5USR

Crystal structure of human NFS1-ISD11 in complex with E. coli acyl-carrier protein at 3.09 angstroms


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of human Fe-S assembly subcomplex reveals unexpected cysteine desulfurase architecture and acyl-ACP-ISD11 interactions.

Cory, S.A.Van Vranken, J.G.Brignole, E.J.Patra, S.Winge, D.R.Drennan, C.L.Rutter, J.Barondeau, D.P.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: E5325-E5334

  • DOI: 10.1073/pnas.1702849114

  • PubMed Abstract: 
  • In eukaryotes, sulfur is mobilized for incorporation into multiple biosynthetic pathways by a cysteine desulfurase complex that consists of a catalytic subunit (NFS1), LYR protein (ISD11), and acyl carrier protein (ACP). This NFS1-ISD11-ACP (SDA) com ...

    In eukaryotes, sulfur is mobilized for incorporation into multiple biosynthetic pathways by a cysteine desulfurase complex that consists of a catalytic subunit (NFS1), LYR protein (ISD11), and acyl carrier protein (ACP). This NFS1-ISD11-ACP (SDA) complex forms the core of the iron-sulfur (Fe-S) assembly complex and associates with assembly proteins ISCU2, frataxin (FXN), and ferredoxin to synthesize Fe-S clusters. Here we present crystallographic and electron microscopic structures of the SDA complex coupled to enzyme kinetic and cell-based studies to provide structure-function properties of a mitochondrial cysteine desulfurase. Unlike prokaryotic cysteine desulfurases, the SDA structure adopts an unexpected architecture in which a pair of ISD11 subunits form the dimeric core of the SDA complex, which clarifies the critical role of ISD11 in eukaryotic assemblies. The different quaternary structure results in an incompletely formed substrate channel and solvent-exposed pyridoxal 5'-phosphate cofactor and provides a rationale for the allosteric activator function of FXN in eukaryotic systems. The structure also reveals the 4'-phosphopantetheine-conjugated acyl-group of ACP occupies the hydrophobic core of ISD11, explaining the basis of ACP stabilization. The unexpected architecture for the SDA complex provides a framework for understanding interactions with acceptor proteins for sulfur-containing biosynthetic pathways, elucidating mechanistic details of eukaryotic Fe-S cluster biosynthesis, and clarifying how defects in Fe-S cluster assembly lead to diseases such as Friedreich's ataxia. Moreover, our results support a lock-and-key model in which LYR proteins associate with acyl-ACP as a mechanism for fatty acid biosynthesis to coordinate the expression, Fe-S cofactor maturation, and activity of the respiratory complexes.


    Organizational Affiliation

    Department of Chemistry, Texas A&M University, College Station, TX 77842.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cysteine desulfurase, mitochondrial
A, C, E, G
426Homo sapiensMutation(s): 0 
Gene Names: NFS1 (NIFS)
EC: 2.8.1.7
Find proteins for Q9Y697 (Homo sapiens)
Go to Gene View: NFS1
Go to UniProtKB:  Q9Y697
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LYR motif-containing protein 4
B, D, F, H
91Homo sapiensMutation(s): 1 
Gene Names: LYRM4 (C6orf149, ISD11)
Find proteins for Q9HD34 (Homo sapiens)
Go to Gene View: LYRM4
Go to UniProtKB:  Q9HD34
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Acyl carrier protein
I, J, K, L
78Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: acpP
Find proteins for P0A6A8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6A8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8Q1
Query on 8Q1

Download SDF File 
Download CCD File 
I, J, K, L
S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
S-dodecanoyl-4'-phosphopantetheine
C23 H45 N2 O8 P S
MVHUOSAYFQKAMT-NRFANRHFSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A, C, E, G
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 125.484α = 90.00
b = 147.780β = 90.00
c = 168.454γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXphasing
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM096100
National Science Foundation (United States)United StatesCHE 1508269
Robert A. WelchUnited StatesA-1647

Revision History 

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-07-05
    Type: Database references
  • Version 1.2: 2017-07-12
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence