5L3K

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.157 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


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

  • DOI: https://doi.org/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.


  • Organizational Affiliation

    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom vgm23@cam.ac.uk tom@cryst.bioc.cam.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha,alpha-trehalose-phosphate synthase
A, B, C, D, E
A, B, C, D, E, F, G, H
487Mycolicibacterium thermoresistibileMutation(s): 0 
Gene Names: RMCT_1906
EC: 2.4.1.347
UniProt
Find proteins for A0A117IMA6 (Mycolicibacterium thermoresistibile)
Explore A0A117IMA6 
Go to UniProtKB:  A0A117IMA6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A117IMA6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
AA [auth H]
I [auth A]
K [auth B]
N [auth C]
Q [auth D]
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
Query on F6P

Download Ideal Coordinates CCD File 
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
Query on PO4

Download Ideal Coordinates CCD File 
CA [auth H]
DA [auth H]
M [auth B]
S [auth D]
T [auth D]
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
Query on EDO

Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.157 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 216.96α = 90
b = 216.96β = 90
c = 159.835γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited States--

Revision History  (Full details and data files)

  • 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