6CSE

Crystal structure of sodium/alanine symporter AgcS with L-alanine bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for substrate binding and specificity of a sodium-alanine symporter AgcS.

Ma, J.Lei, H.T.Reyes, F.E.Sanchez-Martinez, S.Sarhan, M.F.Hattne, J.Gonen, T.

(2019) Proc Natl Acad Sci U S A 116: 2086-2090

  • DOI: 10.1073/pnas.1806206116
  • Primary Citation of Related Structures:  
    6CSE, 6CSF

  • PubMed Abstract: 
  • The amino acid, polyamine, and organocation (APC) superfamily is the second largest superfamily of membrane proteins forming secondary transporters that move a range of organic molecules across the cell membrane. Each transporter in the APC superfamily i ...

    The amino acid, polyamine, and organocation (APC) superfamily is the second largest superfamily of membrane proteins forming secondary transporters that move a range of organic molecules across the cell membrane. Each transporter in the APC superfamily is specific for a unique subset of substrates, even if they possess a similar structural fold. The mechanism of substrate selectivity remains, by and large, elusive. Here, we report two crystal structures of an APC member from Methanococcus maripaludis , the alanine or glycine:cation symporter (AgcS), with l- or d-alanine bound. Structural analysis combined with site-directed mutagenesis and functional studies inform on substrate binding, specificity, and modulation of the AgcS family and reveal key structural features that allow this transporter to accommodate glycine and alanine while excluding all other amino acids. Mutation of key residues in the substrate binding site expand the selectivity to include valine and leucine. These studies provide initial insights into substrate selectivity in AgcS symporters.


    Organizational Affiliation

    Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Monoclonal antibody FAB heavy chain AH214Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Monoclonal antibody FAB light chain BL213Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Sodium/alanine symporter AgcS CM453Methanococcus maripaludis S2Mutation(s): 0 
Gene Names: agcSMMP1511
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Amino Acid/Polyamine/Organocation (APC) Superfamily
Protein: 
AgcS sodium/alanine symporter with bound L-alanine
Find proteins for Q6LX42 (Methanococcus maripaludis (strain S2 / LL))
Explore Q6LX42 
Go to UniProtKB:  Q6LX42
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ALA
Query on ALA

Download Ideal Coordinates CCD File 
M
ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
M
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.231 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.477α = 90
b = 183.477β = 90
c = 349.067γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Data collection, Database references