9N50 | pdb_00009n50

Crosslinked Crystal Structure of Human Mitochondrial Ketosynthase, OXSM, and Crosslinker-crypto Human Mitochondrial Acyl Carrier Protein, C8aBr-mACP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 
    0.220 (Depositor), 0.254 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Role of Human Mitochondrial Ketosynthase in Long-Chain Fatty Acid Biosynthesis.

Suo, Y.Jiang, Z.Heberlig, G.W.Wang, E.Y.Sankaran, B.La Clair, J.J.Burkart, M.D.

(2025) J Am Chem Soc 147: 33248-33255

  • DOI: https://doi.org/10.1021/jacs.5c10318
  • Primary Citation of Related Structures:  
    9N50, 9N51

  • PubMed Abstract: 

    Although ketosynthases in bacterial type II fatty acid biosynthesis have been extensively studied, the human mitochondrial ketosynthase, OXSM, remains incompletely characterized. Contrary to the assumption that the role of mitochondrial fatty acid biosynthesis is limited to the production of the lipoic acid precursor octanoate, recent studies suggest an ability to produce longer chain fatty acids. Here, we employ covalent, dual site-selective cross-linkers to trap the interactions between OXSM and its mitochondrial acyl carrier protein partner, mACP. Two high-resolution crystal structures that capture OXSM bound to mACP provide molecular details of the conformational changes that guide the chain elongation process. We identify key protein • protein and protein • substrate interactions that regulate the transacylation and condensation steps associated with this process. We also observe a conserved gating mechanism previously identified in bacterial type II ketosynthases. Complemented by site-directed mutagenesis and activity analyses, these findings provide detailed insight into the selectivity of the OXSM substrate. This study explores how the OXSM can elongate fatty acids larger than eight carbons, mirroring that of its bacterial type II progenitor.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92037-0358, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-oxoacyl-[acyl-carrier-protein] synthase, mitochondrial
A, B
425Homo sapiensMutation(s): 0 
Gene Names: OXSM
EC: 2.3.1.41
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWU1 (Homo sapiens)
Explore Q9NWU1 
Go to UniProtKB:  Q9NWU1
PHAROS:  Q9NWU1
GTEx:  ENSG00000151093 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NWU1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrial88Homo sapiensMutation(s): 0 
Gene Names: NDUFAB1
UniProt & NIH Common Fund Data Resources
Find proteins for O14561 (Homo sapiens)
Explore O14561 
Go to UniProtKB:  O14561
PHAROS:  O14561
GTEx:  ENSG00000004779 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14561
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BMZ (Subject of Investigation/LOI)
Query on A1BMZ

Download Ideal Coordinates CCD File 
D [auth C]N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-octanamidoethyl)-beta-alaninamide
C19 H38 N3 O8 P
ZIGJSYVYXLXQHO-KRWDZBQOSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work:  0.220 (Depositor), 0.254 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.947α = 90
b = 119.437β = 103.29
c = 78.874γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesAG073807

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-24
    Type: Initial release