6NN7

The structure of human liver pyruvate kinase, hLPYK-GGG


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 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: 10.1107/S2053230X19007209
  • Primary Citation of Related Structures:  
    6NN5, 6NN4, 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) ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyruvate kinase PKLRA, B, C, E [auth D], D [auth E], F, G, H542Homo sapiensMutation(s): 1 
Gene Names: PKLRPK1PKL
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC

Download Ideal Coordinates CCD File 
EA [auth D], Q [auth C]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth E] , CA [auth E] , DA [auth E] , GA [auth D] , IA [auth F] , JA [auth F] , K [auth A] , L [auth A] , 
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
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth E] , FA [auth D] , HA [auth F] , I [auth A] , J [auth A] , KA [auth G] , LA [auth G] , M [auth B] , 
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
 Ligand Interaction
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 = 79.365α = 76.44
b = 106.205β = 80.06
c = 151.711γ = 71.37
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR01GM115340
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR01GM127655
National Science Foundation (NSF, United States)United StatesCHE1403293
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesT32GM08545
American Heart AssociationUnited StatesPRE33960374

Revision History  (Full details and data files)

  • 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