8TGY

Crystal structure of Gdx-Clo from Small Multidrug Resistance family of transporters in complex with guanylurea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.281 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Transport of metformin metabolites by guanidinium exporters of the Small Multidrug Resistance family.

Lucero, R.M.Demirer, K.Yeh, T.J.Stockbridge, R.B.

(2023) Biorxiv 

  • DOI: https://doi.org/10.1101/2023.08.10.552832
  • Primary Citation of Related Structures:  
    8TGY

  • PubMed Abstract: 

    Proteins from the Small Multidrug Resistance (SMR) family are frequently associated with horizontally transferred multidrug resistance gene arrays found in bacteria from wastewater and the human-adjacent biosphere. Recent studies suggest that a subset of SMR transporters might participate in metabolism of the common pharmaceutical metformin by bacterial consortia. Here, we show that both genomic and plasmid-associated transporters of the SMR Gdx functional subtype export byproducts of microbial metformin metabolism, with particularly high export efficiency for guanylurea. We use solid supported membrane electrophysiology to evaluate the transport kinetics for guanylurea and native substrate guanidinium by four representative SMR Gdx homologues. Using an internal reference to normalize independent electrophysiology experiments, we show that transport rates are comparable for genomic and plasmid-associated SMR Gdx homologues, and using a proteoliposome-based transport assay, we show that 2 proton:1 substrate transport stoichiometry is maintained. Additional characterization of guanidinium and guanylurea export properties focuses on the structurally characterized homologue, Gdx-Clo, for which we examined the pH dependence and thermodynamics of substrate binding and solved an x-ray crystal structure with guanylurea bound. Together, these experiments contribute in two main ways. By providing the first detailed kinetic examination of the structurally characterized SMR Gdx homologue Gdx-Clo, they provide a functional framework that will inform future mechanistic studies of this model transport protein. Second, this study casts light on a potential role for SMR Gdx transporters in microbial handling of metformin and its microbial metabolic byproducts, providing insight into how native transport physiologies are co-opted to contend with new selective pressures.


  • Organizational Affiliation

    Program in Chemical Biology.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Multidrug resistance protein, SMR familyA,
B [auth E],
C [auth G],
D [auth B]
105Clostridia bacteriumMutation(s): 0 
Gene Names: HMPREF1982_00479
Membrane Entity: Yes 
UniProt
Find proteins for U2EQ00 (Clostridiales bacterium oral taxon 876 str. F0540)
Explore U2EQ00 
Go to UniProtKB:  U2EQ00
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU2EQ00
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
L10 MonobodyE [auth C],
F [auth D],
G [auth F],
H
91Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DMU
Query on DMU

Download Ideal Coordinates CCD File 
M [auth C],
P [auth D]
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
LDA
Query on LDA

Download Ideal Coordinates CCD File 
J [auth E]
K [auth B]
L [auth B]
N [auth C]
O [auth C]
J [auth E],
K [auth B],
L [auth B],
N [auth C],
O [auth C],
Q [auth D]
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
9U1 (Subject of Investigation/LOI)
Query on 9U1

Download Ideal Coordinates CCD File 
I [auth E]N-(diaminomethylidene)urea
C2 H6 N4 O
SQSPRWMERUQXNE-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.281 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.914α = 86.77
b = 74.371β = 90.01
c = 107.212γ = 70.26
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35- GM128768

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-02
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references