8ZTQ | pdb_00008ztq

Crystal structure of Sufu from Mycoplasma Pneumonia

• PDB DOI: https://doi.org/10.2210/pdb8ZTQ/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Mycoplasmoides pneumoniae 19294
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-06-07 Released: 2024-12-11 
• Deposition Author(s): Wang, W.M., Ma, D.Y., Gong, W.J., Yao, H., Liu, Y.H., Wang, H.F.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 
  0.299 (Depositor), 0.296 (DCC) 
• R-Value Work: 
  0.271 (Depositor), 0.269 (DCC) 
• R-Value Observed: 
  0.274 (Depositor) 

Starting Model: in silico

Literature

The reduced interaction between SufS and SufU in Mycoplasma penetrans results in diminished sulfotransferase activity.

Ma, D., Yao, H., Liu, Y., Gong, W., Zhao, Y., Wang, R., Wu, C., Wang, W., Wang, H.

(2024) Int J Biol Macromol 284: 138181-138181

• PubMed: 39615726 
• DOI: https://doi.org/10.1016/j.ijbiomac.2024.138181
• Primary Citation of Related Structures:  
  8ZTP, 8ZTQ


• PubMed Abstract: 
  

  Mycoplasma Penetrans (Mpe) is an AIDS-related mycoplasma that is also closely related to respiratory diseases. Proteins involved in the first phase of Fe-S cluster biosynthesis in the SUF-like pathway are essential in Gram-positive bacteria because there is no redundant Fe-S cluster biosynthetic pathway in these proteins. In this study, we characterized two essential proteins: cysteine desulphurase (MpeSufS) and sulfurtransferase (MpeSufU) in Mpe, and resolved their crystal structures. Our results reveal that MpeSufS belongs to type II cysteine desulfurase, and MpeSufU is a Zn ²⁺ -containing sulfurtransferase. Residue Q342 in MpeSufS and the zinc atom in MpeSufU mediate sulfur transfer from MpeSufS to MpeSufU. Mutation of Q342 significantly impacts the cysteine desulfurase activity. This study provides new insights into the regulation of the activity of the SufS-SufU complex, which will help guide the design of drugs for the treatment of mycoplasma infections.

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Organizational Affiliation: 
• Key Laboratory of Chemical Biology and Molecular Engineering of Education Ministry, Key Laboratory of Energy Conversion and Storage Materials of Shanxi Provence, Institute of Molecular Science, Shanxi University, Taiyuan 030006, China.
Department of Pulmonary and Critical Care Medicine, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan 030032, China.
Institute of Biomedical Sciences, Shanxi University, Taiyuan 030006, China.
Key Laboratory of Chemical Biology and Molecular Engineering of Education Ministry, Key Laboratory of Energy Conversion and Storage Materials of Shanxi Provence, Institute of Molecular Science, Shanxi University, Taiyuan 030006, China. Electronic address: [e-mail].
Key Laboratory of Chemical Biology and Molecular Engineering of Education Ministry, Key Laboratory of Energy Conversion and Storage Materials of Shanxi Provence, Institute of Molecular Science, Shanxi University, Taiyuan 030006, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 35.93 kDa 
• Atom Count: 2,371 
• Modeled Residue Count: 293 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogen fixation protein NifU	A, B	156	Mycoplasmoides pneumoniae 19294	Mutation(s): 0  Gene Names: MYPE7420
UniProt
Find proteins for Q8EV25 (Malacoplasma penetrans (strain HF-2)) Explore Q8EV25  Go to UniProtKB:  Q8EV25

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free:  0.299 (Depositor), 0.296 (DCC) 
• R-Value Work:  0.271 (Depositor), 0.269 (DCC) 
• R-Value Observed: 0.274 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.08	α = 90
b = 30.333	β = 122.48
c = 87.209	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-11 
Deposition Author(s): Wang, W.M., Ma, D.Y., Gong, W.J., Yao, H., Liu, Y.H., Wang, H.F.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-12-11
  Type: Initial release
  
• Version 1.1: 2024-12-18
  Changes: Database references