2YLN

Crystal structure of the L-cystine solute receptor of Neisseria gonorrhoeae in the closed conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.109 
  • R-Value Observed: 0.111 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structures of Two Solute Receptors for L-Cystine and L-Cysteine, Respectively, of the Human Pathogen Neisseria Gonorrhoeae.

Bulut, H.Moniot, S.Licht, A.Scheffel, F.Gathmann, S.Saenger, W.Schneider, E.

(2012) J Mol Biol 415: 560

  • DOI: 10.1016/j.jmb.2011.11.030
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • ATP-binding cassette (ABC) transporters are integral membrane proteins that carry a variety of substrates across biological membranes at the expense of ATP. The here considered prokaryotic canonical importers consist of three entities: an extracellul ...

    ATP-binding cassette (ABC) transporters are integral membrane proteins that carry a variety of substrates across biological membranes at the expense of ATP. The here considered prokaryotic canonical importers consist of three entities: an extracellular solute receptor, two membrane-intrinsic proteins forming a translocation pathway, and two cytoplasmic ATP-binding subunits. The ngo0372-74 and ngo2011-14 gene clusters from the human pathogen Neisseria gonorrhoeae were predicted by sequence homology as ABC transporters for the uptake of cystine and cysteine, respectively, and chosen for structural characterization. The structure of the receptor component Ngo0372 was obtained in a ligand-free "open" conformation and in a "closed" conformation when co-crystallized with L-cystine. Our data provide the first structural information of an L-cystine ABC transporter. Dissociation constants of 21 and 33 nM for L-cystine and L-selenocystine, respectively, were determined by isothermal titration calorimetry. In contrast, L-cystathionine and L-djenkolic acid are weak binders, while no binding was detectable for S-methyl-L-cysteine. Mutational analysis of two residues from the binding pocket, Trp97 and Tyr59, revealed that the latter is crucial for L-cystine binding. The structure of the Ngo2014 receptor was obtained in closed conformation in complex with co-purified L-cysteine. The protein binds L-cysteine with a K(d) of 26 nM. Comparison of the structures of both receptors and analysis of the ligand binding sites shed light on the mode of ligand recognition and provides insight into the tight binding of both substrates. Moreover, since L-cystine limitation leads to reduction in virulence of N. gonorrhoeae, Ngo0372 might be suited as target for an antimicrobial vaccine.


    Organizational Affiliation

    Institut fuer Chemie und Biochemie/Kristallographie, Freie Universitaet Berlin, Takustrasse 6, D-14195 Berlin, Germany.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PUTATIVE ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID
A
283Neisseria gonorrhoeaeMutation(s): 1 
Find proteins for Q5F9M1 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090))
Go to UniProtKB:  Q5F9M1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CYS
Query on CYS

Download CCD File 
A
CYSTEINE
C3 H7 N O2 S
XUJNEKJLAYXESH-REOHCLBHSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CYSKd :  21   nM  PDBBind
CYSKd:  21   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.109 
  • R-Value Observed: 0.111 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.73α = 90
b = 63.43β = 96.89
c = 44.65γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-14
    Type: Initial release
  • Version 1.1: 2012-01-25
    Changes: Other