7L16

Crystal structure of sugar-bound melibiose permease MelB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.275 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

X-ray crystallography reveals molecular recognition mechanism for sugar binding in a melibiose transporter MelB.

Guan, L.Hariharan, P.

(2021) Commun Biol 4: 931-931

  • DOI: https://doi.org/10.1038/s42003-021-02462-x
  • Primary Citation of Related Structures:  
    7L16, 7L17

  • PubMed Abstract: 

    Major facilitator superfamily_2 transporters are widely found from bacteria to mammals. The melibiose transporter MelB, which catalyzes melibiose symport with either Na + , Li + , or H + , is a prototype of the Na + -coupled MFS transporters, but its sugar recognition mechanism has been a long-unsolved puzzle. Two high-resolution X-ray crystal structures of a Salmonella typhimurium MelB mutant with a bound ligand, either nitrophenyl-α-D-galactoside or dodecyl-β-D-melibioside, were refined to a resolution of 3.05 or 3.15 Å, respectively. In the substrate-binding site, the interaction of both galactosyl moieties on the two ligands with MelB St  are virturally same, so the sugar specificity determinant pocket can be recognized, and hence the molecular recognition mechanism for sugar binding in MelB has been deciphered. The conserved cation-binding pocket is also proposed, which directly connects to the sugar specificity pocket. These key structural findings have laid a solid foundation for our understanding of the cooperative binding and symport mechanisms in Na + -coupled MFS transporters, including eukaryotic transporters such as MFSD2A.


  • Organizational Affiliation

    Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA. Lan.Guan@ttuhsc.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Melibiose carrier protein485Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Mutation(s): 2 
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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMO (Subject of Investigation/LOI)
Query on LMO

Download Ideal Coordinates CCD File 
B [auth A]dodecyl 6-O-alpha-D-galactopyranosyl-beta-D-glucopyranoside
C24 H46 O11
HBVAWIPMNSJELA-RWNQQKCBSA-N
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.275 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.372α = 90
b = 127.372β = 90
c = 103.905γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2021-08-04 
  • Deposition Author(s): Guan, L.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM122759
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR21NS105863

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-04
    Type: Initial release
  • Version 1.1: 2021-08-25
    Changes: Advisory, Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection, Refinement description