7AK7

Structure of Salmonella TacT2 toxin bound to TacA2 antitoxin

• PDB DOI: https://doi.org/10.2210/pdb7AK7/pdb

• Classification: TOXIN
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-09-30 Released: 2021-08-18 
• Deposition Author(s): Grabe, G.J., Morgan, R.M.L., Hare, S.A., Helaine, S.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom), European Research Council (ERC), Biotechnology and Biological Sciences Research Council (BBSRC), Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.263 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 

Literature

Auxiliary interfaces support the evolution of specific toxin-antitoxin pairing.

Grabe, G.J., Giorgio, R.T., Hall, A.M.J., Morgan, R.M.L., Dubois, L., Sisley, T.A., Rycroft, J.A., Hare, S.A., Helaine, S.

(2021) Nat Chem Biol 17: 1296-1304

• PubMed: 34556858 
• DOI: https://doi.org/10.1038/s41589-021-00862-y
• Primary Citation of Related Structures:  
  7AK7, 7AK8, 7AK9


• PubMed Abstract: 
  

  Toxin-antitoxin (TA) systems are a large family of genes implicated in the regulation of bacterial growth and its arrest in response to attacks. These systems encode nonsecreted toxins and antitoxins that specifically pair, even when present in several paralogous copies per genome. Salmonella enterica serovar Typhimurium contains three paralogous TacAT systems that block bacterial translation. We determined the crystal structures of the three TacAT complexes to understand the structural basis of specific TA neutralization and the evolution of such specific pairing. In the present study, we show that alteration of a discrete structural add-on element on the toxin drives specific recognition by their cognate antitoxin underpinning insulation of the three pairs. Similar to other TA families, the region supporting TA-specific pairing is key to neutralization. Our work reveals that additional TA interfaces beside the main neutralization interface increase the safe space for evolution of pairing specificity.

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Organizational Affiliation: 

