3HQP

Crystal structure of Leishmania mexicana pyruvate kinase (LmPYK) in complex with ATP, Oxalate and fructose 2,6 bisphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The allosteric mechanism of pryuvate kinase from Leishmania mexicana: a rock and lock model

Morgan, H.P.McNae, I.W.Nowicki, M.W.Hannaert, V.Michels, P.A.M.Fothergill-Gilmore, L.A.Walkinshaw, M.D.

(2010) J Biol Chem 285: 12892-12898

  • DOI: https://doi.org/10.1074/jbc.M109.079905
  • Primary Citation of Related Structures:  
    3HQN, 3HQO, 3HQP, 3HQQ

  • PubMed Abstract: 

    Allosteric regulation provides a rate management system for enzymes involved in many cellular processes. Ligand-controlled regulation is easily recognizable, but the underlying molecular mechanisms have remained elusive. We have obtained the first complete series of allosteric structures, in all possible ligated states, for the tetrameric enzyme, pyruvate kinase, from Leishmania mexicana. The transition between inactive T-state and active R-state is accompanied by a simple symmetrical 6 degrees rigid body rocking motion of the A- and C-domain cores in each of the four subunits. However, formation of the R-state in this way is only part of the mechanism; eight essential salt bridge locks that form across the C-C interface provide tetramer rigidity with a coupled 7-fold increase in rate. The results presented here illustrate how conformational changes coupled with effector binding correlate with loss of flexibility and increase in thermal stability providing a general mechanism for allosteric control.


  • Organizational Affiliation

    Structural Biochemistry Group, Institute of Structural and Molecular Biology, University of Edinburgh, Michael Swann Building, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate kinase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
499Leishmania mexicanaMutation(s): 0 
Gene Names: PYK
EC: 2.7.1.40
UniProt
Find proteins for Q27686 (Leishmania mexicana)
Explore Q27686 
Go to UniProtKB:  Q27686
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ27686
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
BC [auth I]
CA [auth B]
FB [auth F]
GD [auth M]
JA [auth C]
BC [auth I],
CA [auth B],
FB [auth F],
GD [auth M],
JA [auth C],
KC [auth J],
MB [auth G],
ND [auth N],
QA [auth D],
SC [auth K],
UB [auth H],
V [auth A],
XA [auth E],
YD [auth P],
ZC [auth L]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
FDP
Query on FDP

Download Ideal Coordinates CCD File 
AC [auth I]
BA [auth B]
EB [auth F]
FD [auth M]
IA [auth C]
AC [auth I],
BA [auth B],
EB [auth F],
FD [auth M],
IA [auth C],
JC [auth J],
LB [auth G],
MD [auth N],
PA [auth D],
PD [auth O],
RC [auth K],
TB [auth H],
U [auth A],
WA [auth E],
XD [auth P],
YC [auth L]
2,6-di-O-phosphono-beta-D-fructofuranose
C6 H14 O12 P2
YXWOAJXNVLXPMU-ZXXMMSQZSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CC [auth I]
DC [auth I]
LC [auth J]
NB [auth G]
QD [auth O]
CC [auth I],
DC [auth I],
LC [auth J],
NB [auth G],
QD [auth O],
YA [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
OXL
Query on OXL

Download Ideal Coordinates CCD File 
AA [auth B]
DB [auth F]
ED [auth M]
HA [auth C]
IC [auth J]
AA [auth B],
DB [auth F],
ED [auth M],
HA [auth C],
IC [auth J],
KB [auth G],
LD [auth N],
OA [auth D],
QC [auth K],
SB [auth H],
T [auth A],
VA [auth E],
WD [auth P],
XC [auth L],
ZB [auth I]
OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
K
Query on K

Download Ideal Coordinates CCD File 
AD [auth L]
CB [auth F]
DA [auth B]
DD [auth M]
EC [auth I]
AD [auth L],
CB [auth F],
DA [auth B],
DD [auth M],
EC [auth I],
GA [auth C],
GB [auth F],
HC [auth J],
HD [auth M],
JB [auth G],
KA [auth C],
KD [auth N],
MC [auth J],
NA [auth D],
OB [auth G],
OD [auth N],
PC [auth K],
RA [auth D],
RB [auth H],
RD [auth O],
S [auth A],
SD [auth O],
TC [auth K],
UA [auth E],
VB [auth H],
VD [auth P],
W [auth A],
WC [auth L],
YB [auth I],
Z [auth B],
ZA [auth E],
ZD [auth P]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth F]
BB [auth F]
BD [auth M]
CD [auth M]
EA [auth C]
AB [auth F],
BB [auth F],
BD [auth M],
CD [auth M],
EA [auth C],
FA [auth C],
FC [auth J],
GC [auth J],
HB [auth G],
IB [auth G],
ID [auth N],
JD [auth N],
LA [auth D],
MA [auth D],
NC [auth K],
OC [auth K],
PB [auth H],
Q [auth A],
QB [auth H],
R [auth A],
SA [auth E],
TA [auth E],
TD [auth P],
UC [auth L],
UD [auth P],
VC [auth L],
WB [auth I],
X [auth B],
XB [auth I],
Y [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.486α = 89.73
b = 151.14β = 80.17
c = 160.319γ = 71.64
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary