5L6S

Crystal structure of E. coli ADP-glucose pyrophosphorylase (AGPase) in complex with a positive allosteric regulator beta-fructose-1,6-diphosphate (FBP) - AGPase*FBP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis of Glycogen Biosynthesis Regulation in Bacteria.

Cifuente, J.O.Comino, N.Madariaga-Marcos, J.Lopez-Fernandez, S.Garcia-Alija, M.Agirre, J.Albesa-Jove, D.Guerin, M.E.

(2016) Structure 24: 1613-1622

  • DOI: 10.1016/j.str.2016.06.023
  • Primary Citation of Related Structures:  
    5L6S, 5L6V

  • PubMed Abstract: 
  • ADP-glucose pyrophosphorylase (AGPase) catalyzes the rate-limiting step of bacterial glycogen and plant starch biosynthesis, the most common carbon storage polysaccharides in nature. A major challenge is to understand how AGPase activity is regulated ...

    ADP-glucose pyrophosphorylase (AGPase) catalyzes the rate-limiting step of bacterial glycogen and plant starch biosynthesis, the most common carbon storage polysaccharides in nature. A major challenge is to understand how AGPase activity is regulated by metabolites in the energetic flux within the cell. Here we report crystal structures of the homotetrameric AGPase from Escherichia coli in complex with its physiological positive and negative allosteric regulators, fructose-1,6-bisphosphate (FBP) and AMP, and sucrose in the active site. FBP and AMP bind to partially overlapping sites located in a deep cleft between glycosyltransferase A-like and left-handed β helix domains of neighboring protomers, accounting for the fact that sensitivity to inhibition by AMP is modulated by the concentration of the activator FBP. We propose a model in which the energy reporters regulate EcAGPase catalytic activity by intra-protomer interactions and inter-protomer crosstalk, with a sensory motif and two regulatory loops playing a prominent role.


    Organizational Affiliation

    Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain; Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia, 48940, Spain; Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Bizkaia, Spain; IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain. Electronic address: mrcguerin@cicbiogune.es.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucose-1-phosphate adenylyltransferaseABCDEFGHIJKLMNOP431Escherichia coli K-12Mutation(s): 0 
Gene Names: glgCb3430JW3393
EC: 2.7.7.27
Find proteins for P0A6V1 (Escherichia coli (strain K12))
Explore P0A6V1 
Go to UniProtKB:  P0A6V1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FBP
Query on FBP

Download Ideal Coordinates CCD File 
C, G, I, L
1,6-di-O-phosphono-beta-D-fructofuranose
C6 H14 O12 P2
RNBGYGVWRKECFJ-ARQDHWQXSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, P
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.16α = 90
b = 148.9β = 113.1
c = 177.49γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-09-07
    Type: Initial release
  • Version 1.1: 2016-09-14
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary