1A3W | pdb_00001a3w

PYRUVATE KINASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH FBP, PG, MN2+ AND K+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.323 (Depositor) 
  • R-Value Work: 
    0.218 (Depositor) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1A3W

This is version 1.5 of the entry. See complete history

Literature

The allosteric regulation of pyruvate kinase by fructose-1,6-bisphosphate.

Jurica, M.S.Mesecar, A.Heath, P.J.Shi, W.Nowak, T.Stoddard, B.L.

(1998) Structure 6: 195-210

  • DOI: https://doi.org/10.1016/s0969-2126(98)00021-5
  • Primary Citation Related Structures: 
    1A3W, 1A3X

  • PubMed Abstract: 

    Yeast pyruvate kinase (PK) catalyzes the final step in glycolysis. The enzyme therefore represents an important control point and is allosterically activated by fructose-1,6-bisphosphate (FBP). In mammals the enzyme is found as four different isozymes with different regulatory properties: two of these isozymes are produced by alternate splicing. The allosteric regulation of PK is directly related to proliferation of certain cell types, as demonstrated by the expression of an allosterically regulated isozyme in tumor cells. A model for the allosteric transition from the inactive (T) state to the active (R) state has been proposed previously, but until now the FBP-binding site had not been identified. We report here the structures of PK from yeast complexed with a substrate analog and catalytic metal ions in the presence and absence of bound FBP. The allosteric site is located 40 A from the active site and is entirely located in the enzyme regulatory (C) domain. A phosphate-binding site for the allosteric activator is created by residues encoded by a region of the gene corresponding to the alternately spliced exon of mammalian isozymes. FBP activation appears to induce several conformational changes among active-site sidechains through a mechanism that is most likely to involve significant domain motions, as previously hypothesized. The structure and location of the allosteric activator site agrees with the pattern of alternate genetic splicing of the PK gene in multicellular eukaryotes that distinguishes between a non-regulated isozyme and the regulated fetal isozymes. The conformational differences observed between the active sites of inactive and fully active PK enzymes is in agreement with the recently determined thermodynamic mechanism of allosteric activation through a 'metal relay' that increases the affinity of the enzyme for its natural phosphoenolpyruvate substrate.


  • Organizational Affiliation
    • Molecular and Cellular Biology, Program of the University of Washington, Fred Hutchinson Cancer Research Center, Seattle 98104, USA.

Macromolecule Content 

  • Total Structure Weight: 110.41 kDa 
  • Atom Count: 7,581 
  • Modeled Residue Count: 981 
  • Deposited Residue Count: 1,000 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PYRUVATE KINASE
A, B
500Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.1.40
UniProt
Find proteins for P00549 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00549 
Go to UniProtKB:  P00549
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00549
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FBP

Query on FBP



Download:Ideal Coordinates CCD File
D [auth A],
H [auth B]
1,6-di-O-phosphono-beta-D-fructofuranose
C6 H14 O12 P2
RNBGYGVWRKECFJ-ARQDHWQXSA-N
PGA

Query on PGA



Download:Ideal Coordinates CCD File
C [auth A],
G [auth B]
2-PHOSPHOGLYCOLIC ACID
C2 H5 O6 P
ASCFNMCAHFUBCO-UHFFFAOYSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.323 (Depositor) 
  • R-Value Work:  0.218 (Depositor) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.4α = 90
b = 102.7β = 112.3
c = 110.9γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-05-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.4: 2023-08-02
    Changes: Database references, Refinement description, Structure summary
  • Version 1.5: 2024-05-22
    Changes: Data collection