Biological Assembly 1  

 3D View: Structure

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.31 kDa 
• Atom Count: 1006 
• Residue Count: 136 
• Unique protein chains: 1

2MPN

3D NMR structure of the transmembrane domain of the full-length inner membrane protein YgaP from Escherichia coli

• DOI: 10.2210/pdb2MPN/pdb
• BMRB: 19994

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-05-29 Released: 2014-06-25 
• Deposition Author(s): Eichmann, C., Tzitzilonis, C., Bordignon, E., Maslennikov, I., Choe, S., Riek, R.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: target function 

Literature

Solution NMR Structure and Functional Analysis of the Integral Membrane Protein YgaP from Escherichia coli.

Eichmann, C., Tzitzilonis, C., Bordignon, E., Maslennikov, I., Choe, S., Riek, R.

(2014) J Biol Chem 289: 23482-23503

• PubMed: 24958726 
• DOI: 10.1074/jbc.M114.571935
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The solution NMR structure of the α-helical integral membrane protein YgaP from Escherichia coli in mixed 1,2-diheptanoyl-sn-glycerol-3-phosphocholine/1-myristoyl-2-hydroxy-sn-glycero-3-phospho-(1'-rac-glycerol) micelles is presented. In these micelles, YgaP forms a homodimer with the two transmembrane helices being the dimer interface, whereas the N-terminal cytoplasmic domain includes a rhodanese-fold in accordance to its sequence homology to the rhodanese family of sulfurtransferases. The enzymatic sulfur transfer activity of full-length YgaP as well as of the N-terminal rhodanese domain only was investigated performing a series of titrations with sodium thiosulfate and potassium cyanide monitored by NMR and EPR. The data indicate the thiosulfate concentration-dependent addition of several sulfur atoms to the catalytic Cys-63, which process can be reversed by the addition of potassium cyanide. The catalytic reaction induces thereby conformational changes within the rhodanese domain, as well as on the transmembrane α-helices of YgaP. These results provide insights into a potential mechanism of YgaP during the catalytic thiosulfate activity in vivo.

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Organizational Affiliation: 

From the Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland and the Structural Biology Laboratory, The Salk Institute, La Jolla, California 92037 [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Inner membrane protein YgaP	A, B	68	Escherichia coli K-12	Mutation(s): 0  Gene Names: b2668, JW2643, ygaP, ygaP b2668 JW2643
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Rhodaneses	Protein:  YgaP rhodanese homodimeric transmembrane domain
Find proteins for P55734 (Escherichia coli (strain K12)) Go to UniProtKB:  P55734

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: target function 
• OLDERADO: 2MPN Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-05-29 
• Released Date: 2014-06-25 
Deposition Author(s): Eichmann, C., Tzitzilonis, C., Bordignon, E., Maslennikov, I., Choe, S., Riek, R.

Revision History 

• Version 1.0: 2014-06-25
  Type: Initial release
  
• Version 1.1: 2014-08-13
  Changes: Database references
• Version 1.2: 2014-09-17
  Changes: Database references