4RSM

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

• PDB DOI:  https://doi.org/10.2210/pdb4RSM/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-11-08 Released: 2014-12-10 
• Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Morisco, L.L., Wasserman, S.R., Chamala, S., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Lafleur, J., Hillerich, B., Siedel, R.D., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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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 

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

• PubMed: 26560079 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 137.87 kDa 
• Atom Count: 10,269 
• Modelled Residue Count: 1,257 
• Deposited Residue Count: 1,308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic binding protein/LacI transcriptional regulator	A, B, C, D	327	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: MSMEG_3599, MSMEI_3516, thpA
UniProt
Find proteins for A0QYB5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QYB5  Go to UniProtKB:  A0QYB5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3VB	E [auth A], F [auth B], G [auth C], H [auth D]	D-Threitol C4 H10 O4 UNXHWFMMPAWVPI-QWWZWVQMSA-N

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 = 62.723	α = 90
b = 128.288	β = 93.05
c = 66.579	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-10 
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Morisco, L.L., Wasserman, S.R., Chamala, S., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Lafleur, J., Hillerich, B., Siedel, R.D., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• 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