8ODQ

SufS-SufU complex from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural and Biochemical Characterization of Mycobacterium tuberculosis Zinc SufU-SufS Complex.

Elchennawi, I.Carpentier, P.Caux, C.Ponge, M.Ollagnier de Choudens, S.

(2023) Biomolecules 13

  • DOI: https://doi.org/10.3390/biom13050732
  • Primary Citation of Related Structures:  
    8ODQ

  • PubMed Abstract: 

    Iron-sulfur (Fe-S) clusters are inorganic prosthetic groups in proteins composed exclusively of iron and inorganic sulfide. These cofactors are required in a wide range of critical cellular pathways. Iron-sulfur clusters do not form spontaneously in vivo; several proteins are required to mobilize sulfur and iron, assemble and traffic-nascent clusters. Bacteria have developed several Fe-S assembly systems, such as the ISC, NIF, and SUF systems. Interestingly, in Mycobacterium tuberculosis ( Mtb ), the causative agent of tuberculosis (TB), the SUF machinery is the primary Fe-S biogenesis system. This operon is essential for the viability of Mtb under normal growth conditions, and the genes it contains are known to be vulnerable, revealing the Mtb SUF system as an interesting target in the fight against tuberculosis. In the present study, two proteins of the Mtb SUF system were characterized for the first time: Rv1464( sufS ) and Rv1465( sufU ). The results presented reveal how these two proteins work together and thus provide insights into Fe-S biogenesis/metabolism by this pathogen. Combining biochemistry and structural approaches, we showed that Rv1464 is a type II cysteine-desulfurase enzyme and that Rv1465 is a zinc-dependent protein interacting with Rv1464. Endowed with a sulfurtransferase activity, Rv1465 significantly enhances the cysteine-desulfurase activity of Rv1464 by transferring the sulfur atom from persulfide on Rv1464 to its conserved Cys40 residue. The zinc ion is important for the sulfur transfer reaction between SufS and SufU, and His354 in SufS plays an essential role in this reaction. Finally, we showed that Mtb SufS-SufU is more resistant to oxidative stress than E. coli SufS-SufE and that the presence of zinc in SufU is likely responsible for this improved resistance. This study on Rv1464 and Rv1465 will help guide the design of future anti-tuberculosis agents.


  • Organizational Affiliation

    CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, 38000 Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteine desulfuraseA [auth B]418Mycobacterium tuberculosisMutation(s): 0 
Gene Names: csd
UniProt
Find proteins for P9WQ69 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WQ69 
Go to UniProtKB:  P9WQ69
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WQ69
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteine desulfuraseB [auth D]418Mycobacterium tuberculosisMutation(s): 0 
Gene Names: csd
UniProt
Find proteins for P9WQ69 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WQ69 
Go to UniProtKB:  P9WQ69
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WQ69
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogen fixation proteinC [auth A],
D [auth C]
166Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
UniProt
Find proteins for O53156 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O53156 
Go to UniProtKB:  O53156
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO53156
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLP (Subject of Investigation/LOI)
Query on PLP

Download Ideal Coordinates CCD File 
H [auth B],
I [auth D]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
MPO
Query on MPO

Download Ideal Coordinates CCD File 
J [auth D]3[N-MORPHOLINO]PROPANE SULFONIC ACID
C7 H15 N O4 S
DVLFYONBTKHTER-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
M [auth A],
O [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
E [auth B]
F [auth B]
G [auth B]
K [auth D]
L [auth D]
E [auth B],
F [auth B],
G [auth B],
K [auth D],
L [auth D],
N [auth C]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TSY
Query on TSY
A [auth B]L-PEPTIDE LINKINGC3 H7 N O2 S3CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.25α = 92.4
b = 75.553β = 109.57
c = 75.602γ = 99.71
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)Francelabex ARCANE, ANR-11-LABX-0003-01
Agence Nationale de la Recherche (ANR)FranceCBH-EUR-GS (ANR-17-EURE-0003)
Agence Nationale de la Recherche (ANR)FranceLabex GRAL (ANR-10-LABX-49-01)

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-31
    Type: Initial release
  • Version 1.1: 2023-06-07
    Changes: Database references