9DDD | pdb_00009ddd

SufS-SufU complex from Mycobacterium Tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb9DDD/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Mycobacterium tuberculosis
• Expression System: Mycolicibacterium smegmatis MC2 155, Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2024-08-27 Released: 2025-07-30 
• Deposition Author(s): Stuteley, S.M., Bashiri, G.
• Funding Organization(s): Health Research Council (HRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.203 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Models: in silico

Literature

Feedback regulation of iron-sulfur cluster biogenesis.

Stuteley, S.M., Chen, J., Wang, J., Dawes, S., Baker, E.N., Squire, C.J., Pandelia, M.E., Bashiri, G.

(2025) bioRxiv 

• PubMed: 40667192 
• DOI: https://doi.org/10.1101/2025.06.15.659787
• Primary Citation Related Structures: 
  9DCL, 9DDD


• PubMed Abstract: 
  

  Iron-sulfur (Fe-S) clusters are ubiquitous cofactors in biological systems. Given their central role in bacterial metabolism and pathogenesis, the biogenesis of Fe-S clusters is tightly controlled. We reveal a feedback regulatory mechanism involving the sulfide producing SufS/SufU complex within the sulfur utilization (SUF) system of Mycobacterium tuberculosis , the bacterium that causes tuberculosis. In this mechanism, [2Fe-2S] clusters compete with zinc ions for binding to the sulfide transfer protein SufU. Cluster binding induces SufU tetramerization, which prevents its interaction with the cysteine desulfurase SufS, thereby inhibiting SufS activation and limiting sulfide supply for Fe-S cluster biogenesis. These findings uncover an unrecognized regulatory mechanism in M. tuberculosis , ensuring strict control of Fe-S cluster production.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 125.52 kDa 
• Atom Count: 8,668 
• Modeled Residue Count: 1,098 
• Deposited Residue Count: 1,158 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable cysteine desulfurase	A, B	417	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: csd, Rv1464, MTV007.11 EC: 2.8.1.7
UniProt
Find proteins for P9WQ69 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WQ69  Go to UniProtKB:  P9WQ69

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Possible nitrogen fixation related protein	C, D	162	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: Rv1465
UniProt
Find proteins for O53156 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O53156  Go to UniProtKB:  O53156

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ALA (Subject of Investigation/LOI)	E [auth A], F [auth B]	ALANINE C3 H7 N O2 QNAYBMKLOCPYGJ-REOHCLBHSA-N
ZN (Subject of Investigation/LOI)	G [auth C], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS	A, B	L-PEPTIDE LINKING	C3 H7 N O2 S2		CYS
LLP	A, B	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.203 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.799	α = 91.03
b = 73.616	β = 100.22
c = 76.349	γ = 110.02

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Stuteley, S.M., Bashiri, G.

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Funding Organization	Location	Grant Number
Health Research Council (HRC)	New Zealand	--

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release