8Q1F

D10N,P146A variant of beta-phosphoglucomutase from Lactococcus lactis in complex with native beta-glucose 1,6-bisphosphate intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.01 Å
  • R-Value Free: 0.135 
  • R-Value Work: 0.115 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Peri active site catalysis of proline isomerisation is the molecular basis of allomorphy in beta-phosphoglucomutase.

Cruz-Navarrete, F.A.Baxter, N.J.Flinders, A.J.Buzoianu, A.Cliff, M.J.Baker, P.J.Waltho, J.P.

(2024) Commun Biol 7: 909-909

  • DOI: https://doi.org/10.1038/s42003-024-06577-9
  • Primary Citation of Related Structures:  
    8Q1C, 8Q1D, 8Q1E, 8Q1F

  • PubMed Abstract: 

    Metabolic regulation occurs through precise control of enzyme activity. Allomorphy is a post-translational fine control mechanism where the catalytic rate is governed by a conformational switch that shifts the enzyme population between forms with different activities. β-Phosphoglucomutase (βPGM) uses allomorphy in the catalysis of isomerisation of β-glucose 1-phosphate to glucose 6-phosphate via β-glucose 1,6-bisphosphate. Herein, we describe structural and biophysical approaches to reveal its allomorphic regulatory mechanism. Binding of the full allomorphic activator β-glucose 1,6-bisphosphate stimulates enzyme closure, progressing through NAC I and NAC III conformers. Prior to phosphoryl transfer, loops positioned on the cap and core domains are brought into close proximity, modulating the environment of a key proline residue. Hence accelerated isomerisation, likely via a twisted anti/C4-endo transition state, leads to the rapid predominance of active cis-P βPGM. In contrast, binding of the partial allomorphic activator fructose 1,6-bisphosphate arrests βPGM at a NAC I conformation and phosphoryl transfer to both cis-P βPGM and trans-P βPGM occurs slowly. Thus, allomorphy allows a rapid response to changes in food supply while not otherwise impacting substantially on levels of important metabolites.


  • Organizational Affiliation

    School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-phosphoglucomutase
A, B
221Lactococcus lactis subsp. lactis Il1403Mutation(s): 2 
Gene Names: JCM5805K_2499
EC: 5.4.2.6
UniProt
Find proteins for P71447 (Lactococcus lactis subsp. lactis (strain IL1403))
Explore P71447 
Go to UniProtKB:  P71447
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP71447
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B16 (Subject of Investigation/LOI)
Query on B16

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
1,6-di-O-phosphono-beta-D-glucopyranose
C6 H14 O12 P2
RWHOZGRAXYWRNX-DVKNGEFBSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
G [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth A],
N [auth B],
O [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
K [auth B]
L [auth B]
D [auth A],
E [auth A],
F [auth A],
K [auth B],
L [auth B],
M [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.01 Å
  • R-Value Free: 0.135 
  • R-Value Work: 0.115 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.023α = 90
b = 79.663β = 97.614
c = 79.848γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Consejo Nacional de Ciencia y Tecnologia (CONACYT)Mexico472448
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M021637/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/S007965/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-07
    Type: Initial release