Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 470.22 kDa 
• Atom Count: 29007 
• Modelled Residue Count: 3741 
• Deposited Residue Count: 4336 
• Unique protein chains: 1

6NN7

The structure of human liver pyruvate kinase, hLPYK-GGG

• PDB DOI: 10.2210/pdb6NN7/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-01-14 Released: 2019-06-19 
• Deposition Author(s): McFarlane, J.S., Ronnebaum, T.A., Meneely, K.M., Fenton, A.W., Lamb, A.L.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI), National Science Foundation (NSF, United States), American Heart Association

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.251 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 

Literature

Changes in the allosteric site of human liver pyruvate kinase upon activator binding include the breakage of an intersubunit cation-pi bond.

McFarlane, J.S., Ronnebaum, T.A., Meneely, K.M., Chilton, A., Fenton, A.W., Lamb, A.L.

(2019) Acta Crystallogr F Struct Biol Commun 75: 461-469

• PubMed: 31204694 
• DOI: 10.1107/S2053230X19007209
• Primary Citation of Related Structures:  
  6NN4, 6NN5, 6NN7, 6NN8


• PubMed Abstract: 
  

Human liver pyruvate kinase (hLPYK) converts phosphoenolpyruvate to pyruvate in the final step of glycolysis. hLPYK is allosterically activated by fructose-1,6-bisphosphate (Fru-1,6-BP). The allosteric site, as defined by previous structural studies, is located in domain C between the phosphate-binding loop (residues 444-449) and the allosteric loop (residues 527-533). In this study, the X-ray crystal structures of four hLPYK variants were solved to make structural correlations with existing functional data. The variants are D499N, W527H, Δ529/S531G (called GGG here) and S531E. The results revealed a conformational toggle between the open and closed positions of the allosteric loop. In the absence of Fru-1,6-BP the open position is stabilized, in part, by a cation-π bond between Trp527 and Arg538' (from an adjacent monomer). In the S531E variant glutamate binds in place of the 6'-phosphate of Fru-1,6-BP in the allosteric site, leading to partial allosteric activation. Finally, the structure of the D499N mutant does not provide structural evidence for the previously observed allosteric activation of the D499N variant.

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Organizational Affiliation: 

Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside, Lawrence, KS 66045, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase PKLR	A, B, C, E [auth D], D [auth E], F, G, H	542	Homo sapiens	Mutation(s): 1  Gene Names: PKLR, PK1, PKL EC: 2.7.1.40
UniProt & NIH Common Fund Data Resources
Find proteins for P30613 (Homo sapiens) Explore P30613  Go to UniProtKB:  P30613
PHAROS:  P30613

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	EA [auth D], Q [auth C]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
GOL	BA [auth E], CA [auth E], DA [auth E], GA [auth D], IA [auth F], JA [auth F], K [auth A], L [auth A], MA [auth G], NA [auth H], O [auth B], OA [auth H], P [auth B], Y [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	AA [auth E], FA [auth D], HA [auth F], I [auth A], J [auth A], KA [auth G], LA [auth G], M [auth B], N [auth B], R [auth C], S [auth C], T [auth C], U [auth C], V [auth C], W [auth C], X [auth C], Z [auth E]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.251 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.365	α = 76.44
b = 106.205	β = 80.06
c = 151.711	γ = 71.37

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-01-14 
• Released Date: 2019-06-19 
Deposition Author(s): McFarlane, J.S., Ronnebaum, T.A., Meneely, K.M., Fenton, A.W., Lamb, A.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	R01GM115340
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	R01GM127655
National Science Foundation (NSF, United States)	United States	CHE1403293
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	T32GM08545
American Heart Association	United States	PRE33960374

Revision History  

• Version 1.0: 2019-06-19
  Type: Initial release
  
• Version 1.1: 2019-11-13
  Changes: Database references
• Version 1.2: 2019-11-27
  Changes: Author supporting evidence