2WIT | pdb_00002wit

CRYSTAL STRUCTURE OF THE SODIUM-COUPLED GLYCINE BETAINE SYMPORTER BETP FROM CORYNEBACTERIUM GLUTAMICUM WITH BOUND SUBSTRATE

• PDB DOI: https://doi.org/10.2210/pdb2WIT/pdb
• Entry: 2WIT supersedes: 2W8A

• Classification: MEMBRANE PROTEIN
• Organism(s): Corynebacterium glutamicum
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2009-05-17 Released: 2009-05-26 
• Deposition Author(s): Ressl, S., Terwisscha Van Scheltinga, A.C., Vonrhein, C., Ott, V., Ziegler, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free: 
  0.265 (Depositor), 0.294 (DCC) 
• R-Value Work: 
  0.257 (Depositor) 
• R-Value Observed: 
  0.257 (Depositor) 

Literature

Molecular Basis of Transport and Regulation in the Na(+)/Betaine Symporter Betp.

Ressl, S., Terwisscha Van Scheltinga, A.C., Vonrhein, C., Ott, V., Ziegler, C.

(2009) Nature 458: 47

• PubMed: 19262666 
• DOI: https://doi.org/10.1038/nature07819
• Primary Citation Related Structures: 
  2WIT


• PubMed Abstract: 
  

  Osmoregulated transporters sense intracellular osmotic pressure and respond to hyperosmotic stress by accumulation of osmolytes to restore normal hydration levels. Here we report the determination of the X-ray structure of a member of the family of betaine/choline/carnitine transporters, the Na(+)-coupled symporter BetP from Corynebacterium glutamicum, which is a highly effective osmoregulated uptake system for glycine betaine. Glycine betaine is bound in a tryptophan box occluded from both sides of the membrane with aromatic side chains lining the transport pathway. BetP has the same overall fold as three unrelated Na(+)-coupled symporters. Whereas these are crystallized in either the outward-facing or the inward-facing conformation, the BetP structure reveals a unique intermediate conformation in the Na(+)-coupled transport cycle. The trimeric architecture of BetP and the break in three-fold symmetry by the osmosensing C-terminal helices suggest a regulatory mechanism of Na(+)-coupled osmolyte transport to counteract osmotic stress.

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Organizational Affiliation: 
• Max Planck Institute of Biophysics, Department of Structural Biology, 60438 Frankfurt am Main, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 185.47 kDa 
• Atom Count: 11,737 
• Modeled Residue Count: 1,541 
• Deposited Residue Count: 1,698 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCINE BETAINE TRANSPORTER BETP	A, B, C	566	Corynebacterium glutamicum	Mutation(s): 3  Membrane Entity: Yes
UniProt
Find proteins for P54582 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore P54582  Go to UniProtKB:  P54582

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BET	D [auth A], E [auth B], F [auth C]	TRIMETHYL GLYCINE C5 H12 N O2 KWIUHFFTVRNATP-UHFFFAOYSA-O

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free:  0.265 (Depositor), 0.294 (DCC) 
• R-Value Work:  0.257 (Depositor) 
• R-Value Observed: 0.257 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.095	α = 90
b = 129.422	β = 90
c = 182.942	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
SHELXD	phasing
SHARP	phasing
BUSTER-TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-26 
Deposition Author(s): Ressl, S., Terwisscha Van Scheltinga, A.C., Vonrhein, C., Ott, V., Ziegler, C.
• This entry supersedes: 2W8A

Revision History  

• Version 1.0: 2009-05-26
  Type: Initial release
  
• Version 1.1: 2013-01-30
  Changes: Database references, Derived calculations, Refinement description, Source and taxonomy, Version format compliance
• Version 1.2: 2013-03-20
  Changes: Database references
• Version 1.3: 2015-05-13
  Changes: Database references
• Version 1.4: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations, Other