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- PDB-8v3u: ACAD11 D220A with 4-hydroxyvaleryl-CoA -

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Basic information

Entry
Database: PDB / ID: 8v3u
TitleACAD11 D220A with 4-hydroxyvaleryl-CoA
ComponentsAcyl-Coenzyme A dehydrogenase family, member 11
KeywordsOXIDOREDUCTASE / acyl-CoA dehydrogenases / Dihedral / mitochondrial
Function / homology
Function and homology information


very-long-chain fatty acyl-CoA dehydrogenase activity / long-chain fatty acyl-CoA dehydrogenase activity / medium-chain fatty acyl-CoA dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / mitochondrial membrane / peroxisome / flavin adenine dinucleotide binding / nucleus
Similarity search - Function
Acyl-CoA dehydrogenase family member 10/11, N-terminal / : / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain ...Acyl-CoA dehydrogenase family member 10/11, N-terminal / : / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Protein kinase-like domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Acyl-CoA dehydrogenase family member 11
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsZhang, J. / Bartlett, A. / Rashan, E. / Yuan, P. / Pagliarini, D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM131795 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK098672 United States
Other private
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: ACAD10 and ACAD11 enable mammalian 4-hydroxy acid lipid catabolism.
Authors: Edrees H Rashan / Abigail K Bartlett / Daven B Khana / Jingying Zhang / Raghav Jain / Gina Wade / Luciano A Abriata / Andrew J Smith / Zakery N Baker / Taylor Cook / Alana Caldwell / Autumn ...Authors: Edrees H Rashan / Abigail K Bartlett / Daven B Khana / Jingying Zhang / Raghav Jain / Gina Wade / Luciano A Abriata / Andrew J Smith / Zakery N Baker / Taylor Cook / Alana Caldwell / Autumn R Chevalier / Patrick Forny / Brian F Pfleger / Matteo Dal Peraro / Peng Yuan / Daniel Amador-Noguez / Judith A Simcox / David J Pagliarini /
Abstract: Fatty acid β-oxidation is a central catabolic pathway with broad health implications. However, various fatty acids, including 4-hydroxy acids (4-HAs), are largely incompatible with β-oxidation ...Fatty acid β-oxidation is a central catabolic pathway with broad health implications. However, various fatty acids, including 4-hydroxy acids (4-HAs), are largely incompatible with β-oxidation machinery before being modified. Here we reveal that two atypical acyl-CoA dehydrogenases, ACAD10 and ACAD11, drive 4-HA catabolism in mice. Unlike other ACADs, ACAD10 and ACAD11 feature kinase domains that phosphorylate the 4-hydroxy position as a requisite step in converting 4-hydroxyacyl-CoAs into conventional 2-enoyl-CoAs. Through cryo-electron microscopy and molecular modeling, we identified an atypical dehydrogenase binding pocket capable of accommodating this phosphorylated intermediate. We further show that ACAD10 is mitochondrial and necessary for catabolizing shorter-chain 4-HAs, whereas ACAD11 is peroxisomal and enables longer-chain 4-HA catabolism. Mice lacking ACAD11 accumulate 4-HAs in their plasma and females are susceptible to body weight and fat gain, concurrent with decreased adipocyte differentiation and adipokine expression. Collectively, we present that ACAD10 and ACAD11 are the primary gatekeepers of mammalian 4-HA catabolism.
History
DepositionNov 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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 / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acyl-Coenzyme A dehydrogenase family, member 11
B: Acyl-Coenzyme A dehydrogenase family, member 11
C: Acyl-Coenzyme A dehydrogenase family, member 11
D: Acyl-Coenzyme A dehydrogenase family, member 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)352,2998
Polymers349,1574
Non-polymers3,1424
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Acyl-Coenzyme A dehydrogenase family, member 11


Mass: 87289.188 Da / Num. of mol.: 4 / Mutation: D220A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Acad11 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0R4J0I6
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
Has ligand of interestY
Has protein modificationN

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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: ACAD11 D220A with FAD and 4-hydroxyvaleryl-CoA / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
Details: 50mM HEPES, 50mM NaCl, 2% glycerol, 50uM FAD, 100uM 4-hydroxyvaleryl-CoA
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: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 54.06 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 2789

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Processing

EM software
IDNameVersionCategory
7Coot0.9.8model fitting
19PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 722751
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 242249 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 2WBI

2wbi


Accession code: 2WBI / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 28.47 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002712204
ELECTRON MICROSCOPYf_angle_d0.476916604
ELECTRON MICROSCOPYf_chiral_restr0.04171868
ELECTRON MICROSCOPYf_plane_restr0.00392088
ELECTRON MICROSCOPYf_dihedral_angle_d4.82961688

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