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- PDB-8jzo: CryoEM structure of the NADP-dependent malic enzyme MaeB -

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Basic information

Entry
Database: PDB / ID: 8jzo
TitleCryoEM structure of the NADP-dependent malic enzyme MaeB
ComponentsNADP-dependent malic enzyme
KeywordsLIPID BINDING PROTEIN / Type III secretion system / inositol phosphate phosphatase / bacteria effector
Function / homology
Function and homology information


malolactic enzyme activity / malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) / malate dehydrogenase (decarboxylating) (NADP+) activity / oxaloacetate decarboxylase activity / malate metabolic process / acyltransferase activity / NAD binding / manganese ion binding / identical protein binding / cytosol
Similarity search - Function
NAD(P)-dependent malic enzyme / Malic enzyme, NAD-binding domain, bacterial type / : / Phosphate acetyltransferase, domain 2 / Phosphate acetyltransferase, domain 1 / Phosphate acetyl/butaryl transferase / Phosphate acetyl/butaryl transferase / Malic enzyme, conserved site / Malic enzymes signature. / Malic enzyme, N-terminal domain ...NAD(P)-dependent malic enzyme / Malic enzyme, NAD-binding domain, bacterial type / : / Phosphate acetyltransferase, domain 2 / Phosphate acetyltransferase, domain 1 / Phosphate acetyl/butaryl transferase / Phosphate acetyl/butaryl transferase / Malic enzyme, conserved site / Malic enzymes signature. / Malic enzyme, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding / Malic enzyme, N-terminal domain superfamily / Malic enzyme, N-terminal domain / Malic enzyme, NAD binding domain / Malic enzyme, NAD binding domain / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP-dependent malic enzyme
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsJiang, W.X. / Cheng, X.Q. / Wu, M. / Ma, L.X. / Xing, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2021YFC2100100 China
CitationJournal: To Be Published
Title: CryoEM structure of the NADP-dependent malic enzyme in complex with oxaloacetate
Authors: Jiang, W.X. / Cheng, X.Q. / Wu, M. / Ma, L.X. / Xing, Q.
History
DepositionJul 6, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADP-dependent malic enzyme
B: NADP-dependent malic enzyme
C: NADP-dependent malic enzyme
D: NADP-dependent malic enzyme
E: NADP-dependent malic enzyme
F: NADP-dependent malic enzyme


Theoretical massNumber of molelcules
Total (without water)495,0446
Polymers495,0446
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "C"
d_2ens_1chain "B"
d_3ens_1chain "A"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 1 - 759 / Label seq-ID: 1 - 759

Dom-IDAuth asym-IDLabel asym-ID
d_1CC
d_2BB
d_3AA
d_4DD
d_5EE
d_6FF

NCS oper:
IDCodeMatrixVector
1given(0.764936670419, -0.644094605792, -0.00374553570375), (-0.644105413525, -0.764920692303, -0.00495487181191), (0.000326368442886, 0.00620268296949, -0.999980709918)93.3682654826, 256.369319724, 73.2594140908
2given(-0.501270454569, 0.865262884972, 0.00693334445881), (-0.86528084449, -0.501286845948, 0.000747153969125), (0.00412207897447, -0.00562476393872, 0.999975684952)75.0976288079, 253.080232512, 0.173636141904
3given(0.169703043673, 0.985438404926, 0.0105842839186), (0.985488772931, -0.169653219126, -0.00544643611109), (-0.00357146947492, 0.0113549697565, -0.999929152124)-12.078479945, 14.0298799631, 73.2545362398
4given(-0.498044476003, -0.867122873809, -0.0070442629615), (0.867129760933, -0.498073067863, 0.00303261842615), (-0.00613821046892, -0.00459791120278, 0.99997059036)256.848813655, 60.7790844983, 0.957664302389
5given(-0.939465750631, -0.342554084386, 0.00779760615749), (-0.342494467007, 0.939485394319, 0.00804573992216), (-0.0100818381679, 0.00488806013052, -0.999937229734)249.824460891, 43.9308442075, 74.3167746307

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Components

#1: Protein
NADP-dependent malic enzyme / NADP-ME


Mass: 82507.266 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: maeB, ypfF, b2463, JW2447
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P76558, malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: NADP-dependent malic enzyme / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Source (recombinant)Organism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 39 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108061 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 155.02 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003835310
ELECTRON MICROSCOPYf_angle_d0.588947904
ELECTRON MICROSCOPYf_chiral_restr0.04555562
ELECTRON MICROSCOPYf_plane_restr0.00496300
ELECTRON MICROSCOPYf_dihedral_angle_d7.88844884
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CCELECTRON MICROSCOPYNCS constraints0.041797325748
ens_1d_3CCELECTRON MICROSCOPYNCS constraints0.0417948235331
ens_1d_4CCELECTRON MICROSCOPYNCS constraints0.000707051411184
ens_1d_5CCELECTRON MICROSCOPYNCS constraints0.000707879292648
ens_1d_6CCELECTRON MICROSCOPYNCS constraints0.0417993318485

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