Active-site flexibility and substrate specificity in a bacterial virulence factor: crystallographic snapshots of an epoxide hydrolase

. Author manuscript; available in PMC: 2018 May 2.

Published in final edited form as: Structure. 2017 Apr 6;25(5):697–707.e4. doi: 10.1016/j.str.2017.03.002

Key Resources Table

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies





Bacterial and Virus Strains
E. coli TOP10 Bacterial Strain	Gift from Dr. George O’Toole	N/A




Biological Samples





Chemicals, Peptides, and Recombinant Proteins
(±)-epibromohydrin	Sigma Aldrich	Cat#E1012
1,2-cyclohexane oxide	Sigma Aldrich	Cat#C102504
4-(±)-vinyl-1-cyclohexene 1,2-(±)-epoxide	Sigma Aldrich	Cat#152544
1,2-(±)-epoxyhexane	Sigma Aldrich	Cat#377171
1,2-(±)-epoxyoctane	Sigma Aldrich	Cat#260258
(R)-epoxyoctane	Sigma Aldrich	Cat#45366
cis-stilbene oxide	Sigma Aldrich	Cat#308323
1,2-(±)-styrene oxide	Sigma Aldrich	Cat#W513504
(R)-styrene oxide	Sigma Aldrich	Cat#540099
(S)-styrene oxide	Sigma Aldrich	Cat#540102
(+)-limonene 1,2-epoxide	Sigma Aldrich	Cat#218324
(−)-limonene 1,2-epoxide	Sigma Aldrich	Cat#218332
fosfomycin sodium	Sigma Aldrich	Cat#34089
(R)-1-(4-nitrophenyl)-oxirane	Sigma Aldrich	Cat#69167
(S)-1-(4-nitrophenyl)-oxirane	Sigma Aldrich	Cat#75914
(±)-propylene oxide	Sigma Aldrich	Cat#56671
3-bromo-1,2-propanediol	Sigma Aldrich	Cat#226130
trans-1,2-cyclohexane diol	Sigma Aldrich	Cat#141712
1-phenyl-1,2-ethanediol	Sigma Aldrich	Cat#P24055
1,2-hexanediol	Sigma Aldrich	Cat#213691
1,2-octanediol	Sigma Aldrich	Cat#213705
(±)-1-(4-nitrophenyl)-ethane-1,2-diol	Sigma Aldrich	Cat#R416576
(±)-trans-oxirane-2,3-dicarboxylic acid	TCI America	Cat#E0350
cis-oxirane-2,3-dicarboxylic acid	TCI America	Cat#E0449
(S)-1,2-epoxyhexane	Maybridge Chemical	Cat#MAY00281CE
(S)-1,2-epoxyoctane	Enamine	Cat#BBV-39745467
(R)-1,2-epoxyhexane	This study	N/A
(±)19,20-dihydroxy-4Z,7Z,10Z,13Z,16Z-docosapentaenoic acid	Cayman Chemical	Cat#10007001
(±)19,20-dihydroxy-4Z,7Z,10Z,13Z,16Z-docosapentaenoic acid	This study (Morisseau et al., 2010)	N/A
(±)17,18-dihydroxy-5Z,8Z,11Z,14Z-eicosatetraenoic acid	This Study (Morisseau et al., 2010)	N/A
(±)14,15-dihydroxy-5Z,8Z,11Z,17Z-eicosatetraenoic acid	Cayman Chemical	Cat#10006998
(±)19,20-epoxy-4Z,7Z,10Z,13Z,16Z-docosapentaenoic acid	Cayman Chemical	Cat#10175
(±)16,17-epoxy-4Z,7Z,10Z,13Z,19Z-docosapentaenoic acid	Cayman Chemical	Cat#10174
(±)-(4Z,7Z,10Z)-12-[3-(2Z,5Z)-2,5-octadien-1-yl-2-oxiranyl]-4,7,10-dodecatrienoic acid	Cayman Chemical	CAT#10464; CAS ID: 895127-64-7
(±)17,18-epoxy-5Z,8Z,11Z,14Z-eicosatetraenoic acid	This Study (Morisseau et al., 2010)	N/A
(±)14,15-epoxy-5Z,8Z,11Z,17Z-eicosatetraenoic acid	Cayman Chemical	Cat#10173; CAS ID: 131339-24-7
(±)11,12-epoxy-5Z,8Z,14Z,17Z- eicosatetraenoic acid	Cayman Chemical	Cat#10462; CAS ID: 504435-15-8
(±)13-(3-pentyl-2-oxiranyl)-8Z,11Z-tridecadienoic acid	Cayman Chemical	Cat#10007527; CAS ID: 351533-80-7
Epoxy-Fatty Acids, Mixture of 14	This study (Morisseau et al., 2010)	N/A

Critical Commercial Assays





Deposited Data
Crystal Structure: Cif_E153Q-(S)-2-Butyloxirane	This study	PDB ID: 5TNL
Crystal Structure: Cif_E153Q-(S)-2-Hexyloxirane	This study	PDB ID: 5TNN
Crystal Structure: Cif_E153Q-(R)-2-Hexyloxirane	This study	PDB ID: 5TNM
Crystal Structure: Cif_E153Q-rac-2-Hexyloxirane	This study	PDB ID: 5TNK
Crystal Structure: Cif_E153Q-(S)-2-phenyloxirane	This study	PDB ID: 5TNI
Crystal Structure: Cif_E153Q-(R)-2-phenyloxirane	This study	PDB ID: 5TNQ
Crystal Structure: Cif_E153Q-rac-2-phenyloxirane	This study	PDB ID: 5TNP
Crystal Structure: Cif_E153Q-7-oxabicyclo[4.1.0]heptane	This study	PDB ID: 5TND
Crystal Structure: Cif_E153Q-3-Vinyl-7-oxabicyclo[4.1.0]heptane	This study	PDB ID: 5TNJ
Crystal Structure: Cif_E153Q-(2R,3S)-2,3-diphenyloxirane	This study	PDB ID: 5TNE
Crystal Structure: Cif_D129S + 7-oxabicyclo[4.1.0]heptane	This study	PDB ID: 5TNS
Crystal Structure: Cif_E153Q-rac-cis-16,17-EDP	This study	PDB ID: 5TNR
Crystal Structure: Cif_E153Q-rac-cis-19,20-EDP	This study	PDB ID: 5TNF
Crystal Structure: Cif_E153Q-rac-cis-14,15-EEQ	This study	PDB ID: 5TNG
Crystal Structure: Cif_E153Q-rac-cis-17,18-EEQ	This study	PDB ID: 5TNH

Experimental Models: Cell Lines





Experimental Models: Organisms/Strains






Oligonucleotides




Recombinant DNA
pDPM73: C-terminal His6-tagged Cif	Gift from Dr. George O’Toole (MacEachran et al., 2007)	N/A
pMQ70::Cif_E153Q: C-terminal His6-tagged Cif_E153Q	This lab (Bahl et al., 2016)	N/A
pMQ70::Cif_D129S: C-terminal His6-tagged Cif_D129S	This lab (Bahl et al., 2015)	N/A

Software and Algorithms




Other