6R1B

Crystal structure of UgpB from Mycobacterium tuberculosis in complex with glycerophosphocholine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis of Glycerophosphodiester Recognition by theMycobacterium tuberculosisSubstrate-Binding Protein UgpB.

Fenn, J.S.Nepravishta, R.Guy, C.S.Harrison, J.Angulo, J.Cameron, A.D.Fullam, E.

(2019) Acs Chem.Biol. 14: 1879-1887

  • DOI: 10.1021/acschembio.9b00204

  • PubMed Abstract: 
  • <i>Mycobacterium tuberculosis </i> ( <i>Mtb </i>) is the causative agent of tuberculosis (TB) and has evolved an incredible ability to survive latently within the human host for decades. The <i>Mtb </i> pathogen encodes for a low number of ATP-bind ...

    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.


    Organizational Affiliation

    School of Life Sciences , University of Warwick , Coventry , West Midlands CV4 7AL , United Kingdom.,School of Pharmacy , University of East Anglia , Norwich Research Park, Norwich , Norfolk NR4 7TJ , United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative Sn-glycerol-3-phosphate-binding lipoprotein UgpB
A
394Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: ugpB
Find proteins for P71619 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P71619
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Putative Sn-glycerol-3-phosphate-binding lipoprotein UgpB
B
395Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: ugpB
Find proteins for P71619 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P71619
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Putative Sn-glycerol-3-phosphate-binding lipoprotein UgpB
C
384Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: ugpB
Find proteins for P71619 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P71619
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Putative Sn-glycerol-3-phosphate-binding lipoprotein UgpB
D
382Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: ugpB
Find proteins for P71619 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P71619
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CH5
Query on CH5

Download SDF File 
Download CCD File 
A, B, C, D
2-(((R)-2,3-DIHYDROXYPROPYL)PHOSPHORYLOXY)-N,N,N-TRIMETHYLETHANAMINIUM
GLYCERO-3-PHOSPHOCHOLINE
C8 H21 N O6 P
SUHOQUVVVLNYQR-MRVPVSSYSA-O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLZ
Query on MLZ
A, B, C, D
L-PEPTIDE LINKINGC7 H16 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.110α = 90.00
b = 169.860β = 90.00
c = 213.310γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
PHASERphasing
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom104193/ Z / 14/ Z
Royal SocietyUnited KingdomR G 1 2 0 4 0 5
Medical Research Council (United Kingdom)United KingdomMR / J 0 0 3 9 6 4 / 1
Engineering and Physical Sciences Research CouncilUnited KingdomE P /M 0 2 7 5 0 3 /1

Revision History 

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2019-10-02
    Type: Data collection, Database references