5WKP

Crystal Structure of the Human mitochondrial Cysteine Desulfurase in complex with ISD11 and Iron-Sulfur Cluster Scaffold Protein ISCU1, and E. coli ACP1 protein at 3.15A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure and functional dynamics of the mitochondrial Fe/S cluster synthesis complex.

Boniecki, M.T.Freibert, S.A.Muhlenhoff, U.Lill, R.Cygler, M.

(2017) Nat Commun 8: 1287-1287

  • DOI: 10.1038/s41467-017-01497-1
  • Primary Citation of Related Structures:  5WGB, 5WLW

  • PubMed Abstract: 
  • Iron-sulfur (Fe/S) clusters are essential protein cofactors crucial for many cellular functions including DNA maintenance, protein translation, and energy conversion. De novo Fe/S cluster synthesis occurs on the mitochondrial scaffold protein ISCU an ...

    Iron-sulfur (Fe/S) clusters are essential protein cofactors crucial for many cellular functions including DNA maintenance, protein translation, and energy conversion. De novo Fe/S cluster synthesis occurs on the mitochondrial scaffold protein ISCU and requires cysteine desulfurase NFS1, ferredoxin, frataxin, and the small factors ISD11 and ACP (acyl carrier protein). Both the mechanism of Fe/S cluster synthesis and function of ISD11-ACP are poorly understood. Here, we present crystal structures of three different NFS1-ISD11-ACP complexes with and without ISCU, and we use SAXS analyses to define the 3D architecture of the complete mitochondrial Fe/S cluster biosynthetic complex. Our structural and biochemical studies provide mechanistic insights into Fe/S cluster synthesis at the catalytic center defined by the active-site Cys of NFS1 and conserved Cys, Asp, and His residues of ISCU. We assign specific regulatory rather than catalytic roles to ISD11-ACP that link Fe/S cluster synthesis with mitochondrial lipid synthesis and cellular energy status.


    Organizational Affiliation

    Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, Canada, S7N 5E5.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cysteine desulfurase, mitochondrial
A, E
406Homo sapiensGene 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, F
91Homo sapiensGene 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
C, G
77Escherichia coli (strain K12)Gene Names: acpP
Find proteins for P0A6A8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6A8
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
D, H
150Homo sapiensGene Names: ISCU (NIFUN)
Find proteins for Q9H1K1 (Homo sapiens)
Go to Gene View: ISCU
Go to UniProtKB:  Q9H1K1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8Q1
Query on 8Q1

Download SDF File 
Download CCD File 
C, G
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
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, E
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 98.360α = 90.00
b = 123.290β = 90.00
c = 151.724γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-11-15
    Type: Initial release