6EU6 | pdb_00006eu6

Sensor Amt Protein

• PDB DOI: https://doi.org/10.2210/pdb6EU6/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Candidatus Kuenenia stuttgartensis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2017-10-28 Released: 2018-01-24 
• Deposition Author(s): Pflueger, T., Hernandez, C., Andrade, S.L.A.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.184 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

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

• PubMed: 29323112 
• DOI: https://doi.org/10.1038/s41467-017-02637-3
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Institute for Biochemistry, University of Freiburg, Albertstr. 21, Freiburg, 79104, Germany.
European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestr. 85, Hamburg, D-22603, Germany.
Center for Medicine, Institute for Exercise and Occupational Medicine, Medical Center, University of Freiburg, Hugstetterstr. 55, Freiburg, 79106, Germany.
Faculty of Medicine, University of Freiburg, Freiburg, 79106, Germany.
Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Vitkevicha str. 1, Pushchino, 142290, Russia.
Department of Microbiology, Radboud University, Institute for Water and Wetland Research, Heyendaalseweg 135, Nijmegen, NL-6525 AJ, The Netherlands.
Institute for Biochemistry, University of Freiburg, Albertstr. 21, Freiburg, 79104, Germany. [e-mail].
BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 1, Freiburg, 79104, Germany. [e-mail].

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)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 44.97 kDa 
• Atom Count: 3,278 
• Modeled Residue Count: 405 
• Deposited Residue Count: 405 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ammonium transporter	A	405	Candidatus Kuenenia stuttgartensis	Mutation(s): 0  Gene Names: amtb, kuste3690 Membrane Entity: Yes
UniProt
Find proteins for Q1Q357 (Kuenenia stuttgartiensis) Explore Q1Q357  Go to UniProtKB:  Q1Q357

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LMT	E [auth A]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
ZDM	D [auth A]	nonyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside C21 H40 O11 KCCBGPCYGBPHBR-ZESVGKPKSA-N
MES	B [auth A], C [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4	H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NH4	F [auth A], G [auth A]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.184 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.745	α = 90
b = 99.745	β = 90
c = 89.069	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-01-24 
Deposition Author(s): Pflueger, T., Hernandez, C., Andrade, S.L.A.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	AN-676/3
German Research Foundation	Germany	AN-676/4
German Research Foundation	Germany	RTG 2202

Revision History  

• 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
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description