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- PDB-6ris: The Kb42S variant of the molybdenum storage protein -

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Basic information

Entry
Database: PDB / ID: 6ris
TitleThe Kb42S variant of the molybdenum storage protein
Components(Molybdenum storage protein subunit ...) x 2
KeywordsMETAL BINDING PROTEIN / amino acid kinase family / Mo storage / polyoxomolybdate cluster / ATP hydrolysis
Function / homology
Function and homology information


nutrient reservoir activity / molybdenum ion binding / cytoplasm
Similarity search - Function
Molybdenum storage protein subunit alpha/beta / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Molybdenum storage protein subunit beta / Molybdenum storage protein subunit alpha
Similarity search - Component
Biological speciesAzotobacter vinelandii DJ (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsErmler, U. / Bruenle, S.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: Molybdate pumping into the molybdenum storage protein via an ATP-powered piercing mechanism.
Authors: Steffen Brünle / Martin L Eisinger / Juliane Poppe / Deryck J Mills / Julian D Langer / Janet Vonck / Ulrich Ermler /
Abstract: The molybdenum storage protein (MoSto) deposits large amounts of molybdenum as polyoxomolybdate clusters in a heterohexameric (αβ) cage-like protein complex under ATP consumption. Here, we suggest ...The molybdenum storage protein (MoSto) deposits large amounts of molybdenum as polyoxomolybdate clusters in a heterohexameric (αβ) cage-like protein complex under ATP consumption. Here, we suggest a unique mechanism for the ATP-powered molybdate pumping process based on X-ray crystallography, cryoelectron microscopy, hydrogen-deuterium exchange mass spectrometry, and mutational studies of MoSto from . First, we show that molybdate, ATP, and Mg consecutively bind into the open ATP-binding groove of the β-subunit, which thereafter becomes tightly locked by fixing the previously disordered N-terminal arm of the α-subunit over the β-ATP. Next, we propose a nucleophilic attack of molybdate onto the γ-phosphate of β-ATP, analogous to the similar reaction of the structurally related UMP kinase. The formed instable phosphoric-molybdic anhydride becomes immediately hydrolyzed and, according to the current data, the released and accelerated molybdate is pressed through the cage wall, presumably by turning aside the Metβ149 side chain. A structural comparison between MoSto and UMP kinase provides valuable insight into how an enzyme is converted into a molecular machine during evolution. The postulated direct conversion of chemical energy into kinetic energy via an activating molybdate kinase and an exothermic pyrophosphatase reaction to overcome a proteinous barrier represents a novelty in ATP-fueled biochemistry, because normally, ATP hydrolysis initiates large-scale conformational changes to drive a distant process.
History
DepositionApr 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Molybdenum storage protein subunit beta
A: Molybdenum storage protein subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,00011
Polymers57,4512
Non-polymers1,5499
Water4,576254
1
B: Molybdenum storage protein subunit beta
A: Molybdenum storage protein subunit alpha
hetero molecules

B: Molybdenum storage protein subunit beta
A: Molybdenum storage protein subunit alpha
hetero molecules

B: Molybdenum storage protein subunit beta
A: Molybdenum storage protein subunit alpha
hetero molecules

B: Molybdenum storage protein subunit beta
A: Molybdenum storage protein subunit alpha
hetero molecules

B: Molybdenum storage protein subunit beta
A: Molybdenum storage protein subunit alpha
hetero molecules

B: Molybdenum storage protein subunit beta
A: Molybdenum storage protein subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,00066
Polymers344,70612
Non-polymers9,29454
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Unit cell
Length a, b, c (Å)116.390, 116.390, 237.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11B-439-

HOH

21A-410-

HOH

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Components

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Molybdenum storage protein subunit ... , 2 types, 2 molecules BA

#1: Protein Molybdenum storage protein subunit beta / MoSto subunit beta


Mass: 28205.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Gene: mosB, Avin_43210 / Variant: DJ / ATCC BAA-1303 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P84253
#2: Protein Molybdenum storage protein subunit alpha / Mo storage protein subunit alpha / MoSto subunit alpha


Mass: 29245.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Gene: mosA, Avin_43200 / Variant: DJ / ATCC BAA-1303 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P84308

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Non-polymers , 5 types, 263 molecules

#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 4.04 Å3/Da / Density % sol: 69.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M Na-citrate, pH 5.6, 1 M ammonium phosphate, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.738 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.738 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 104313 / % possible obs: 99.4 % / Redundancy: 8.1 % / Net I/σ(I): 13.4
Reflection shellResolution: 2.1→2.2 Å / Num. unique obs: 13361

