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- PDB-9ejn: Crystal structure of magnesium-transporting ATPase MgtA in an E1-... -

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Basic information

Entry
Database: PDB / ID: 9ejn
TitleCrystal structure of magnesium-transporting ATPase MgtA in an E1-like magnesium-bound state
ComponentsMagnesium-transporting ATPase, P-type 1
KeywordsMETAL TRANSPORT / Membrane protein / P-Type Atpase / Magnesium Ion
Function / homology
Function and homology information


P-type Mg2+ transporter / P-type magnesium transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
P-type ATPase, subfamily IIIB / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / P-type ATPase, cytoplasmic domain N / : / P-type ATPase actuator domain / P-type ATPase, haloacid dehalogenase domain ...P-type ATPase, subfamily IIIB / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / P-type ATPase, cytoplasmic domain N / : / P-type ATPase actuator domain / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Magnesium-transporting ATPase, P-type 1
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis CV56 (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 Å
AuthorsKhan, M.B. / Primeau, J.O. / Basu, P.C. / Morth, J.P. / Lemieux, M.J. / Young, H.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Res Sq / Year: 2026
Title: Distinct transport cycle and lipid regulation of a Mg2+-transporting P-type ATPase, MgtA.
Authors: Howard Young / Muhammad Bashir Khan / Joseph Primeau / Paramita Chaudhuri-Basu / Lucie Bergdoll / Ludovic Renault / J Preben Morth / M Joanne Lemieux
Abstract: P-type ATPases represent an evolutionarily conserved superfamily of ion, lipid, and peptide pumps found across all domains of life. Among the substrates transported by P-type ATPases, Mg2+ is of ...P-type ATPases represent an evolutionarily conserved superfamily of ion, lipid, and peptide pumps found across all domains of life. Among the substrates transported by P-type ATPases, Mg2+ is of critical importance in bacterial, fungal, and plant cellular homeostasis. A bacterial P-type ATPase found in Gram-negative bacteria, Mg2+ transporter A (MgtA), facilitates the transport of Mg2+ from the periplasm to the cytoplasm under conditions of Mg2+ starvation. MgtA is a cardiolipin-sensitive integral membrane ion-transporter that scavenges Mg2+ during bacterial infection and pathogenesis. Here, we determined cryo-EM structures of MgtA capturing three distinct states along the Mg2+ transport cycle, including a phosphorylated E2-P intermediate (2.6 Å resolution), an E1-like conformation stabilized by the peptide regulator MgtR (2.7 Å resolution), and an E1-like ATP-bound state (2.8 Å resolution). These three conformations reveal the binding of Mg2+ in the transmembrane domain coordinated in a novel site involving Ser702 and Asn706 on M5, Ser773 and Asp777 on M7, and Ser821 and Thr824 on M8. In the E2-P conformation, the phosphate analog BeF3 is bound in close proximity to the catalytic aspartate, Asp361, suggesting that it represents a covalent aspartylphosphate intermediate. In the presence of AMPPCP, Mg2+ remains bound in the transmembrane domain and the ATP analog is bound in a catalytically competent conformation. Overall, the structures reveal distinct steps in the transport cycle of MgtA compared to other P-type ATPases, as well as lipid binding sites that fill gaps in our understanding of transport regulation.
History
DepositionNov 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Database references / Structure summary / Category: audit_author / citation_author
Revision 1.2Jun 10, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Magnesium-transporting ATPase, P-type 1
C: Magnesium-transporting ATPase, P-type 1
B: Magnesium-transporting ATPase, P-type 1
D: Magnesium-transporting ATPase, P-type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)406,1138
Polymers406,0164
Non-polymers974
Water00
1
A: Magnesium-transporting ATPase, P-type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5282
Polymers101,5041
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Magnesium-transporting ATPase, P-type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5282
Polymers101,5041
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Magnesium-transporting ATPase, P-type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5282
Polymers101,5041
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Magnesium-transporting ATPase, P-type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5282
Polymers101,5041
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)180.403, 66.595, 218.666
Angle α, β, γ (deg.)90.000, 90.151, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Magnesium-transporting ATPase, P-type 1 / Mg(2+) transport ATPase / P-type 1


