5WS9 | pdb_00005ws9

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

• PDB DOI: https://doi.org/10.2210/pdb5WS9/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-12-06 Released: 2017-11-15 
• Deposition Author(s): Zhong, W., Cai, Q., El Sahili, A., Lescar, J., Dedon, P.C.
• Funding Organization(s): National Research Foundation funding through SMART, Singapore-MIT Alliance for Research and Technology (SMART) Fellowship

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.223 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

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

• PubMed: 29215013 
• DOI: https://doi.org/10.1038/s41467-017-02086-y
• Primary Citation 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.

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Organizational Affiliation: 
• Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore.
NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore.
Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
Tychan Private Ltd, 80 Robinson Road, #17-02, Singapore, 068898, Singapore.
Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore. [e-mail].
School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore. [e-mail].
Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore. [e-mail].
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 208.47 kDa 
• Atom Count: 15,920 
• Modeled Residue Count: 1,884 
• Deposited Residue Count: 1,900 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase	A, B, C, D	475	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: pyk, pykA, Rv1617, MTCY01B2.09 EC: 2.7.1.40
UniProt
Find proteins for P9WKE5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WKE5  Go to UniProtKB:  P9WKE5

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	BA [auth D], I [auth A], O [auth B], U [auth C]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
AMP	G [auth A], M [auth B], T [auth C], Z [auth D]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
PO4	CA [auth D], J [auth A], P [auth B], V [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
OXL	F [auth A], L [auth B], S [auth C], Y [auth D]	OXALATE ION C2 O4 MUBZPKHOEPUJKR-UHFFFAOYSA-L
K	AA [auth D], H [auth A], N [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	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 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.19	α = 90
b = 127.19	β = 90
c = 144.924	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-11-15 
Deposition Author(s): Zhong, W., Cai, Q., El Sahili, A., Lescar, J., Dedon, P.C.

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Funding Organization	Location	Grant Number
National Research Foundation funding through SMART	Singapore	S916137
Singapore-MIT Alliance for Research and Technology (SMART) Fellowship	Singapore	S900184

Revision History  

• 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