2NS1

Crystal structure of the e. coli ammonia channel AMTB complexed with the signal transduction protein GLNK


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.962 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inhibitory complex of the transmembrane ammonia channel, AmtB, and the cytosolic regulatory protein, GlnK, at 1.96

Gruswitz, F.O'Connell III, J.Stroud, R.M.

(2007) Proc.Natl.Acad.Sci.USA 104: 42-47

  • DOI: 10.1073/pnas.0609796104

  • PubMed Abstract: 
  • Ammonia conductance is highly regulated. A P(II) signal transduction protein, GlnK, is the final regulator of transmembrane ammonia conductance by the ammonia channel AmtB in Escherichia coli. The complex formed between AmtB and inhibitory GlnK at 1. ...

    Ammonia conductance is highly regulated. A P(II) signal transduction protein, GlnK, is the final regulator of transmembrane ammonia conductance by the ammonia channel AmtB in Escherichia coli. The complex formed between AmtB and inhibitory GlnK at 1.96-A resolution shows that the trimeric channel is blocked directly by GlnK and how, in response to intracellular nitrogen status, the ability of GlnK to block the channel is regulated by uridylylation/deuridylylation at Y51. ATP and Mg(2+) augment the interaction of GlnK. The hydrolyzed product, adenosine 5'-diphosphate orients the surface of GlnK for AmtB blockade. 2-Oxoglutarate diminishes AmtB/GlnK association, and sites for 2-oxoglutarate are evaluated.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Genentech Hall, School of Medicine, University of California, 600 16th Street, San Francisco, CA 94158-2517, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ammonia channel
A
412Escherichia 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
B
116Escherichia coli (strain K12)Mutation(s): 1 
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
BOG
Query on BOG

Download SDF File 
Download CCD File 
A
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.962 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.162 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 102.032α = 90.00
b = 102.032β = 90.00
c = 363.849γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
PHASERphasing
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Source and taxonomy, Version format compliance