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- PDB-6eu6: Sensor Amt Protein -

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Basic information

Entry
Database: PDB / ID: 6eu6
TitleSensor Amt Protein
ComponentsAmmonium transporter
KeywordsMEMBRANE PROTEIN / Ammonium transporter / Signalling / histidine kinase
Function / homology
Function and homology information


ammonium homeostasis / ammonium channel activity / phosphorelay sensor kinase activity / plasma membrane
Similarity search - Function
Ammonium transporter / Ammonium transporter AmtB-like domain / Ammonium Transporter Family / Ammonium/urea transporter / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain ...Ammonium transporter / Ammonium transporter AmtB-like domain / Ammonium Transporter Family / Ammonium/urea transporter / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
AMMONIUM ION / Ammonium transporter
Similarity search - Component
Biological speciesKuenenia stuttgartiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsPflueger, T. / Hernandez, C. / Andrade, S.L.A.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research FoundationAN-676/3 Germany
German Research FoundationAN-676/4 Germany
German Research FoundationRTG 2202 Germany
CitationJournal: Nat Commun / Year: 2018
Title: Signaling ammonium across membranes through an ammonium sensor histidine kinase.
Authors: Tobias Pflüger / Camila F Hernández / Philipp Lewe / Fabian Frank / Haydyn Mertens / Dmitri Svergun / Manfred W Baumstark / Vladimir Y Lunin / Mike S M Jetten / Susana L A Andrade /
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 ...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.
History
DepositionOct 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_symm_contact ...pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ammonium transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9658
Polymers43,4641
Non-polymers1,5027
Water1,874104
1
A: Ammonium transporter
hetero molecules

A: Ammonium transporter
hetero molecules

A: Ammonium transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,89624
Polymers130,3913
Non-polymers4,50521
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area17640 Å2
ΔGint-162 kcal/mol
Surface area35380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.745, 99.745, 89.069
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ammonium transporter


Mass: 43463.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kuenenia stuttgartiensis (bacteria) / Gene: amtb, kuste3690 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q1Q357

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Sugars , 2 types, 2 molecules

#3: Sugar ChemComp-ZDM / nonyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside / nonyl-beta-D-maltoside


Type: saccharide / Mass: 468.536 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C21H40O11 / Comment: detergent*YM
#4: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 4 types, 109 molecules

#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M MES/NaOH pH 7.0 24 % (w/v) of polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2015
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→86.38 Å / Num. obs: 33401 / % possible obs: 100 % / Observed criterion σ(F): 2 / Redundancy: 10.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.037 / Net I/σ(I): 12.1
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 10.5 % / Rmerge(I) obs: 1.461 / Num. unique obs: 2466 / CC1/2: 0.735 / Rpim(I) all: 0.469 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B2H

2b2h


Resolution: 1.98→86.38 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.27 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.116 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1845 1694 4.8 %RANDOM
Rwork0.15203 ---
obs0.15356 33401 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.018 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.98→86.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3067 0 96 104 3267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193248
X-RAY DIFFRACTIONr_bond_other_d0.0020.023179
X-RAY DIFFRACTIONr_angle_refined_deg1.9641.9684408
X-RAY DIFFRACTIONr_angle_other_deg1.02137280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.245406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.25323.077117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91315496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0541512
X-RAY DIFFRACTIONr_chiral_restr0.1620.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023581
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02777
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0793.4021624
X-RAY DIFFRACTIONr_mcbond_other3.083.3991623
X-RAY DIFFRACTIONr_mcangle_it3.9395.0812030
X-RAY DIFFRACTIONr_mcangle_other3.9395.0842031
X-RAY DIFFRACTIONr_scbond_it4.7864.0281624
X-RAY DIFFRACTIONr_scbond_other4.7794.0241621
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7985.8332373
X-RAY DIFFRACTIONr_long_range_B_refined8.28329.1133962
X-RAY DIFFRACTIONr_long_range_B_other8.27429.0633941
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 131 -
Rwork0.257 2466 -
obs--99.81 %

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