1AQF

PYRUVATE KINASE FROM RABBIT MUSCLE WITH MG, K, AND L-PHOSPHOLACTATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Ligand-induced domain movement in pyruvate kinase: structure of the enzyme from rabbit muscle with Mg2+, K+, and L-phospholactate at 2.7 A resolution.

Larsen, T.M.Benning, M.M.Wesenberg, G.E.Rayment, I.Reed, G.H.

(1997) Arch.Biochem.Biophys. 345: 199-206

  • DOI: 10.1006/abbi.1997.0257

  • PubMed Abstract: 
  • The structure of rabbit muscle pyruvate kinase crystallized as a complex with Mg2+, K+, and L-phospholactate (L-P-lactate) has been solved and refined to 2.7 A resolution. The crystals, grown from solutions of polyethylene glycol 8000 at pH 7.5, belo ...

    The structure of rabbit muscle pyruvate kinase crystallized as a complex with Mg2+, K+, and L-phospholactate (L-P-lactate) has been solved and refined to 2.7 A resolution. The crystals, grown from solutions of polyethylene glycol 8000 at pH 7.5, belong to the space group P2(1) and have unit cell parameters a = 144.4 A, b = 112.6 A, c = 171.2 A, and beta = 93.7 degrees. The asymmetric unit contains two tetramers. The crystal structure reveals that the eight subunits within the asymmetric unit adopt several different conformations. These conformations are characterized by differences in the relative positions of protein domains A and B, resulting in different degrees of closure of the active site cleft that occupies the interface between these two domains. The global conformational differences may be described as rotations of the B domain with respect to the (beta/alpha)8-barrel of the A domain. Carbon atoms of the backbone in domain B rotate >20 degrees from the most open to the most closed subunit. The different conformations among subunits within the asymmetric unit are accompanied by 3-3.8 A shifts in the position of Mg2+ and a significant change in the orientation of the phenyl ring of Phe 243. In all of the subunits, Mg2+ coordinates to the protein through the carboxylate side chains of Glu 271 and Asp 295. In the subunit having the most closed conformation, Mg2+ also coordinates to the carboxylate oxygen, the bridging ester oxygen, and a nonbridging phosphoryl oxygen of L-P-lactate. Mg2+ to L-P-lactate coordination is missing in subunits exhibiting a more open conformation. K+ coordinates to four protein ligands and to a phosphoryl oxygen of the L-P-lactate. The position and liganding of K+ are unaffected by the different conformations of the subunits. The side chain of Arg 72, Mg2+, and K+ provides a locus of positive charge for the phosphate moiety of the analog in the closed subunit.


    Organizational Affiliation

    Institute for Enzyme Research, Graduate School, University of Wisconsin-Madison, 53705, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PYRUVATE KINASE
A, B, C, D, E, F, G, H
530Oryctolagus cuniculusMutation(s): 0 
Gene Names: PKM (PKM2)
EC: 2.7.1.40
Find proteins for P11974 (Oryctolagus cuniculus)
Go to Gene View: PKM
Go to UniProtKB:  P11974
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PEQ
Query on PEQ

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
L-PHOSPHOLACTATE
C3 H7 O6 P
CSZRNWHGZPKNKY-REOHCLBHSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 144.400α = 90.00
b = 112.600β = 93.70
c = 171.200γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-09-16
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance