4RSM

Crystal structure of carbohydrate transporter msmeg_3599 from mycobacterium smegmatis str. mc2 155, target efi-510970, in complex with d-threitol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

A General Strategy for the Discovery of Metabolic Pathways: d-Threitol, l-Threitol, and Erythritol Utilization in Mycobacterium smegmatis.

Huang, H.Carter, M.S.Vetting, M.W.Al-Obaidi, N.Patskovsky, Y.Almo, S.C.Gerlt, J.A.

(2015) J.Am.Chem.Soc. 137: 14570-14573

  • DOI: 10.1021/jacs.5b08968
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We describe a general integrated bioinformatic and experimental strategy to discover the in vitro enzymatic activities and in vivo functions (metabolic pathways) of uncharacterized enzymes discovered in microbial genome projects using the ligand spec ...

    We describe a general integrated bioinformatic and experimental strategy to discover the in vitro enzymatic activities and in vivo functions (metabolic pathways) of uncharacterized enzymes discovered in microbial genome projects using the ligand specificities of the solute binding proteins (SBPs) for ABC transporters. Using differential scanning fluorimetry, we determined that the SBP for an ABC transporter encoded by the genome of Mycobacterium smegmatis is stabilized by d-threitol. Using sequence similarity networks and genome neighborhood networks to guide selection of target proteins for pathway enzymes, we applied both in vitro and in vivo experimental approaches to discover novel pathways for catabolism of d-threitol, l-threitol, and erythritol.


    Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine , Bronx, New York 10461, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Periplasmic binding protein/LacI transcriptional regulator
A, B, C, D
327Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: thpA
Find proteins for A0QYB5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QYB5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3VB
Query on 3VB

Download SDF File 
Download CCD File 
A, B, C, D
D-Threitol
C4 H10 O4
UNXHWFMMPAWVPI-QWWZWVQMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 62.723α = 90.00
b = 128.288β = 93.05
c = 66.579γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
ARP/wARPmodel building
SHELXphasing
SHELXmodel building
REFMACrefinement
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2015-01-14
    Type: Structure summary
  • Version 1.2: 2015-06-10
    Type: Non-polymer description
  • Version 1.3: 2016-06-01
    Type: Database references
  • Version 1.4: 2018-01-24
    Type: Structure summary