4M64

3D crystal structure of Na+/melibiose symporter of Salmonella typhimurium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.359 
  • R-Value Work: 0.312 
  • R-Value Observed: 0.314 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure-based mechanism for Na(+)/melibiose symport by MelB.

Ethayathulla, A.S.Yousef, M.S.Amin, A.Leblanc, G.Kaback, H.R.Guan, L.

(2014) Nat Commun 5: 3009-3009

  • DOI: https://doi.org/10.1038/ncomms4009
  • Primary Citation of Related Structures:  
    4M64

  • PubMed Abstract: 

    The bacterial melibiose permease (MelB) belongs to the glycoside-pentoside-hexuronide:cation symporter family, a part of the major facilitator superfamily (MFS). Structural information regarding glycoside-pentoside-hexuronide:cation symporter family transporters and other Na(+)-coupled permeases within MFS has been lacking, although a wealth of biochemical and biophysical data are available. Here we present the three-dimensional crystal structures of Salmonella typhimurium MelBSt in two conformations, representing an outward partially occluded and an outward inactive state of MelBSt. MelB adopts a typical MFS fold and contains a previously unidentified cation-binding motif. Three conserved acidic residues form a pyramidal-shaped cation-binding site for Na(+), Li(+) or H(+), which is in close proximity to the sugar-binding site. Both cosubstrate-binding sites are mainly contributed by the residues from the amino-terminal domain. These two structures and the functional data presented here provide mechanistic insights into Na(+)/melibiose symport. We also postulate a structural foundation for the conformational cycling necessary for transport catalysed by MFS permeases in general.


  • Organizational Affiliation

    Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Melibiose carrier protein
A, B, C, D
486Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Mutation(s): 1 
Gene Names: melBSTM4299
Membrane Entity: Yes 
UniProt
Find proteins for P30878 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P30878 
Go to UniProtKB:  P30878
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30878
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.359 
  • R-Value Work: 0.312 
  • R-Value Observed: 0.314 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.206α = 90
b = 127.206β = 90
c = 206.303γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-15
    Type: Initial release
  • Version 1.1: 2014-01-29
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references
  • Version 1.3: 2024-04-03
    Changes: Refinement description