Department of Microbiology, Harvard Medical School, Boston, MA, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A4B2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 82.05 kDa 
• Atom Count: 5,253 
• Modelled Residue Count: 625 
• Deposited Residue Count: 728 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyltransferase	A, B	166	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 2  Gene Names:  A3104_12120, A3S30_09335, A3T81_08410, A3U32_18895, A3V03_06630, A3V89_04715, A3W57_09370, A3W75_08380, A3X15_08985, A3X55_16410, A3Y76_14810, A4N07_10055, A4O05_19285, A4O41_13420, A4R48_14945, A6D61_23370, AAA76_04890, AAB27_06080, AAB79_07335, AAC35_12485, ADQ28_16395, AF497_17060, AGM99_01705, AHN93_01715, AKH62_11990, AL144_08340, AL168_06480, AL184_07135, AQ530_03720, AU613_02445, AVA38_05020, AVC05_08125, AVL16_17225, AWT30_10165, AXX99_06220, B1265_01705, B1398_23245, B1642_15800, B1P38_05125, B2E31_22085, B4V59_04040, B4W90_15110, B6362_05795, B7Q27_01705, B8Y16_22745, B8Z46_15755, B9C90_11205, B9C96_14245, B9M14_07745, B9O84_03860, BBQ66_22395, BIC00_15285, BIC13_14710, BK110_14120, BKM50_18920, BMS46_01705, BMU56_14770, BZ203_07155, BZZ88_08270, C5W43_08435, CA117_06825, CB102_09090, CB198_03545, CB570_03095, CB646_12985, CBM67_08535, CBM76_05080, CBZ90_21895, CC339_11425, CC403_11745, CC453_16245, CC652_15015, CC971_08570, CCP17_01700, CDZ72_15910, CE70_13730, CED07_02455, CEQ70_07710, CFF58_07755, CFF59_21595, CHN22_20110, CIX60_06815, CPS79_04970, CQO33_23140, CSG22_03750, CVR97_08925, D4361_13195, D4387_09195, D4422_08350, D5823_02245, D5N86_13565, D5N95_11060, D5O82_11205, D5P17_16870, D5X47_12830, D5Y28_14825, D6422_03935, D6J79_15995, D8S24_15270, DD95_21775, DLB93_15585, DLR28_22745, DMI89_21300, DMO92_15470, DN165_12420, DNB97_07960, DNM27_06425, DNZ37_16415, DO533_20150, DP680_12765, DPB42_04130, DPD91_13885, DPF41_22710, DPF68_06925, DPS76_13305, DQD22_13230, DQR44_14440, DRM14_09995, DRR75_21965, DRT38_11500, DRT61_02580, DRV05_13390, DSF94_15305, DTF68_14145, DU071_20475, DU657_04175, DU879_07275, DWU22_16770, DY580_18910, DYM27_17255, E0935_09170, E1A11_12005, E6W45_15420, EBD14_13825, EBK21_16640, EC404_21665, EEQ30_21810, EER35_15280, EHB09_19970, EL822_14495, ELS01_18365, EPB30_15210, EQG93_09755, EVY71_07905, F0D96_14080, F2P00_16195, F3Q97_09870, F3R12_05240, F9G02_11145, F9O44_17810, FEM52_15650, FGZ46_10925, FQC24_13060, G0038_10890, G0040_04675, G0042_08320, G0045_13120, G0047_14485, G0048_13540, G0051_12080, G0052_16430, G0059_11660, G0061_12550, G0062_13130, G0063_16480, G0067_14185, G0069_13405, G0070_09580, G0071_13165, G0072_10940, G0074_13530, G0076_16085, G0077_13470, G0080_15595, G0084_16165, G0086_14475, G0087_13540, G0088_12550, G0089_06955, G0090_15400, G0094_13455, G0100_13300, G0101_10015, G0102_12635, G0111_18015, G0113_14145, G0117_15065, G0123_13540, G0124_10550, G0148_10680, G0157_12960, G0170_15225, G0A05_04970, G0A32_22495, G0A39_21715, G0A43_21070, G0A44_10190, G0A46_23355, G0A50_09160, G0A51_09465, G0A52_05930, G0A53_08765, G0A58_08665, G0A60_22620, G0A61_13425, G0A63_05005, G0A66_09670, G0A67_23690, G0A68_05880, G0A70_09080, G0A73_10190, G0A76_21905, G0A79_05455, G0A92_11430, G0A96_13675, G0A97_21725, G0B03_22870, G0B05_23635, G0B07_23665, G0B08_05105, G0B12_23035, G0B96_04990, G0C03_13210, G0C04_15865, G0E15_14995, G0E20_06345, G0G84_17325, G0J24_22425, G0J26_22635, G0J27_06420, G0J28_22920, G0J31_06945, G0J33_21870, G0J34_23190, G0J36_22945, G0J37_21650, G0J40_23005, G0J43_01745, G0J44_22205, G0J45_23245, G0J46_23065, G0J47_22375, G0J49_23025, G0J50_01755, G0J51_22440, G0J53_09480, G0J55_22080, G0J58_09970, G0J59_11780, G0J62_09150, G0J65_12065, G0J66_08650, G0J67_13775, G0J69_14065, G0J71_10850