Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 270291.63 
• Atom Count: 15666 
• Residue Count: 2380 
• Unique protein chains: 3

5USR

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

• DOI: 10.2210/pdb5USR/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens, Escherichia coli (strain K12)
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): 1 


• Deposited: 2017-02-13 Released: 2017-06-21 
• Deposition Author(s): Cory, S.A., Barondeau, D.P.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences; National Science Foundation (United States); Robert A. Welch 

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Experimental Data Snapshot

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

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

• PubMed: 28634302 
• 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) 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cysteine desulfurase, mitochondrial	A, C, E, G	426	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
LYR motif-containing protein 4	B, D, F, H	91	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Acyl carrier protein	I, J, K, L	78	Escherichia 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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
8Q1	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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, C, E, G	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

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 = 125.484	α = 90.00
b = 147.780	β = 90.00
c = 168.454	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
PHENIX	phasing
PDB_EXTRACT	data extraction
SCALEPACK	data scaling
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-02-13 
• Released Date: 2017-06-21 
• Deposition Author(s): Cory, S.A., Barondeau, D.P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences	United States	R01GM096100
National Science Foundation (United States)	United States	CHE 1508269
Robert A. Welch	United States	A-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