8Q1C | pdb_00008q1c

Substrate-free D10N,P146A variant of beta-phosphoglucomutase from Lactococcus lactis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 
    0.270 (Depositor), 0.279 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.220 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8Q1C

This is version 1.0 of the entry. See complete history

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 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.

Macromolecule Content 

  • Total Structure Weight: 48.97 kDa 
  • Atom Count: 3,591 
  • Modeled Residue Count: 438 
  • Deposited Residue Count: 442 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS

Query on TRS



Download:Ideal Coordinates CCD File
F [auth A],
I [auth B]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PO4

Query on PO4



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO

Query on EDO



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

Query on MG



Download:Ideal Coordinates CCD File
C [auth A],
G [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free:  0.270 (Depositor), 0.279 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.220 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.65α = 90
b = 117.251β = 98.637
c = 53.25γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



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