5Z8O

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), 0.240 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (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 of 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.

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 
• Modelled 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), 0.240 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (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