8KG1 | pdb_00008kg1

Crystal structure of the cargo cysteine desulfurase from Mycobacterium smegmatis

• PDB DOI: https://doi.org/10.2210/pdb8KG1/pdb

• Classification: TRANSFERASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Mycolicibacterium smegmatis MC2 155
• Mutation(s): No 


• Deposited: 2023-08-17 Released: 2024-11-20 
• Deposition Author(s): Liu, X., Tang, Y., Liu, Y., Ma, M., Gao, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.185 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Literature

The structural and functional analysis of mycobacteria cysteine desulfurase-loaded encapsulin.

Tang, Y., Liu, Y., Zhang, M., Lan, W., Ma, M., Chen, C., Wu, S., Chen, R., Yan, Y., Feng, L., Li, Y., Guddat, L.W., Gao, Y., Liu, X., Rao, Z.

(2024) Commun Biol 7: 1656-1656

• PubMed: 39702509 
• DOI: https://doi.org/10.1038/s42003-024-07299-8
• Primary Citation Related Structures: 
  8KG1, 8WOL, 8WON


• PubMed Abstract: 
  

  Encapsulin nanocompartments loaded with dedicated cargo proteins via unique targeting peptides, play a key role in stress resistance, iron storage and natural product biosynthesis. Mmp1 and cysteine desulfurase (Enc-CD) have been identified as the most abundant representatives of family 2 encapsulin systems. However, the molecular assembly, catalytic mechanism, and physiological functions of the Mmp1 encapsulin system have not been studied in detail. Here we isolate and characterize an Enc-CD-loaded Mmp1 encapsulin system from Mycobacterium smegmatis mc ² 155. The cryo-EM structure of the Mmp1 encapsulin and the crystal structure of the naked cargo Enc-CD have been determined. The structure shows that the Mmp1 protomer assembles two conformation models, the icosahedron (T = 1) and homodecamer, with the resolution of 2.60 Å and 2.69 Å. The Enc-CD at 2.10 Å resolution is dimeric and loaded into the Mmp1 (T = 1) encapsulin through the N-terminal long disordered region. Mmp1 encapsulin protects Enc-CD against oxidation as well as to maintain structural stability. These studies provide new insights into the mechanism by which Enc-CD-loaded encapsulin stores sulfur and provides a framework for discovery of new anti-mycobacterial therapeutics.

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Organizational Affiliation: 
• College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, China.
Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
School of Life Sciences, Tianjin University, Tianjin, China.
School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China. [e-mail].
College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, China. [e-mail].
College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, China. [e-mail].
Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China. [e-mail].
Laboratory of Structural Biology, Tsinghua University, Beijing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 93.05 kDa 
• Atom Count: 6,774 
• Modeled Residue Count: 810 
• Deposited Residue Count: 852 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cysteine desulfurase	A, B	426	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: MSMEI_4425 EC: 2.8.1.7
UniProt
Find proteins for A0R0X2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R0X2  Go to UniProtKB:  A0R0X2

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.185 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.092	α = 90
b = 112.092	β = 90
c = 120.813	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-11-20 
Deposition Author(s): Liu, X., Tang, Y., Liu, Y., Ma, M., Gao, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32171259
National Natural Science Foundation of China (NSFC)	China	32201033

Revision History  

• Version 1.0: 2024-11-20
  Type: Initial release
  
• Version 1.1: 2026-06-03
  Changes: Database references