4RS3 | pdb_00004rs3

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

• PDB DOI: https://doi.org/10.2210/pdb4RS3/pdb

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


• Deposited: 2014-11-06 Released: 2014-11-19 
• 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)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.163 (Depositor), 0.178 (DCC) 
• R-Value Work: 
  0.124 (Depositor) 
• R-Value Observed: 
  0.125 (Depositor) 

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 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.

---

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)

Macromolecule Content 

• Total Structure Weight: 36.56 kDa 
• Atom Count: 2,647 
• Modeled Residue Count: 315 
• Deposited Residue Count: 327 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter, carbohydrate uptake transporter-2 (CUT2) family, periplasmic sugar-binding protein	A	327	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: MSMEG_3598, MSMEI_3515 EC: 3.6.3.17
UniProt
Find proteins for A0QYB3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QYB3  Go to UniProtKB:  A0QYB3

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XYL	B [auth A]	Xylitol C5 H12 O5 HEBKCHPVOIAQTA-SCDXWVJYSA-N
IMD	N [auth A], O [auth A], P [auth A], Q [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	HA [auth A], IA [auth A], JA [auth A], KA [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.163 (Depositor), 0.178 (DCC) 
• R-Value Work:  0.124 (Depositor) 
• R-Value Observed: 0.125 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.841	α = 90
b = 63.07	β = 90
c = 73.134	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
ARP/wARP	model building
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-19 
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: 2014-11-19
  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
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-10-16
  Changes: Data collection, Database references, Structure summary