6DZX

Crystal structure of the N. meningitides methionine-binding protein in its D-methionine bound conformation.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures of the Neisseria meningitides methionine-binding protein MetQ in substrate-free form and bound to l- and d-methionine isomers.

Nguyen, P.T.Lai, J.Y.Kaiser, J.T.Rees, D.C.

(2019) Protein Sci 28: 1750-1757

  • DOI: https://doi.org/10.1002/pro.3694
  • Primary Citation of Related Structures:  
    6CVA, 6DZX, 6OJA

  • PubMed Abstract: 

    The bacterial periplasmic methionine-binding protein MetQ is involved in the import of methionine by the cognate MetNI methionine ATP binding cassette (ABC) transporter. The MetNIQ system is one of the few members of the ABC importer family that has been structurally characterized in multiple conformational states. Critical missing elements in the structural analysis of MetNIQ are the structure of the substrate-free form of MetQ, and detailing how MetQ binds multiple methionine derivatives, including both l- and d-methionine isomers. In this study, we report the structures of the Neisseria meningitides MetQ in substrate-free form and in complexes with l-methionine and with d-methionine, along with the associated binding constants determined by isothermal titration calorimetry. Structures of the substrate-free (N238A) and substrate-bound N. meningitides MetQ are related by a "Venus-fly trap" hinge-type movement of the two domains accompanying methionine binding and dissociation. l- and d-methionine bind to the same site on MetQ, and this study emphasizes the important role of asparagine 238 in ligand binding and affinity. A thermodynamic analysis demonstrates that ligand-free MetQ associates with the ATP-bound form of MetNI ∼40 times more tightly than does liganded MetQ, consistent with the necessity of dissociating methionine from MetQ for transport to occur.


  • Organizational Affiliation

    Howard Hughes Medical Institute and Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipoprotein
A, B, C, D, E
A, B, C, D, E, F
247Neisseria meningitidis alpha153Mutation(s): 0 
Gene Names: sfbANME_0028
UniProt
Find proteins for C6S9R8 (Neisseria meningitidis alpha153)
Explore C6S9R8 
Go to UniProtKB:  C6S9R8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6S9R8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.663α = 114.83
b = 87.933β = 104.12
c = 91.639γ = 105.39
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2019-08-14
    Changes: Data collection, Database references
  • Version 1.2: 2019-09-25
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-20
    Changes: Author supporting evidence