8TRW | pdb_00008trw

Structure of human LIAS

• PDB DOI: https://doi.org/10.2210/pdb8TRW/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia
• Mutation(s): No 


• Deposited: 2023-08-10 Released: 2025-06-11 
• Deposition Author(s): Esakova, O.A., Warui, D.M., Neti, S.S., Alumasa, J.N., Booker, S.J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States), Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Literature

Structural basis for catalysis by human lipoyl synthase.

Esakova, O.A., Warui, D.M., Neti, S.S., Alumasa, J.N., Booker, S.J.

(2025) Nat Commun 16: 6355-6355

• PubMed: 40640146 
• DOI: https://doi.org/10.1038/s41467-025-61393-x
• Primary Citation of Related Structures:  
  8TRW, 8TSK, 8UGO, 8V0J, 9C19


• PubMed Abstract: 
  

  Lipoic acid is an essential cofactor in five mitochondrial multiprotein complexes. In each complex, it is tethered in an amide linkage to the side chain of a conserved lysyl residue on a lipoyl carrier protein or lipoyl domain to afford the lipoyl cofactor. Lipoyl synthase catalyzes the last step in the biosynthesis of the lipoyl cofactor, the addition of two sulfur atoms to carbons 6 and 8 of an octanoyllysyl residue of the H protein, the lipoyl carrier protein of the glycine cleavage system. Lipoyl synthase, a member of the radical S-adenosylmethionine superfamily, contains two [Fe ₄ S ₄ ] clusters, one of which is sacrificed during catalysis to supply the appended sulfur atoms. Herein, we use X-ray crystallography to characterize several stages in lipoyl synthase catalysis and present a structure of an intermediate wherein the enzyme is cross-linked to the H protein substrate through a 6-mercaptooctanoyl ligand to a [Fe ₃ S ₄ ] cluster.

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Organizational Affiliation: 
• Department of Chemistry, The Pennsylvania State University, University Park, PA, USA. [e-mail].
Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA. [e-mail].
Department of Chemistry, The Pennsylvania State University, University Park, PA, USA.
Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA.
Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA.
Department of Chemistry, The Pennsylvania State University, University Park, PA, USA. [e-mail].
Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA. [e-mail].
Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, USA. [e-mail].
Howard Hughes Medical Institute, Chevy Chase, MD, USA. [e-mail].
Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 42.84 kDa 
• Atom Count: 2,849 
• Modeled Residue Count: 294 
• Deposited Residue Count: 368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoyl synthase, mitochondrial	A	368	Homo sapiens	Mutation(s): 0  Gene Names: LIAS EC: 2.8.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for O43766 (Homo sapiens) Explore O43766  Go to UniProtKB:  O43766
PHAROS:  O43766 GTEx:  ENSG00000121897

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose	B [auth E]	2		N/A
Glycosylation Resources
GlyTouCan:  G92130SN GlyCosmos:  G92130SN

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4 (Subject of Investigation/LOI)	E [auth A], F [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
DTT	C [auth A]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.353	α = 90
b = 88.789	β = 90
c = 108.166	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-11 
Deposition Author(s): Esakova, O.A., Warui, D.M., Neti, S.S., Alumasa, J.N., Booker, S.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM-122595
National Science Foundation (NSF, United States)	United States	MCB1716686
Howard Hughes Medical Institute (HHMI)	United States	SJB

Revision History  

• Version 1.0: 2025-06-11
  Type: Initial release
  
• Version 1.1: 2026-03-04
  Changes: Database references