5L3K | pdb_00005l3k

Structure of Mycobacterium thermoresistibile trehalose-6-phosphate synthase in a ternary complex with ADP and fructose-6-phosphate

• PDB DOI: https://doi.org/10.2210/pdb5L3K/pdb

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


• Deposited: 2016-05-23 Released: 2017-06-07 
• 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: 2.31 Å
• R-Value Free: 
  0.213 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1128/mBio.02272-19
• Primary Citation 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].
Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil.
Department of Chemistry, University of Warwick, Coventry, United Kingdom.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 442.92 kDa 
• Atom Count: 29,978 
• Modeled Residue Count: 3,597 
• Deposited Residue Count: 3,896 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha,alpha-trehalose-phosphate synthase	A, B, C, D, E, F, G, H	487	Mycolicibacterium thermoresistibile	Mutation(s): 0  Gene Names: RMCT_1906 EC: 2.4.1.347
UniProt
Find proteins for A0A117IMA6 (Mycolicibacterium thermoresistibile) Explore A0A117IMA6  Go to UniProtKB:  A0A117IMA6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	AA [auth H], I [auth A], K [auth B], N [auth C], Q [auth D], U [auth E], W [auth F], Z [auth G]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
F6P	L [auth B], O [auth C], R [auth D], V [auth E], X [auth F]	6-O-phosphono-beta-D-fructofuranose C6 H13 O9 P BGWGXPAPYGQALX-ARQDHWQXSA-N
PO4	CA [auth H], DA [auth H], M [auth B], S [auth D], T [auth D], Y [auth F]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	BA [auth H], J [auth A], P [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free:  0.213 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 216.96	α = 90
b = 216.96	β = 90
c = 159.835	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-06-07 
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: 2017-06-07
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence
• Version 1.2: 2020-01-22
  Changes: Database references
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary