5LHT

ATP Phosphoribosyltransferase from Mycobacterium tuberculosis in complex with the allosteric activator 3-(2-Thienyl)-L-alanine

• PDB DOI:  https://doi.org/10.2210/pdb5LHT/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-07-12 Released: 2017-07-05 
• Deposition Author(s): de Chiara, C., Pisco, J.P., de Carvalho, L.P., Smerdon, S.J., Walker, P.A., Ogrodowicz, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.229 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 

Literature

Uncoupling conformational states from activity in an allosteric enzyme.

Pisco, J.P., Chiara, C., Pacholarz, K.J., Garza-Garcia, A., Ogrodowicz, R.W., Walker, P.A., Barran, P.E., Smerdon, S.J., Carvalho, L.P.S.

(2017) Nat Commun 8: 203-203

• PubMed: 28781362 
• DOI: https://doi.org/10.1038/s41467-017-00224-0
• Primary Citation of Related Structures:  
  5LHT, 5LHU


• PubMed Abstract: 
  

ATP-phosphoribosyltransferase (ATP-PRT) is a hexameric enzyme in conformational equilibrium between an open and seemingly active state and a closed and presumably inhibited form. The structure-function relationship of allosteric regulation in this system is still not fully understood. Here, we develop a screening strategy for modulators of ATP-PRT and identify 3-(2-thienyl)-L-alanine (TIH) as an allosteric activator of this enzyme. Kinetic analysis reveals co-occupancy of the allosteric sites by TIH and L-histidine. Crystallographic and native ion-mobility mass spectrometry data show that the TIH-bound activated form of the enzyme closely resembles the inhibited L-histidine-bound closed conformation, revealing the uncoupling between ATP-PRT open and closed conformations and its functional state. These findings suggest that dynamic processes are responsible for ATP-PRT allosteric regulation and that similar mechanisms might also be found in other enzymes bearing a ferredoxin-like allosteric domain.Active and inactive state ATP-phosphoribosyltransferases (ATP-PRTs) are believed to have different conformations. Here the authors show that in both states, ATP-PRT has a similar structural arrangement, suggesting that dynamic alterations are involved in ATP-PRT regulation by allosteric modulators.

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Related Citations: 

• Mechanism of feedback allosteric inhibition of ATP phosphoribosyltransferase.
  Pedreno, S., Pisco, J.P., Larrouy-Maumus, G., Kelly, G., de Carvalho, L.P.
  (2012) Biochemistry 51: 8027

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Organizational Affiliation: 

Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 32.33 kDa 
• Atom Count: 2,274 
• Modelled Residue Count: 284 
• Deposited Residue Count: 294 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP phosphoribosyltransferase	A	294	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: hisG, Rv2121c, MTCY261.17c EC: 2.4.2.17
UniProt
Find proteins for P9WMN1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WMN1  Go to UniProtKB:  P9WMN1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TIH	B [auth A]	BETA(2-THIENYL)ALANINE C7 H9 N O2 S WTOFYLAWDLQMBZ-LURJTMIESA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TIH	Binding MOAD:  5LHT	Kd: 2.00e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.229 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.512	α = 90
b = 117.512	β = 90
c = 127.356	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-07-05 
Deposition Author(s): de Chiara, C., Pisco, J.P., de Carvalho, L.P., Smerdon, S.J., Walker, P.A., Ogrodowicz, R.

Revision History  

• Version 1.0: 2017-07-05
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Database references