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- EMDB-27945: Cryo-EM structure of human ME3 in the presence of citrate -

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Basic information

Entry
Database: EMDB / ID: EMD-27945
TitleCryo-EM structure of human ME3 in the presence of citrate
Map data
Sample
  • Complex: Cryo-EM structure human ME3 in the presence of NADP
    • Protein or peptide: NADP-dependent malic enzyme, mitochondrial
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
KeywordsME1 / ME2 / ME3 / NAD(P)-dependent malic enzymes / integrated structural techniques / crystal structures / cryo-EM structures / drug discovery / allosteric mechanism / HYDROLASE
Function / homology
Function and homology information


malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) / oxygen metabolic process / malate dehydrogenase (decarboxylating) (NADP+) activity / malic enzyme activity / oxaloacetate decarboxylase activity / malate metabolic process / Pyruvate metabolism / pyruvate metabolic process / NADP+ binding / aerobic respiration ...malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) / oxygen metabolic process / malate dehydrogenase (decarboxylating) (NADP+) activity / malic enzyme activity / oxaloacetate decarboxylase activity / malate metabolic process / Pyruvate metabolism / pyruvate metabolic process / NADP+ binding / aerobic respiration / NAD binding / mitochondrial matrix / mitochondrion / metal ion binding
Similarity search - Function
Malic enzyme, conserved site / Malic enzymes signature. / Malic oxidoreductase / 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 ...Malic enzyme, conserved site / Malic enzymes signature. / Malic oxidoreductase / 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, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsYu X / Grell TAJ / Shaffer PL / Steele R / Sharma S / Thompson AA / Tresadern G / Ortiz-Meoz RF / Mason M / Gomez-Tamayo JC ...Yu X / Grell TAJ / Shaffer PL / Steele R / Sharma S / Thompson AA / Tresadern G / Ortiz-Meoz RF / Mason M / Gomez-Tamayo JC / Riley D / Wagner MV / Wadia J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Heliyon / Year: 2022
Title: Integrative structural and functional analysis of human malic enzyme 3: A potential therapeutic target for pancreatic cancer.
Authors: Tsehai A J Grell / Mark Mason / Aaron A Thompson / Jose Carlos Gómez-Tamayo / Daniel Riley / Michelle V Wagner / Ruth Steele / Rodrigo F Ortiz-Meoz / Jay Wadia / Paul L Shaffer / Gary ...Authors: Tsehai A J Grell / Mark Mason / Aaron A Thompson / Jose Carlos Gómez-Tamayo / Daniel Riley / Michelle V Wagner / Ruth Steele / Rodrigo F Ortiz-Meoz / Jay Wadia / Paul L Shaffer / Gary Tresadern / Sujata Sharma / Xiaodi Yu /
Abstract: Malic enzymes (ME1, ME2, and ME3) are involved in cellular energy regulation, redox homeostasis, and biosynthetic processes, through the production of pyruvate and reducing agent NAD(P)H. Recent ...Malic enzymes (ME1, ME2, and ME3) are involved in cellular energy regulation, redox homeostasis, and biosynthetic processes, through the production of pyruvate and reducing agent NAD(P)H. Recent studies have implicated the third and least well-characterized isoform, mitochondrial NADP-dependent malic enzyme 3 (ME3), as a therapeutic target for pancreatic cancers. Here, we utilized an integrated structure approach to determine the structures of ME3 in various ligand-binding states at near-atomic resolutions. ME3 is captured in the open form existing as a stable tetramer and its dynamic Domain C is critical for activity. Catalytic assay results reveal that ME3 is a non-allosteric enzyme and does not require modulators for activity while structural analysis suggests that the inner stability of ME3 Domain A relative to ME2 disables allostery in ME3. With structural information available for all three malic enzymes, the foundation has been laid to understand the structural and biochemical differences of these enzymes and could aid in the development of specific malic enzyme small molecule drugs.
History
DepositionAug 25, 2022-
Header (metadata) releaseFeb 8, 2023-
Map releaseFeb 8, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27945.png

Downloads & links

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Map

FileDownload / File: emd_27945.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 200 pix.
= 208. Å		1.04 Å/pix.
x 200 pix.
= 208. Å		1.04 Å/pix.
x 200 pix.
= 208. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.017513607 - 0.060844254
Average (Standard dev.)0.0005048596 (±0.0035334732)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 208.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27945_msk_1.map
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Additional map: #1

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Additional map: #2

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Half map: #1

Fileemd_27945_half_map_1.map
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Half map: #2

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Sample components

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Entire : Cryo-EM structure human ME3 in the presence of NADP

EntireName: Cryo-EM structure human ME3 in the presence of NADP
Components
  • Complex: Cryo-EM structure human ME3 in the presence of NADP
    • Protein or peptide: NADP-dependent malic enzyme, mitochondrial
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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Supramolecule #1: Cryo-EM structure human ME3 in the presence of NADP

SupramoleculeName: Cryo-EM structure human ME3 in the presence of NADP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: NADP-dependent malic enzyme, mitochondrial

MacromoleculeName: NADP-dependent malic enzyme, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
EC number: malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.15125 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGAALGTGTR LAPWPGRACG ALPRWTPTAP AQGCHSKPGP ARPVPLKKRG YDVTRNPHLN KGMAFTLEER LQLGIHGLIP PCFLSQDVQ LLRIMRYYER QQSDLDKYII LMTLQDRNEK LFYRVLTSDV EKFMPIVYTP TVGLACQHYG LTFRRPRGLF I TIHDKGHL ...String:
MGAALGTGTR LAPWPGRACG ALPRWTPTAP AQGCHSKPGP ARPVPLKKRG YDVTRNPHLN KGMAFTLEER LQLGIHGLIP PCFLSQDVQ LLRIMRYYER QQSDLDKYII LMTLQDRNEK LFYRVLTSDV EKFMPIVYTP TVGLACQHYG LTFRRPRGLF I TIHDKGHL ATMLNSWPED NIKAVVVTDG ERILGLGDLG CYGMGIPVGK LALYTACGGV NPQQCLPVLL DVGTNNEELL RD PLYIGLK HQRVHGKAYD DLLDEFMQAV TDKFGINCLI QFEDFANANA FRLLNKYRNK YCMFNDDIQG TASVAVAGIL AAL RITKNK LSNHVFVFQG AGEAAMGIAH LLVMALEKEG VPKAEATRKI WMVDSKGLIV KGRSHLNHEK EMFAQDHPEV NSLE EVVRL VKPTAIIGVA AIAGAFTEQI LRDMASFHER PIIFALSNPT SKAECTAEKC YRVTEGRGIF ASGSPFKSVT LEDGK TFIP GQGNNAYVFP GVALGVIAGG IRHIPDEIFL LTAEQIAQEV SEQHLSQGRL YPPLSTIRDV SLRIAIKVLD YAYKHN LAS YYPEPKDKEA FVRSLVYTPD YDSFTLDSYT WPKEAMNVQT V

UniProtKB: NADP-dependent malic enzyme, mitochondrial

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Macromolecule #2: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAP
Molecular weightTheoretical: 743.405 Da
Chemical component information

ChemComp-NAP:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 174701
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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