3TUI

Inward facing conformations of the MetNI methionine ABC transporter: CY5 native crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Inward facing conformations of the MetNI methionine ABC transporter: Implications for the mechanism of transinhibition.

Johnson, E.Nguyen, P.T.Yeates, T.O.Rees, D.C.

(2012) Protein Sci. 21: 84-96

  • DOI: 10.1002/pro.765
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Two new crystal structures of the Escherichia coli high affinity methionine uptake ATP Binding Cassette (ABC) transporter MetNI, purified in the detergents cyclohexyl-pentyl-β-D-maltoside (CY5) and n-decyl-β-D-maltopyranoside (DM), have been solved i ...

    Two new crystal structures of the Escherichia coli high affinity methionine uptake ATP Binding Cassette (ABC) transporter MetNI, purified in the detergents cyclohexyl-pentyl-β-D-maltoside (CY5) and n-decyl-β-D-maltopyranoside (DM), have been solved in inward facing conformations to resolutions of 2.9 and 4.0 Å, respectively. Compared to the previously reported 3.7 Å resolution structure of MetNI purified in n-dodecyl-β-D-maltopyranoside (DDM), the higher resolution of the CY5 data enabled significant improvements to the structural model in several regions, including corrections to the sequence registry, and identification of ADP in the nucleotide binding site. CY5 crystals soaked with selenomethionine established details of the methionine binding site in the C2 regulatory domain of the ABC subunit, including the displacement of the side chain of MetN residue methionine 301 by the exogenous ligand. When compared to the CY5 or DDM structures, the DM structure exhibits a significant repositioning of the dimeric C2 domains, including an unexpected register shift in the intermolecular β-sheet hydrogen bonding between monomers, and a narrowing of the nucleotide binding space. The immediate proximity of the exogenous methionine binding site to the conformationally variable dimeric interface provides an indication of how methionine binding to the regulatory domains might mediate the phenomenon of transinhibition.


    Organizational Affiliation

    Division of Chemistry and Chemical Engineering 114-96, California Institute of Technology, Pasadena, CA 91125, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-methionine transport system permease protein metI
A, B, E, F
217Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: metI (yaeE)
Find proteins for P31547 (Escherichia coli (strain K12))
Go to UniProtKB:  P31547
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Methionine import ATP-binding protein MetN
C, D, G, H
366Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: metN (abc)
EC: 3.6.3.-
Find proteins for P30750 (Escherichia coli (strain K12))
Go to UniProtKB:  P30750
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
C, D, G, H
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.240 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 83.430α = 90.00
b = 140.080β = 96.39
c = 150.070γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-30
    Type: Initial release
  • Version 1.1: 2011-12-28
    Type: Database references