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: 1.60 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

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:  
    4RS3, 4RSM

  • 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 specificities of the solute binding proteins (SBPs) for ABC transporters ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Periplasmic binding protein/LacI transcriptional regulatorA, B, C, D327Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_3599MSMEI_3516thpA
UniProt
Find proteins for A0QYB5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QYB5 
Go to UniProtKB:  A0QYB5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0QYB5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.723α = 90
b = 128.288β = 93.05
c = 66.579γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
ARP/wARPmodel building
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

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