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 
  • R-Value Observed: 0.209 

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/acschembio.9b00204
  • Primary Citation of Related Structures:  
    6R1B

  • PubMed Abstract: 

    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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative Sn-glycerol-3-phosphate-binding lipoprotein UgpB394Mycobacterium tuberculosisMutation(s): 0 
Gene Names: ugpBERS007679_03701
UniProt
Find proteins for P71619 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P71619 
Go to UniProtKB:  P71619
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP71619
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Putative Sn-glycerol-3-phosphate-binding lipoprotein UgpB395Mycobacterium tuberculosisMutation(s): 0 
Gene Names: ugpBERS007679_03701
UniProt
Find proteins for P71619 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P71619 
Go to UniProtKB:  P71619
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP71619
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Putative Sn-glycerol-3-phosphate-binding lipoprotein UgpB384Mycobacterium tuberculosisMutation(s): 0 
Gene Names: ugpBERS007679_03701
UniProt
Find proteins for P71619 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P71619 
Go to UniProtKB:  P71619
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP71619
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Putative Sn-glycerol-3-phosphate-binding lipoprotein UgpB382Mycobacterium tuberculosisMutation(s): 0 
Gene Names: ugpBERS007679_03701
UniProt
Find proteins for P71619 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P71619 
Go to UniProtKB:  P71619
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP71619
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CH5 (Subject of Investigation/LOI)
Query on CH5

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
M [auth C],
P [auth D]
2-(((R)-2,3-DIHYDROXYPROPYL)PHOSPHORYLOXY)-N,N,N-TRIMETHYLETHANAMINIUM
C8 H21 N O6 P
SUHOQUVVVLNYQR-MRVPVSSYSA-O
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
L [auth B],
O [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
J [auth B],
N [auth C],
Q [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MLZ
Query on MLZ
A
L-PEPTIDE LINKINGC7 H16 N2 O2LYS
Binding Affinity Annotations 
IDSourceBinding Affinity
CH5 Binding MOAD:  6R1B Kd: 3600 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.11α = 90
b = 169.86β = 90
c = 213.31γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2019-10-02
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description