6EU6

Sensor Amt Protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Signaling ammonium across membranes through an ammonium sensor histidine kinase.

Pfluger, T.Hernandez, C.F.Lewe, P.Frank, F.Mertens, H.Svergun, D.Baumstark, M.W.Lunin, V.Y.Jetten, M.S.M.Andrade, S.L.A.

(2018) Nat Commun 9: 164-164

  • DOI: 10.1038/s41467-017-02637-3
  • Primary Citation of Related Structures:  
    6EU6

  • PubMed Abstract: 
  • Sensing and uptake of external ammonium is essential for anaerobic ammonium-oxidizing (anammox) bacteria, and is typically the domain of the ubiquitous Amt/Rh ammonium transporters. Here, we report on the structure and function of an ammonium sensor/transducer from the anammox bacterium "Candidatus Kuenenia stuttgartiensis" that combines a membrane-integral ammonium transporter domain with a fused histidine kinase ...

    Sensing and uptake of external ammonium is essential for anaerobic ammonium-oxidizing (anammox) bacteria, and is typically the domain of the ubiquitous Amt/Rh ammonium transporters. Here, we report on the structure and function of an ammonium sensor/transducer from the anammox bacterium "Candidatus Kuenenia stuttgartiensis" that combines a membrane-integral ammonium transporter domain with a fused histidine kinase. It contains a high-affinity ammonium binding site not present in assimilatory Amt proteins. The levels of phosphorylated histidine in the kinase are coupled to the presence of ammonium, as conformational changes during signal recognition by the Amt module are transduced internally to modulate the kinase activity. The structural analysis of this ammonium sensor by X-ray crystallography and small-angle X-ray-scattering reveals a flexible, bipartite system that recruits a large uptake transporter as a sensory module and modulates its functionality to achieve a mechanistic coupling to a kinase domain in order to trigger downstream signaling events.


    Organizational Affiliation

    BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 1, Freiburg, 79104, Germany. andrade@bio.chemie.uni-freiburg.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ammonium transporterA405Candidatus Kuenenia stuttgartiensisMutation(s): 0 
Gene Names: amtbkuste3690
Membrane Entity: Yes 
UniProt
Find proteins for Q1Q357 (Kuenenia stuttgartiensis)
Explore Q1Q357 
Go to UniProtKB:  Q1Q357
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LMT
Query on LMT

Download Ideal Coordinates CCD File 
E [auth A]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
ZDM
Query on ZDM

Download Ideal Coordinates CCD File 
D [auth A]nonyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside
C21 H40 O11
KCCBGPCYGBPHBR-ZESVGKPKSA-N
 Ligand Interaction
MES
Query on MES

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NH4
Query on NH4

Download Ideal Coordinates CCD File 
F [auth A], G [auth A]AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.745α = 90
b = 99.745β = 90
c = 89.069γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyAN-676/3
German Research FoundationGermanyAN-676/4
German Research FoundationGermanyRTG 2202

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-24
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Author supporting evidence
  • Version 1.2: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations