Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A3B1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 785.24 kDa 
• Atom Count: 45056 
• Modelled Residue Count: 6214 
• Deposited Residue Count: 6896 
• Unique protein chains: 1

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

• PDB DOI: 10.2210/pdb5L6S/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-05-31 Released: 2016-09-07 
• Deposition Author(s): Cifuente, J.O., Albesa-Jove, D., Comino, N., Madariaga-Marcos, J., Agirre, J., Lopez-Fernandez, S., Garcia-Alija, M., Guerin, M.E.

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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 

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

• PubMed: 27545622 
• 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 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.

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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: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-1-phosphate adenylyltransferase	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	431	Escherichia coli K-12	Mutation(s): 0  Gene Names: glgC, b3430, JW3393 EC: 2.7.7.27
UniProt
Find proteins for P0A6V1 (Escherichia coli (strain K12)) Explore P0A6V1  Go to UniProtKB:  P0A6V1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FBP	EB [auth L], MA [auth G], UA [auth I], Z [auth C]	1,6-di-O-phosphono-beta-D-fructofuranose C6 H14 O12 P2 RNBGYGVWRKECFJ-ARQDHWQXSA-N
SO4	AA [auth D], AB [auth K], BA [auth D], BB [auth L], CA [auth D], CB [auth L], DA [auth D], DB [auth L], EA [auth E], FA [auth E], FB [auth P], GA [auth E], GB [auth P], HA [auth F], IA [auth F], JA [auth G], KA [auth G], LA [auth G], NA [auth H], OA [auth H], PA [auth H], Q [auth A], QA [auth H], R [auth A], RA [auth I], S [auth A], SA [auth I], T [auth B], TA [auth I], U [auth B], V [auth B], VA [auth J], W [auth C], WA [auth J], X [auth C], XA [auth J], Y [auth C], YA [auth K], ZA [auth K]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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 = 161.16	α = 90
b = 148.9	β = 113.1
c = 177.49	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-05-31 
• Released Date: 2016-09-07 
Deposition Author(s): Cifuente, J.O., Albesa-Jove, D., Comino, N., Madariaga-Marcos, J., Agirre, J., Lopez-Fernandez, S., Garcia-Alija, M., Guerin, M.E.

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