Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 55.49 kDa 
• Atom Count: 4,078 
• Modelled Residue Count: 467 
• Deposited Residue Count: 487 
• Unique protein chains: 1

 5JIO

Structure of Mycobacterium thermoresistibile trehalose-6-phosphate synthase ternary complex with ADP and Glucose-6-phosphate.

• PDB DOI: 10.2210/pdb5JIO/pdb

• Classification: TRANSFERASE
• Organism(s): Mycolicibacterium thermoresistibile
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-04-22 Released: 2017-05-10 
• Deposition Author(s): Mendes, V., Verma, N., Blaszczyk, M., Blundell, T.L.
• Funding Organization(s): Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 0.179 
• R-Value Work: 0.152 
• R-Value Observed: 0.153 

Literature

Mycobacterial OtsA Structures Unveil Substrate Preference Mechanism and Allosteric Regulation by 2-Oxoglutarate and 2-Phosphoglycerate.

Mendes, V., Acebron-Garcia-de-Eulate, M., Verma, N., Blaszczyk, M., Dias, M.V.B., Blundell, T.L.

(2019) mBio 10

• PubMed: 31772052 
• DOI: 10.1128/mBio.02272-19
• Primary Citation of Related Structures:  
  5JIJ, 5JIO, 5K41, 5K42, 5K44, 5K5C, 5L3K


• PubMed Abstract: 
  

Trehalose is an essential disaccharide for mycobacteria and a key constituent of several cell wall glycolipids with fundamental roles in pathogenesis. Mycobacteria possess two pathways for trehalose biosynthesis. However, only the OtsAB pathway was found to be essential in Mycobacterium tuberculosis , with marked growth and virulence defects of OtsA mutants and strict essentiality of OtsB2. Here, we report the first mycobacterial OtsA structures from Mycobacterium thermoresistibile in both apo and ligand-bound forms. Structural information reveals three key residues in the mechanism of substrate preference that were further confirmed by site-directed mutagenesis. Additionally, we identify 2-oxoglutarate and 2-phosphoglycerate as allosteric regulators of OtsA. The structural analysis in this work strongly contributed to define the mechanisms for feedback inhibition, show different conformational states of the enzyme, and map a new allosteric site. IMPORTANCE Mycobacterial infections are a significant source of mortality worldwide, causing millions of deaths annually. Trehalose is a multipurpose disaccharide that plays a fundamental structural role in these organisms as a component of mycolic acids, a molecular hallmark of the cell envelope of mycobacteria. Here, we describe the first mycobacterial OtsA structures. We show mechanisms of substrate preference and show that OtsA is regulated allosterically by 2-oxoglutarate and 2-phosphoglycerate at an interfacial site. These results identify a new allosteric site and provide insight on the regulation of trehalose synthesis through the OtsAB pathway in mycobacteria.

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Organizational Affiliation: 

Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha,alpha-trehalose-phosphate synthase	A	487	Mycolicibacterium thermoresistibile	Mutation(s): 0  Gene Names: RMCT_1906 EC: 2.4.1.347
UniProt
Find proteins for G7CGT2 (Mycolicibacterium thermoresistibile (strain ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316)) Explore G7CGT2  Go to UniProtKB:  G7CGT2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
G6P	C [auth A]	6-O-phosphono-alpha-D-glucopyranose C6 H13 O9 P NBSCHQHZLSJFNQ-DVKNGEFBSA-N
EDO	D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 0.179 
• R-Value Work: 0.152 
• R-Value Observed: 0.153 
• Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.357	α = 90
b = 105.357	β = 90
c = 158.866	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-05-10 
Deposition Author(s): Mendes, V., Verma, N., Blaszczyk, M., Blundell, T.L.

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Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	--

Revision History  

• Version 1.0: 2017-05-10
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence
• Version 2.0: 2020-01-22
  Changes: Atomic model, Database references
• Version 2.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary