5Z8O | pdb_00005z8o

Structural of START superfamily protein MSMEG_0129 from Mycobacterium smegmatis

• PDB DOI: https://doi.org/10.2210/pdb5Z8O/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-01-31 Released: 2018-03-21 
• Deposition Author(s): Zheng, S., Liu, W., Bi, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.236 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.213 (DCC) 

Starting Model: experimental

Literature

Structural and genetic analysis of START superfamily protein MSMEG_0129 from Mycobacterium smegmatis.

Zheng, S., Zhou, Y., Fleming, J., Zhou, Y., Zhang, M., Li, S., Li, H., Sun, B., Liu, W., Bi, L.

(2018) FEBS Lett 592: 1445-1457

• PubMed: 29512898 
• DOI: https://doi.org/10.1002/1873-3468.13024
• Primary Citation Related Structures: 
  5Z8O


• PubMed Abstract: 
  

  Mycobacterium tuberculosis is a notorious pathogen that continues to threaten human health. Rv0164, an antigen of both T- and B cells conserved across mycobacteria, and MSMEG_0129, its close homolog in Mycobacterium smegmatis, are predicted members of the START domain superfamily, but their molecular function is unknown. Here, gene knockout studies demonstrate MSMEG_0129 is essential for bacterial growth, suggesting Rv0164 may be a potential drug target. The MSMEG_0129 crystal structure determined at 1.95 Å reveals a fold similar to that in polyketide aromatase/cyclases ZhuI and TcmN from Streptomyces sp. Structural comparisons and docking simulations, however, infer that MSMEG_0129 and Rv0164 are unlikely to catalyze polyketide aromatization/cyclization, but probably play an irreplaceable role during mycobacterial growth, for example, in lipid transfer during cell envelope synthesis.

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Organizational Affiliation: 
• School of Stomatology and Medicine, Foshan University, China.
Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
Shenyang Chest Hospital, Dadong, China.
Institute of Immunology, The Third Military Medical University, Chongqing, China.
Guangdong Province Key Laboratory of TB Systems Biology and Translational Medicine, Foshan, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.68 kDa 
• Atom Count: 2,766 
• Modeled Residue Count: 291 
• Deposited Residue Count: 294 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclase/dehydrase	A, B	147	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: MSMEI_0126
UniProt
Find proteins for I7FVL6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore I7FVL6  Go to UniProtKB:  I7FVL6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.236 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.213 (DCC) 

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.76	α = 90
b = 109.76	β = 90
c = 56.5	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
Rosetta	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-21 
Deposition Author(s): Zheng, S., Liu, W., Bi, L.

Revision History  

• Version 1.0: 2018-03-21
  Type: Initial release
  
• Version 1.1: 2018-05-09
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description