2NUU

Regulating the Escherichia coli ammonia channel: the crystal structure of the AmtB-GlnK complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The crystal structure of the Escherichia coli AmtB-GlnK complex reveals how GlnK regulates the ammonia channel

Conroy, M.J.Durand, A.Lupo, D.Li, X.-D.Bullough, P.A.Winkler, F.K.Merrick, M.

(2007) Proc.Natl.Acad.Sci.Usa 104: 1213-1218

  • DOI: 10.1073/pnas.0610348104

  • PubMed Abstract: 
  • Amt proteins are ubiquitous channels for the conduction of ammonia in archaea, eubacteria, fungi, and plants. In Escherichia coli, previous studies have indicated that binding of the PII signal transduction protein GlnK to the ammonia channel AmtB re ...

    Amt proteins are ubiquitous channels for the conduction of ammonia in archaea, eubacteria, fungi, and plants. In Escherichia coli, previous studies have indicated that binding of the PII signal transduction protein GlnK to the ammonia channel AmtB regulates the channel thereby controlling ammonium influx in response to the intracellular nitrogen status. Here, we describe the crystal structure of the complex between AmtB and GlnK at a resolution of 2.5 A. This structure of PII in a complex with one of its targets reveals physiologically relevant conformations of both AmtB and GlnK. GlnK interacts with AmtB almost exclusively via a long surface loop containing Y51 (T-loop), the tip of which inserts deeply into the cytoplasmic pore exit, blocking ammonia conduction. Y51 of GlnK is also buried in the pore exit, explaining why uridylylation of this residue prevents complex formation.


    Organizational Affiliation

    Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ammonia channel
A, B, C, D, E, F
415Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: amtB (ybaG)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Amt/Mep/Rh proteins
Protein: 
AmtB ammonia channel (mutant)
Find proteins for P69681 (Escherichia coli (strain K12))
Go to UniProtKB:  P69681
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nitrogen regulatory protein P-II 2
G, H, I, J, K, L
112Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: glnK (ybaI)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Amt/Mep/Rh proteins
Protein: 
AmtB ammonia channel (mutant)
Find proteins for P0AC55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AC55
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
G, H, J, L
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 99.691α = 90.00
b = 107.865β = 90.00
c = 280.162γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
XDSdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-21
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description