4RS3

Crystal structure of carbohydrate transporter A0QYB3 from Mycobacterium smegmatis str. MC2 155, target EFI-510969, in complex with xylitol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.125 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Structures With Same Primary Citation

  • 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
ABC transporter, carbohydrate uptake transporter-2 (CUT2) family, periplasmic sugar-binding protein
A
327Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_3598MSMEI_3515xypA
EC: 3.6.3.17
Find proteins for A0QYB3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QYB3
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XYL
Query on XYL

Download CCD File 
A
D-XYLITOL
C5 H12 O5
HEBKCHPVOIAQTA-SCDXWVJYSA-N
 Ligand Interaction
IMD
Query on IMD

Download CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.125 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.841α = 90
b = 63.07β = 90
c = 73.134γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
ARP/wARPmodel building
REFMACrefinement
XDSdata reduction
SCALAdata scaling
SHELXphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2014-12-31
    Changes: Structure summary
  • Version 1.2: 2016-06-01
    Changes: Database references
  • Version 1.3: 2018-01-24
    Changes: Structure summary