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4ndo

4ndo


Resolution: 2.1→49.298 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.213 2793 5.01 %
Rwork0.1872 --
obs0.1885 55719 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→49.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3797 0 89 254 4140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043992
X-RAY DIFFRACTIONf_angle_d0.7745459
X-RAY DIFFRACTIONf_dihedral_angle_d10.3243243
X-RAY DIFFRACTIONf_chiral_restr0.049634
X-RAY DIFFRACTIONf_plane_restr0.005705
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.13630.34211230.36052523X-RAY DIFFRACTION96
2.1363-2.17520.33631300.32812555X-RAY DIFFRACTION97
2.1752-2.2170.44551170.40932570X-RAY DIFFRACTION98
2.217-2.26230.40011520.37712574X-RAY DIFFRACTION98
2.2623-2.31140.36191250.3042579X-RAY DIFFRACTION99
2.3114-2.36520.2531390.2492599X-RAY DIFFRACTION99
2.3652-2.42440.27391540.21672615X-RAY DIFFRACTION99
2.4244-2.48990.23751630.20292563X-RAY DIFFRACTION99
2.4899-2.56320.22581300.19092614X-RAY DIFFRACTION99
2.5632-2.64590.2051390.18352633X-RAY DIFFRACTION100
2.6459-2.74050.22141420.1912618X-RAY DIFFRACTION100
2.7405-2.85020.22651450.18872639X-RAY DIFFRACTION100
2.8502-2.97990.1891350.18452660X-RAY DIFFRACTION100
2.9799-3.13690.20411590.17982650X-RAY DIFFRACTION100
3.1369-3.33340.20271310.1782672X-RAY DIFFRACTION100
3.3334-3.59080.19851280.16752691X-RAY DIFFRACTION100
3.5908-3.9520.19611280.16192725X-RAY DIFFRACTION100
3.952-4.52350.17441480.14662723X-RAY DIFFRACTION100
4.5235-5.69780.17971550.16312754X-RAY DIFFRACTION100
5.6978-49.31160.20571500.19032969X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.11980.6918-4.23441.24780.01856.63790.09810.5560.4063-0.1090.01270.3494-0.23-1.049-0.04120.32490.0102-0.07830.4383-0.00520.393925.23827.939220.4157
24.1902-1.28220.59812.23550.04592.3139-0.04530.13970.0419-0.21570.0599-0.22760.04830.04370.02950.3818-0.03010.00350.3124-0.0570.327660.496810.61039.3336
30.46260.1325-0.45460.6069-0.59461.96310.0620.0392-0.01160.0604-0.01470.1073-0.1435-0.0495-0.04510.3517-0.0036-0.0050.297-0.02890.344854.667816.255422.6825
43.5615-0.6131-1.50322.13791.29392.7659-0.1725-0.2513-0.230.07570.03030.18660.2457-0.07220.15140.3486-0.0132-0.01530.3173-0.02520.317244.52994.176312.3992
53.301-2.60920.34043.65-0.98921.45950.00030.0021-0.13290.171-0.05510.2093-0.0029-0.1170.03460.2773-0.03670.01220.3329-0.00430.268137.794330.426748.1697
60.26710.24690.26570.23590.08410.9607-0.04010.03340.0958-0.004-0.02150.0381-0.0150.04620.08010.29190.0134-0.00140.3378-0.0030.326737.845533.925835.1525
73.299-1.42122.00252.4837-0.5321.95870.13760.3999-0.4996-0.2724-0.0278-0.06160.13660.1661-0.05880.3771-0.0260.05250.393-0.00740.419751.881229.917942.7437
80.9538-0.04621.00570.40170.72871.8129-0.05490.0364-0.0438-0.12390.047-0.0268-0.0856-0.02240.01490.2351-0.02690.01290.2461-0.01050.242239.422523.458236.677
92.15540.4328-2.87862.062-1.53254.2963-0.07830.2957-0.2648-0.34230.13041.1711-0.1063-0.5712-0.10480.3530.0064-0.08030.5009-0.01850.559717.456426.299841.228
108.1154-3.8129-0.73136.63051.00993.5085-0.13010.0864-0.368-0.29940.0681.01230.2456-0.59090.01410.4399-0.1037-0.01080.51690.00590.542418.993916.790143.4008
116.3736-5.10811.83065.6949-2.41834.87510.28490.1694-0.5748-0.4012-0.02650.34820.3291-0.495-0.25010.3291-0.0694-0.01280.3548-0.02740.357731.252114.985538.9774
122.72620.83120.32270.98891.85934.44760.0565-0.2074-0.02220.2088-0.03630.13430.2646-0.10120.00750.29720.00420.02940.36170.01970.316730.013327.093552.9393
133.7755-2.449-0.97883.02161.59172.7645-0.2396-0.22-0.50510.42220.26170.45150.6047-0.1171-0.0260.4096-0.04770.01820.40940.00120.44230.320814.100351.3712
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 3 through 37 )
2X-RAY DIFFRACTION2chain 'B' and (resid 38 through 68 )
3X-RAY DIFFRACTION3chain 'B' and (resid 69 through 168 )
4X-RAY DIFFRACTION4chain 'B' and (resid 169 through 270 )
5X-RAY DIFFRACTION5chain 'A' and (resid 33 through 68 )
6X-RAY DIFFRACTION6chain 'A' and (resid 69 through 123 )
7X-RAY DIFFRACTION7chain 'A' and (resid 124 through 143 )
8X-RAY DIFFRACTION8chain 'A' and (resid 144 through 190 )
9X-RAY DIFFRACTION9chain 'A' and (resid 191 through 204 )
10X-RAY DIFFRACTION10chain 'A' and (resid 205 through 221 )
11X-RAY DIFFRACTION11chain 'A' and (resid 222 through 243 )
12X-RAY DIFFRACTION12chain 'A' and (resid 244 through 261 )
13X-RAY DIFFRACTION13chain 'A' and (resid 262 through 276 )

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