5WS9

Pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate, ATP and allosteric activator AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Allosteric pyruvate kinase-based "logic gate" synergistically senses energy and sugar levels in Mycobacterium tuberculosis.

Zhong, W.Cui, L.Goh, B.C.Cai, Q.Ho, P.Chionh, Y.H.Yuan, M.Sahili, A.E.Fothergill-Gilmore, L.A.Walkinshaw, M.D.Lescar, J.Dedon, P.C.

(2017) Nat Commun 8: 1986-1986

  • DOI: https://doi.org/10.1038/s41467-017-02086-y
  • Primary Citation of Related Structures:  
    5WRP, 5WS8, 5WS9, 5WSA, 5WSB, 5WSC

  • PubMed Abstract: 

    Pyruvate kinase (PYK) is an essential glycolytic enzyme that controls glycolytic flux and is critical for ATP production in all organisms, with tight regulation by multiple metabolites. Yet the allosteric mechanisms governing PYK activity in bacterial pathogens are poorly understood. Here we report biochemical, structural and metabolomic evidence that Mycobacterium tuberculosis (Mtb) PYK uses AMP and glucose-6-phosphate (G6P) as synergistic allosteric activators that function as a molecular "OR logic gate" to tightly regulate energy and glucose metabolism. G6P was found to bind to a previously unknown site adjacent to the canonical site for AMP. Kinetic data and structural network analysis further show that AMP and G6P work synergistically as allosteric activators. Importantly, metabolome profiling in the Mtb surrogate, Mycobacterium bovis BCG, reveals significant changes in AMP and G6P levels during nutrient deprivation, which provides insights into how a PYK OR gate would function during the stress of Mtb infection.


  • Organizational Affiliation

    Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate kinase
A, B, C, D
475Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: pykpykARv1617MTCY01B2.09
EC: 2.7.1.40
UniProt
Find proteins for P9WKE5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WKE5 
Go to UniProtKB:  P9WKE5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WKE5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
BA [auth D],
I [auth A],
O [auth B],
U [auth C]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
AMP
Query on AMP

Download Ideal Coordinates CCD File 
G [auth A],
M [auth B],
T [auth C],
Z [auth D]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
CA [auth D],
J [auth A],
P [auth B],
V [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
OXL
Query on OXL

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B],
S [auth C],
Y [auth D]
OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
K
Query on K

Download Ideal Coordinates CCD File 
AA [auth D],
H [auth A],
N [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A]
K [auth B]
Q [auth C]
R [auth C]
W [auth D]
E [auth A],
K [auth B],
Q [auth C],
R [auth C],
W [auth D],
X [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.19α = 90
b = 127.19β = 90
c = 144.924γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation funding through SMARTSingaporeS916137
Singapore-MIT Alliance for Research and Technology (SMART) FellowshipSingaporeS900184

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2018-01-10
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description