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- EMDB-62542: B. bacteriovorus MaeB acetyl-CoA bound form -

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Basic information

Entry
Database: EMDB / ID: EMD-62542
TitleB. bacteriovorus MaeB acetyl-CoA bound form
Map data
Sample
  • Complex: Malic enzyme B from Bdellovibrio bacteriovorus strain SSB218315 acetyl-CoA bound form
    • Protein or peptide: NADP-dependent malic enzyme
  • Ligand: ACETYL COENZYME *A
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: water
Keywordsoxidoreductase / cryo-EM / allostery / STRUCTURAL PROTEIN
Function / homology
Function and homology information


malic enzyme activity / malate metabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / acyltransferase activity / NAD binding / metal ion binding
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, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding ...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, 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 speciesBdellovibrio bacteriovorus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 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
DepositionNov 28, 2024-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62542.png

Downloads & links

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Map

FileDownload / File: emd_62542.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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: 0.165
Minimum - Maximum-0.80315936 - 1.2240831
Average (Standard dev.)0.00015777665 (±0.022680972)
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_62542_msk_1.map
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Mask #2

Fileemd_62542_msk_2.map
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Mask #3

Fileemd_62542_msk_3.map
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Half map: #2

Fileemd_62542_half_map_1.map
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Half map: #1

Fileemd_62542_half_map_2.map
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Sample components

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Entire : Malic enzyme B from Bdellovibrio bacteriovorus strain SSB218315 a...

EntireName: Malic enzyme B from Bdellovibrio bacteriovorus strain SSB218315 acetyl-CoA bound form
Components
  • Complex: Malic enzyme B from Bdellovibrio bacteriovorus strain SSB218315 acetyl-CoA bound form
    • Protein or peptide: NADP-dependent malic enzyme
  • Ligand: ACETYL COENZYME *A
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: water

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Supramolecule #1: Malic enzyme B from Bdellovibrio bacteriovorus strain SSB218315 a...

SupramoleculeName: Malic enzyme B from Bdellovibrio bacteriovorus strain SSB218315 acetyl-CoA bound form
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bdellovibrio bacteriovorus (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: 6 / Enantiomer: LEVO
Source (natural)Organism: Bdellovibrio bacteriovorus (bacteria)
Molecular weightTheoretical: 84.36593 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: METKTETKTG TTNFDQEALL YHQQGKPGKI EVISSKPCAT EKDLSLAYSP GVAAPCKAIA KDPAKVYDYT AKGNLVAVIS NGTAVLGLG NIGPAAGKPV MEGKGILFKQ FAGIDVFDIE VAATDVDTFC NAVRVLEPTF GGINLEDIKA PECFEIEERL K KEMNIPVF ...String:
METKTETKTG TTNFDQEALL YHQQGKPGKI EVISSKPCAT EKDLSLAYSP GVAAPCKAIA KDPAKVYDYT AKGNLVAVIS NGTAVLGLG NIGPAAGKPV MEGKGILFKQ FAGIDVFDIE VAATDVDTFC NAVRVLEPTF GGINLEDIKA PECFEIEERL K KEMNIPVF HDDQHGTAIV SGAALLNACS ITNRKMEDMR IVVNGAGASA NSCAKIFIAL GARRENIIMC DSQGVIYKGR TA GMNKYKE YFASETEART LTEALRGADV FVGLSVAGAL TPEMLKDMAK DPIIFAMANP EPEITPDKAR AARPDAIIAT GRS DYPNQV NNVLGFPSIF RGALDTRSTQ INEEMKLAAV HALAKLARMD VPDKVSATYG GKSFKFGRDY LIPKPFDTRV LLWV APEVA KAAMKSGVAT RAIEDWDQYR ESLEAQQGPS KVFIRSAINR VHQNSEANGG ELPRIVFPEG TSTKVLKALA TLVEE RICQ PILLGYPERV KEKIKALDIP LLNDVQIVHP SSHPKYFSFV EKLYSLRQRK GINLGEAERL MADPNYFAAM MVNMGE ADG MVSGSSINYA DAVRPILQTI GTYKEGIPAG LNFVLLEDKF LVLADTTVNF NPSAEQCAQI ALQAAKIVEY FGIEPRV AM LSYSNFSGAE GTPRKMKKAA EIARTLRPDL MIEGDMQADT AVNPEIMERL FPFSGLKGGA NVLVFPNLES SNIAYKLI Q QIGKAEVIGP FLTGVRRSAN VLQRTTTVDG IVNSVVFTAL EAQFIKDALK ARGKK

UniProtKB: NADP-dependent malic enzyme

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Macromolecule #2: ACETYL COENZYME *A

MacromoleculeName: ACETYL COENZYME *A / type: ligand / ID: 2 / Number of copies: 12 / Formula: ACO
Molecular weightTheoretical: 809.571 Da
Chemical component information

ChemComp-ACO:
ACETYL COENZYME *A

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Macromolecule #3: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / type: ligand / ID: 3 / 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 #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 6 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
0.06 mMacetyl-coenzyme A
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: 13724 / 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: PDB ENTRY
PDB model - PDB ID:

6zng


Details: The crystal structure of MaeB acetyl-CoA bound form B. bacteriovorus strain HD100 (PDB code ID: 6ZNG) was used as a startup model.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 165921
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-9krv:
B. bacteriovorus MaeB acetyl-CoA bound form

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