Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 632.83 kDa 
• Atom Count: 45,923 
• Modelled Residue Count: 5,716 
• Deposited Residue Count: 5,796 
• Unique protein chains: 1

 6QXL

Crystal Structure of Pyruvate Kinase II (PykA) from Pseudomonas aeruginosa in complex with sodium malonate, magnesium and glucose-6-phosphate

• PDB DOI: 10.2210/pdb6QXL/pdb

• Classification: TRANSFERASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-03-07 Released: 2019-09-11 
• Deposition Author(s): Abdelhamid, Y., Brear, P., Welch, M.
• Funding Organization(s): Yousef Jameel Scholarship

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 0.251 
• R-Value Work: 0.227 
• R-Value Observed: 0.228 

Literature

Evolutionary plasticity in the allosteric regulator-binding site of pyruvate kinase isoform PykA fromPseudomonas aeruginosa.

Abdelhamid, Y., Brear, P., Greenhalgh, J., Chee, X., Rahman, T., Welch, M.

(2019) J Biol Chem 294: 15505-15516

• PubMed: 31484721 
• DOI: 10.1074/jbc.RA119.009156
• Primary Citation of Related Structures:  
  6QXL


• PubMed Abstract: 
  

Unlike many other well-characterized bacteria, the opportunistic human pathogen Pseudomonas aeruginosa relies exclusively on the Entner-Doudoroff pathway (EDP) for glycolysis. Pyruvate kinase (PK) is the main "pacemaker" of the EDP, and its activity is also relevant for P. aeruginosa virulence. Two distinct isozymes of bacterial PK have been recognized, PykA and PykF. Here, using growth and expression analyses of relevant PK mutants, we show that PykA is the dominant isoform in P. aeruginosa Enzyme kinetics assays revealed that PykA displays potent K-type allosteric activation by glucose 6-phosphate and by intermediates from the pentose phosphate pathway. Unexpectedly, the X-ray structure of PykA at 2.4 Å resolution revealed that glucose 6-phosphate binds in a pocket that is distinct from the binding site reported for this metabolite in the PK from Mycobacterium tuberculosis (the only other available bacterial PK structure containing bound glucose 6-phosphate). We propose a mechanism by which glucose 6-phosphate binding at the allosteric site communicates with the PykA active site. Taken together, our findings indicate remarkable evolutionary plasticity in the mechanism(s) by which PK senses and responds to allosteric signals.

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Organizational Affiliation: 

Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase	A, B, C, D, E, F, G, H, I, J, K, L	483	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: pykA, pyk, pykA_1, C8257_26620, CAZ10_21690, DZ940_08845, NCTC13719_04679, PAERUG_E15_London_28_01_14_03018, PAMH19_3832, RW109_RW109_05666 EC: 2.7.1.40
UniProt
Find proteins for Q9HW72 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HW72  Go to UniProtKB:  Q9HW72

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G6P (Subject of Investigation/LOI)	AA [auth E], EA [auth F], HA [auth G], KA [auth H], M [auth A], NA [auth I], P [auth B], QA [auth J], T [auth C], TA [auth K], W [auth D], WA [auth L]	6-O-phosphono-alpha-D-glucopyranose C6 H13 O9 P NBSCHQHZLSJFNQ-DVKNGEFBSA-N
MLI (Subject of Investigation/LOI)	DA [auth E], GA [auth F], JA [auth G], MA [auth H], O [auth A], PA [auth I], S [auth B], SA [auth J], V [auth C], VA [auth K], YA [auth L], Z [auth D]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
GOL	CA [auth E], R [auth B], Y [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	BA [auth E], FA [auth F], IA [auth G], LA [auth H], N [auth A], OA [auth I], Q [auth B], RA [auth J], U [auth C], UA [auth K], X [auth D], XA [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 0.251 
• R-Value Work: 0.227 
• R-Value Observed: 0.228 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.477	α = 90
b = 182.477	β = 90
c = 405.044	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Abdelhamid, Y., Brear, P., Welch, M.

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Funding Organization	Location	Grant Number
Yousef Jameel Scholarship	United Kingdom	--

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2019-09-18
  Changes: Data collection, Database references
• Version 1.2: 2019-10-30
  Changes: Data collection, Database references
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary