6J72

Crystal structure of IniA from Mycobacterium smegmatis with GTP bound

• PDB DOI:  https://doi.org/10.2210/pdb6J72/pdb

• Classification: HYDROLASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-01-16 Released: 2019-09-11 
• Deposition Author(s): Wang, M.F., Guo, X.Y., Hu, J.J., Li, J., Rao, Z.H.
• Funding Organization(s): Chinese Academy of Sciences, Ministry of Science and Technology (China), National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.221 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 

Literature

Mycobacterial dynamin-like protein IniA mediates membrane fission.

Wang, M., Guo, X., Yang, X., Zhang, B., Ren, J., Liu, A., Ran, Y., Yan, B., Chen, F., Guddat, L.W., Hu, J., Li, J., Rao, Z.

(2019) Nat Commun 10: 3906-3906

• PubMed: 31467269 
• DOI: https://doi.org/10.1038/s41467-019-11860-z
• Primary Citation of Related Structures:  
  6J72, 6J73


• PubMed Abstract: 
  

Mycobacterium tuberculosis infection remains a major threat to human health worldwide. Drug treatments against tuberculosis (TB) induce expression of several mycobacterial proteins, including IniA, but its structure and function remain poorly understood. Here, we report the structures of Mycobacterium smegmatis IniA in both the nucleotide-free and GTP-bound states. The structures reveal that IniA folds as a bacterial dynamin-like protein (BDLP) with a canonical GTPase domain followed by two helix-bundles (HBs), named Neck and Trunk. The distal end of its Trunk domain exists as a lipid-interacting (LI) loop, which binds to negatively charged lipids for membrane attachment. IniA does not form detectable nucleotide-dependent dimers in solution. However, lipid tethering indicates nucleotide-independent association of IniA on the membrane. IniA also deforms membranes and exhibits GTP-hydrolyzing dependent membrane fission. These results confirm the membrane remodeling activity of BDLP and suggest that IniA mediates TB drug-resistance through fission activity to maintain plasma membrane integrity.

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Organizational Affiliation: 

Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing, 100084, China.

Biological Assembly 1  

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

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

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content

• Total Structure Weight: 67.28 kDa 
• Atom Count: 4,719 
• Modelled Residue Count: 561 
• Deposited Residue Count: 606 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoniazid inducible gene protein IniA	A	606	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: iniA, MSMEI_0678
UniProt
Find proteins for I7FE16 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore I7FE16  Go to UniProtKB:  I7FE16

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP (Subject of Investigation/LOI)	B [auth A]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
TLA	D [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
MG (Subject of Investigation/LOI)	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GTP	Binding MOAD:  6J72	Kd: 740 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.221 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 
• Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.514	α = 90
b = 91.514	β = 90
c = 139.494	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Wang, M.F., Guo, X.Y., Hu, J.J., Li, J., Rao, Z.H.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	XDB08020200
Ministry of Science and Technology (China)	China	2016YFA0500201
Ministry of Science and Technology (China)	China	2017YFC0840300
Ministry of Science and Technology (China)	China	2014CB542800
Ministry of Science and Technology (China)	China	2014CBA02003
National Natural Science Foundation of China	China	813300237
National Natural Science Foundation of China	China	81520108019
National Natural Science Foundation of China	China	31630020
National Natural Science Foundation of China	China	31500607
Chinese Academy of Sciences	China	XDPB10

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release