3TUI

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 

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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:  
    3TUI, 3TUJ, 3TUZ

  • 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 in inward facing conformations to resolutions of 2 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-methionine transport system permease protein metIA, B, E, F217Escherichia coli K-12Mutation(s): 0 
Gene Names: b0198, JW0194, metI, yaeE
Membrane Entity: Yes 
UniProt
Find proteins for P31547 (Escherichia coli (strain K12))
Explore P31547 
Go to UniProtKB:  P31547
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31547
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Methionine import ATP-binding protein MetNC, D, G, H366Escherichia coli K-12Mutation(s): 1 
Gene Names: abc, b0199, JW0195, metN
EC: 3.6.3 (PDB Primary Data), 7.4.2.11 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P30750 (Escherichia coli (strain K12))
Explore P30750 
Go to UniProtKB:  P30750
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30750
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download Ideal Coordinates CCD File 
I [auth C],
J [auth D],
K [auth G],
L [auth H]		ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.43α = 90
b = 140.08β = 96.39
c = 150.07γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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