC [auth U]
CB [auth J]
FA [auth B]
FC [auth V]
BA [auth A],
BC [auth U],
CB [auth J],
FA [auth B],
FC [auth V],
MB [auth N],
NA [auth E],
NB [auth N],
RA [auth F],
TB [auth Q],
VB [auth R],
YA [auth I]
methyl 2-[(4,6-dimethoxypyrimidin-2-yl)carbamoylsulfamoylmethyl]benzoate
C16 H18 N4 O7 S
XMQFTWRPUQYINF-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
AB [auth J]
DA [auth B]
DC [auth V]
FB [auth L]
HA [auth C]
AB [auth J],
DA [auth B],
DC [auth V],
FB [auth L],
HA [auth C],
HB [auth M],
IC [auth W],
JA [auth D],
KB [auth N],
LA [auth E],
PA [auth F],
RB [auth Q],
UA [auth H],
WA [auth I],
Z [auth A],
ZB [auth U]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
60G BindingDB:  6U9D Ki: 4.4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free:  0.252 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 368.647α = 90
b = 230.307β = 94.57
c = 183.532γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaGrant numbers 1087713 & 1147297

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-15
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references
  • Version 1.2: 2020-10-21
    Changes: Database references, Derived calculations
  • Version 1.3: 2021-01-27
    Changes: Database references
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description