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- EMDB-63586: E. coli MaeB holo form ME domain dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-63586
TitleE. coli MaeB holo form ME domain dimer
Map data
Sample
  • Complex: Malic enzyme B from Escherichia coli holo form
    • Protein or peptide: NADP-dependent malic enzyme
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsoxidoreductase / cryo-EM / allostery / STRUCTURAL PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsSassa M / Yamato H / Tanino H / Fukuda Y / Inoue T
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: J Biol Chem / Year: 2025
Title: Divergent acetyl-CoA binding modes mediate allosteric inhibition of bacterial hybrid-type malic enzymes.
Authors: Munetoshi Sassa / Haruka Yamato / Hiroki Tanino / Yohta Fukuda / Tsuyoshi Inoue /
Abstract: Malic enzymes (MEs) function as the bypass enzyme in the Krebs cycle and have attracted attention in a wide range of scientific and industrial fields. In contrast to eukaryotic MEs, there is ...Malic enzymes (MEs) function as the bypass enzyme in the Krebs cycle and have attracted attention in a wide range of scientific and industrial fields. In contrast to eukaryotic MEs, there is currently a lack of understanding of the structure-function relationships of prokaryotic MEs. Especially, little is known about an allosteric inhibition mechanism by an effector ligand in multi-domain MEs called hybrid-type MEs. Many bacterial hybrid-type MEs are inhibited by acetyl-CoA; however, the proposed acetyl-CoA binding site is not conserved. Here, we determined crystal and cryo-EM structures of hybrid-type MEs from Escherichia coli (EcMaeB) and Bdellovibrio bacteriovorus including complexes with acetyl-CoA. They reveal that these MaeBs have totally different acetyl-CoA binding sites and show different overall structural changes. However, the binding acetyl-CoA molecules induce identical movements of several α helices near the ligand both in EcMaeB and BbMaeB. Enzymatic assays proved that residues at the acetyl-CoA binding site are needed for inhibition. Phylogenetic analysis uncovered that EcMaeB and BbMaeB are classified into different clades of hybrid-type MEs and that the amino acid residues at the acetyl-CoA binding sites in different clades have evolved exclusively from each other. These results not only provide insights into bacterial MEs but also expand our knowledge about allosteric regulation in enzymes.
History
DepositionFeb 27, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63586.png

Downloads & links

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Map

FileDownload / File: emd_63586.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.249
Minimum - Maximum-1.5708923 - 2.825721
Average (Standard dev.)-0.00010359707 (±0.018651268)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 424.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63586_msk_1.map
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Mask #2

Fileemd_63586_msk_2.map
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Mask #3

Fileemd_63586_msk_3.map
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Half map: #2

Fileemd_63586_half_map_1.map
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Half map: #1

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Sample components

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Entire : Malic enzyme B from Escherichia coli holo form

EntireName: Malic enzyme B from Escherichia coli holo form
Components
  • Complex: Malic enzyme B from Escherichia coli holo form
    • Protein or peptide: NADP-dependent malic enzyme
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Malic enzyme B from Escherichia coli holo form

SupramoleculeName: Malic enzyme B from Escherichia coli holo form / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: NADP-dependent malic enzyme

MacromoleculeName: NADP-dependent malic enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+)
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 47.459816 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: DDQLKQSALD FHEFPVPGKI QVSPTKPLAT QRDLALAYSP GVAAPCLEIE KDPLKAYKYT ARGNLVAVIS NGTAVLGLGN IGALAGKPV MEGKGVLFKK FAGIDVFDIE VDELDPDKFI EVVAALEPTF GGINLEDIKA PECFYIEQKL RERMNIPVFH D DQHGTAII ...String:
DDQLKQSALD FHEFPVPGKI QVSPTKPLAT QRDLALAYSP GVAAPCLEIE KDPLKAYKYT ARGNLVAVIS NGTAVLGLGN IGALAGKPV MEGKGVLFKK FAGIDVFDIE VDELDPDKFI EVVAALEPTF GGINLEDIKA PECFYIEQKL RERMNIPVFH D DQHGTAII STAAILNGLR VVEKNISDVR MVVSGAGAAA IACMNLLVAL GLQKHNIVVC DSKGVIYQGR EPNMAETKAA YA VVDDGKR TLDDVIEGAD IFLGCSGPKV LTQEMVKKMA RAPMILALAN PEPEILPPLA KEVRPDAIIC TGRSDYPNQV NNV LCFPFI FRGALDVGAT AINEEMKLAA VRAIAELAHA EQSEVVASAY GDQDLSFGPE YIIPKPFDPR LIVKIAPAVA KAAM ESGVA TRPIADFDVY IDKLTEFVYK TNLFMKPIFS QARK

UniProtKB: NADP-dependent malic enzyme

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Macromolecule #2: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: NAP
Molecular weightTheoretical: 743.405 Da
Chemical component information

ChemComp-NAP:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
1.0 mMMgCl2sodium magnesium
3.0 mMNADP+nicotinamide adenine dinucleotide phosphate
20.0 mMHEPES
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.007 kPa / Details: 20 mA current
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Details: 3 microliters droplet, 3 seconds delay before blotting, 3 seconds blot, 0 second delay before plunging..

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 7099 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: NONE
Startup modelType of model: OTHER
Details: The crystal structure of E. coli MaeB apo form was used as a startup model.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 376425
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

SoftwareName: UCSF Chimera
Output model

PDB-9m2i:
E. coli MaeB holo form ME domain dimer

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