6R1B image
Deposition Date 2019-03-14
Release Date 2019-09-04
Last Version Date 2024-01-24
Entry Detail
PDB ID:
6R1B
Title:
Crystal structure of UgpB from Mycobacterium tuberculosis in complex with glycerophosphocholine
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.27 Å
R-Value Free:
0.25
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Putative Sn-glycerol-3-phosphate-binding lipoprotein UgpB
Mutations:K161(MLZ)
Chain IDs:A
Chain Length:394
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
Polymer Type:polypeptide(L)
Molecule:Putative Sn-glycerol-3-phosphate-binding lipoprotein UgpB
Mutations:K161(MLZ)
Chain IDs:B
Chain Length:395
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
Polymer Type:polypeptide(L)
Molecule:Putative Sn-glycerol-3-phosphate-binding lipoprotein UgpB
Mutations:K161(MLZ)
Chain IDs:C
Chain Length:384
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
Polymer Type:polypeptide(L)
Molecule:Putative Sn-glycerol-3-phosphate-binding lipoprotein UgpB
Mutations:K161(MLZ)
Chain IDs:D
Chain Length:382
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
MLZ A LYS modified residue
Primary Citation
Structural Basis of Glycerophosphodiester Recognition by theMycobacterium tuberculosisSubstrate-Binding Protein UgpB.
Acs Chem.Biol. 14 1879 1887 (2019)
PMID: 31433162 DOI: 10.1021/acschembio.9b00204

Abstact

Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis (TB) and has evolved an incredible ability to survive latently within the human host for decades. The Mtb pathogen encodes for a low number of ATP-binding cassette (ABC) importers for the acquisition of carbohydrates that may reflect the nutrient poor environment within the host macrophages. Mtb UgpB (Rv2833c) is the substrate binding domain of the UgpABCE transporter that recognizes glycerophosphocholine (GPC), indicating that this transporter has a role in recycling glycerophospholipid metabolites. By using a combination of saturation transfer difference (STD) NMR and X-ray crystallography, we report the structural analysis of Mtb UgpB complexed with GPC and have identified that Mtb UgpB not only recognizes GPC but is also promiscuous for a broad range of glycerophosphodiesters. Complementary biochemical analyses and site-directed mutagenesis precisely define the molecular basis and specificity of glycerophosphodiester recognition. Our results provide critical insights into the structural and functional role of the Mtb UgpB transporter and reveal that the specificity of this ABC-transporter is not limited to GPC, therefore optimizing the ability of Mtb to scavenge scarce nutrients and essential glycerophospholipid metabolites via a single transporter during intracellular infection.

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Primary Citation of related structures