Mass: 101503.906 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis CV56 (lactic acid bacteria)
Gene: LL275_1350 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1V0NGB6, P-type Mg2+ transporter
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 3.24 Å3/Da / Density % sol: 61.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 4% tert-butanol, 100 mM MgSo4, 14% 2000 MME, 10% Glycerol, 100 mM MOPS pH 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.2→25 Å / Num. obs: 85323 / % possible obs: 99 % / Redundancy: 1.8 % / CC1/2: 0.85 / Net I/σ(I): 2
Reflection shellResolution: 3.21→3.25 Å / Num. unique obs: 7632 / CC1/2: 0.31

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.55→24.91 Å / SU ML: 0.5861 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 39.6881
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.339 3123 4.97 %
Rwork0.288 59678 -
obs0.2905 62801 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 98.1 Å2
Refinement stepCycle: LAST / Resolution: 3.55→24.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27348 0 4 0 27352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001927824
X-RAY DIFFRACTIONf_angle_d0.474337704
X-RAY DIFFRACTIONf_chiral_restr0.03864564
X-RAY DIFFRACTIONf_plane_restr0.00384704
X-RAY DIFFRACTIONf_dihedral_angle_d12.635710200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.55-3.610.38511660.3762643X-RAY DIFFRACTION99.29
3.61-3.660.4431360.37922751X-RAY DIFFRACTION99.93
3.66-3.730.41061270.36282729X-RAY DIFFRACTION99.1
3.73-3.790.43941600.35142660X-RAY DIFFRACTION99.75
3.79-3.870.38691830.33272686X-RAY DIFFRACTION98.79
3.87-3.950.33461210.30742769X-RAY DIFFRACTION99.62
3.95-4.030.37591340.29762645X-RAY DIFFRACTION99.5
4.03-4.120.30691100.28752820X-RAY DIFFRACTION99.63
4.13-4.230.33191590.28112675X-RAY DIFFRACTION98.99
4.23-4.340.34581280.27632713X-RAY DIFFRACTION99.3
4.34-4.470.34151730.26262680X-RAY DIFFRACTION97.94
4.47-4.610.3131590.26672577X-RAY DIFFRACTION97.06
4.61-4.780.32181370.25912606X-RAY DIFFRACTION93.91
4.78-4.970.28731460.25032713X-RAY DIFFRACTION99.27
4.97-5.190.27871470.25472763X-RAY DIFFRACTION99.59
5.19-5.460.32161460.2682712X-RAY DIFFRACTION99.44
5.46-5.80.34911130.27092760X-RAY DIFFRACTION99.45
5.8-6.240.33711340.28192769X-RAY DIFFRACTION99.49
6.24-6.860.32251260.30112756X-RAY DIFFRACTION98.73
6.86-7.820.31291440.26872772X-RAY DIFFRACTION99.08
7.82-9.750.25691290.23482672X-RAY DIFFRACTION94.15
9.75-24.910.36691450.31152807X-RAY DIFFRACTION96.47
Refinement TLS params.Method: refined / Origin x: -33.8549210642 Å / Origin y: -38.8854656566 Å / Origin z: -42.5361815016 Å
111213212223313233
T0.45703540038 Å2-0.0500227559867 Å20.0910159532009 Å2-0.413852000217 Å20.0766353837672 Å2--1.44483569538 Å2
L0.0118972369659 °20.0158413493282 °2-0.0934796054652 °2-0.0213783274418 °2-0.0137764065852 °2--0.203508778541 °2
S0.00204959926425 Å °-0.0789770143542 Å °0.031539537899 Å °0.13229511278 Å °0.00964812212038 Å °0.0174036093892 Å °-0.0604595653055 Å °0.000306326680849 Å °-0.0269621435351 Å °
Refinement TLS groupSelection details: all

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