6ECH | pdb_00006ech

Pyruvate Kinase Isoform L-type with phosphorylated Ser12 (pS12) in complex with FBP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 
    0.238 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Distinct Hepatic PKA and CDK Signaling Pathways Control Activity-Independent Pyruvate Kinase Phosphorylation and Hepatic Glucose Production.

Gassaway, B.M.Cardone, R.L.Padyana, A.K.Petersen, M.C.Judd, E.T.Hayes, S.Tong, S.Barber, K.W.Apostolidi, M.Abulizi, A.Sheetz, J.B.Aerni, H.R.Gross, S.Kung, C.Samuel, V.T.Shulman, G.I.Kibbey, R.G.Rinehart, J.

(2019) Cell Rep 29: 3394-3404.e9

  • DOI: https://doi.org/10.1016/j.celrep.2019.11.009
  • Primary Citation Related Structures: 
    6ECH, 6ECK

  • PubMed Abstract: 

    Pyruvate kinase is an important enzyme in glycolysis and a key metabolic control point. We recently observed a pyruvate kinase liver isoform (PKL) phosphorylation site at S113 that correlates with insulin resistance in rats on a 3 day high-fat diet (HFD) and suggests additional control points for PKL activity. However, in contrast to the classical model of PKL regulation, neither authentically phosphorylated PKL at S12 nor S113 alone is sufficient to alter enzyme kinetics or structure. Instead, we show that cyclin-dependent kinases (CDKs) are activated by the HFD and responsible for PKL phosphorylation at position S113 in addition to other targets. These CDKs control PKL nuclear retention, alter cytosolic PKL activity, and ultimately influence glucose production. These results change our view of PKL regulation and highlight a previously unrecognized pathway of hepatic CDK activity and metabolic control points that may be important in insulin resistance and type 2 diabetes.


  • Organizational Affiliation
    • Department of Cellular and Molecular Physiology, Yale University, New Haven, CT, USA; Department of Systems Biology Institute, Yale University, New Haven, CT, USA.

Macromolecule Content 

  • Total Structure Weight: 245.83 kDa 
  • Atom Count: 17,686 
  • Modeled Residue Count: 2,108 
  • Deposited Residue Count: 2,200 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pyruvate kinase PKLR
A, B, C, D
550Rattus norvegicusMutation(s): 0 
Gene Names: Pklr
EC: 2.7.1.40
UniProt
Find proteins for P12928 (Rattus norvegicus)
Explore P12928 
Go to UniProtKB:  P12928
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12928
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP

Query on ATP



Download:Ideal Coordinates CCD File
CB [auth D],
J [auth A],
Z [auth B]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
FBP

Query on FBP



Download:Ideal Coordinates CCD File
E [auth A],
LA [auth C],
U [auth B],
YA [auth D]
1,6-di-O-phosphono-beta-D-fructofuranose
C6 H14 O12 P2
RNBGYGVWRKECFJ-ARQDHWQXSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
T [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
BA [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
MB [auth D],
S [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
OXL

Query on OXL



Download:Ideal Coordinates CCD File
AA [auth B],
DB [auth D],
K [auth A],
OA [auth C]
OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
CA [auth B]
DA [auth B]
EA [auth B]
EB [auth D]
FA [auth B]
CA [auth B],
DA [auth B],
EA [auth B],
EB [auth D],
FA [auth B],
FB [auth D],
GA [auth B],
GB [auth D],
HA [auth B],
HB [auth D],
IA [auth B],
IB [auth D],
JA [auth B],
JB [auth D],
KA [auth B],
KB [auth D],
L [auth A],
LB [auth D],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
PA [auth C],
Q [auth A],
QA [auth C],
R [auth A],
RA [auth C],
SA [auth C],
TA [auth C],
UA [auth C],
VA [auth C],
WA [auth C],
XA [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
NB [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
AB [auth D]
BB [auth D]
F [auth A]
G [auth A]
H [auth A]
AB [auth D],
BB [auth D],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
MA [auth C],
NA [auth C],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
ZA [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A, B, C, D
L-PEPTIDE LINKINGC3 H8 N O6 PSER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free:  0.238 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.55α = 90
b = 108.9β = 90
c = 296.84γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.4: 2024-10-09
    Changes: Structure summary