5X5M | pdb_00005x5m

Crystal structure of a hydrolase encoded by lin2189 from Listeria innocua

• PDB DOI: https://doi.org/10.2210/pdb5X5M/pdb

• Classification: HYDROLASE/ANTIBIOTIC
• Organism(s): Listeria innocua Clip11262
• Expression System: Enterobacteria phage L1
• Mutation(s): Yes 


• Deposited: 2017-02-16 Released: 2017-12-06 
• Deposition Author(s): Zhang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 
  0.195 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

GyrI-like proteins catalyze cyclopropanoid hydrolysis to confer cellular protection

Yuan, H., Zhang, J., Cai, Y., Wu, S., Yang, K., Chan, H.C.S., Huang, W., Jin, W.B., Li, Y., Yin, Y., Igarashi, Y., Yuan, S., Zhou, J., Tang, G.L.

(2017) Nat Commun 8: 1485-1485

• PubMed: 29133784 
• DOI: https://doi.org/10.1038/s41467-017-01508-1
• Primary Citation Related Structures: 
  5X5M


• PubMed Abstract: 
  

  GyrI-like proteins are widely distributed in prokaryotes and eukaryotes, and recognized as small-molecule binding proteins. Here, we identify a subfamily of these proteins as cyclopropanoid cyclopropyl hydrolases (CCHs) that can catalyze the hydrolysis of the potent DNA-alkylating agents yatakemycin (YTM) and CC-1065. Co-crystallography and molecular dynamics simulation analyses reveal that these CCHs share a conserved aromatic cage for the hydrolytic activity. Subsequent cytotoxic assays confirm that CCHs are able to protect cells against YTM. Therefore, our findings suggest that the evolutionarily conserved GyrI-like proteins confer cellular protection against diverse xenobiotics via not only binding, but also catalysis.

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Organizational Affiliation: 
• State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China.
Faculty of Life Sciences, University of Bradford, Bradford, West Yorkshire, BD7 1DP, UK.
Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.
Laboratory of Physical Chemistry of Polymers and Membranes, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH B3 495 (Bâtiment CH) Station 6, CH-1015, Lausanne, Switzerland. [e-mail].
State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China. [e-mail].
State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 52.24 kDa 
• Atom Count: 3,920 
• Modeled Residue Count: 410 
• Deposited Residue Count: 432 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lin2189 protein	A, B	216	Listeria innocua Clip11262	Mutation(s): 2  Gene Names: lin2189
UniProt
Find proteins for Q929T5 (Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)) Explore Q929T5  Go to UniProtKB:  Q929T5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7YU	D [auth A], F [auth B]	(+)-Yatakemycin C35 H29 N5 O8 S CMFSXTISUXTEGX-QXPWRNTLSA-N
DMS	C [auth A], E [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free:  0.195 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.63	α = 90
b = 49.295	β = 124.98
c = 80.361	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data processing
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-06 
Deposition Author(s): Zhang, J.

Revision History  

• Version 1.0: 2017-12-06
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description