, G0J73_04195, G0J76_10025, G0J79_11245, G0J81_14005, G0J82_04065, G0J85_13545, G0J89_01755, G0J92_14060, G0J94_04610, G0J96_11350, G0J97_18265, G0K00_22985, G0K02_14220, G0K03_22870, G0K04_03410, G0K05_16970, G0K07_12990, G0K10_13820, G0K13_11725, G0K15_23065, G0K16_11720, G0K18_04915, G0K19_12945, G0K20_15760, G0K23_22845, G0K25_09170, G0K26_10780, G0K28_13685, G0K30_10450, G0K31_06645, G0K32_14525, G0K33_13465, G0K37_10165, G0K38_06915, G0K39_19210, G0K41_01330, G0K42_13670, G0K44_13055, G0K46_15520, G0K47_22675, G0K48_01755, G0K49_15025, G0K52_04605, G0K53_05150, G0K56_04845, G0K58_19750, G0K59_01755, G0K61_09120, G0K65_11540, G0K68_01745, G0K70_11920, G0K72_11520, G0K74_07905, G0K75_13605, G0K78_05725, G0K80_01750, G0K83_07710, G0K84_15620, G0K85_01755, G0K88_002893, G0K89_002653, G0K90_002299, G0K94_003123, G0K95_003254, G0L00_001896, G0L02_003282, G0L03_12250, G0L06_17545, G0L07_17230, G0L10_17595, G0L14_19275, G0L15_13250, G0L18_11955, G0L19_06530, G0L20_07545, G0L24_08975, G0L25_10820, G0L29_10295, G0L31_19505, G0L32_13795, G0L34_15735, G0L35_12260, G0L36_22645, G0L37_19225, G0L38_11830, G0L42_10150, G0L48_15340, G0L49_23575, G0L51_09770, G0L52_08805, G0L55_09755, G0L59_07195, G0L62_08975, G0L63_08580, G0L65_09630, G0L67_08280, G0L68_08295, G0L73_00610, G0L76_11775, G0L77_07140, G0L78_21395, G0L79_07610, G0L83_06545, G0L86_001734, G0L89_08855, G0L91_11580, G0L93_04530, G0L96_08810, G0L98_04525, G0M00_04585, G0M05_08330, G0M06_001524, G0M13_001301, G0M14_10405, G0M16_09985, G0M18_000610, G0M21_06500, G0M22_001518, G0M25_001338, G0M26_07895, G0M29_001533, G0M30_03245, G0M33_07230, G0M35_03415, G0M36_02605, G0M38_05515, G0M39_09815, G0M41_18395, G0M45_096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UniProt
Find proteins for Q8ZKC6 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZKC6  Go to UniProtKB:  Q8ZKC6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CopG family transcriptional regulator	C, D, E, F	99	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names:  STY4517, A2O69_04830, A3104_12125, A3111_16100, A3122_04225, A3146_12185, A3R41_05780, A3S30_09340, A3T21_16590, A3T81_08415, A3U32_18900, A3V03_06635, A3V89_04720, A3W57_09375, A3W75_08385, A3W86_08895, A3X15_08990, A3X55_16415, A3Y76_14815, A3Z96_24840, A4J27_15475, A4N07_10060, A4O05_19290, A4O41_13425, A4R48_14940, A6D61_23375, A9C21_15195, A9S84_16305, A9T17_24610, A9T39_04435, A9U46_16020, A9U64_07345, AAA76_04895, AAB27_06085, AAB39_05200, AAB79_07340, AAC08_17465, AAC35_12490, AAC42_06110, AAC95_01705, AAC98_04620, AAP89_11820, AAQ24_02940, AB424_12745, ABO94_05745, ABP11_11060, ABP54_03380, ABQ69_19040, ADQ28_16390, ADQ45_04785, AE787_07315, AF480_07975, AF488_05300, AF489_07575, AF497_17065, AGC55_17340, AGM99_01710, AGQ32_12045, AH984_04205, AHN93_01720, AIC76_06295, AKH62_11995, AKH68_21495, AKI16_06210, AL144_08345, AL151_04855, AL154_03280, AL166_08595, AL168_06485, AL170_10390, AL174_18775, AL184_07140, APH22_16760, APP08_09505, APY91_14235, AQ530_03725, AS118_18525, AT354_15380, AU613_02440, AU805_09140, AU830_10285, AU839_09530, AU951_00620, AU965_04915, AVA38_05025, AVB77_03230, AVB94_07720, AVC05_08130, AVC09_00615, AVD75_11750, AVD94_20895, AVG17_14180, AVL02_10840, AVL16_17220, AVM19_15250, AVM22_23420, AWT30_10170, AXM10_05785, AXM23_10860, AXR84_09430, AXU58_11130, AXX99_06225, B1265_01710, B1398_23250, B1642_15805, B1B86_01710, B1B89_08315, B1I91_16585, B1P38_05130, B1Q82_03960, B2E31_22090, B4V59_04045, B4W90_15115, B5A40_15890, B6362_05800, B6G98_03955, B6M25_08550, B6M43_04700, B7071_21440, B7890_21810, B7J30_20630, B7Q27_01710, B8Y16_22750, B8Y36_13865, B8Z46_15760, B9653_06255, B9C61_11525, B9C71_12215, B9C90_11200, B9C91_15880, B9C96_14250, B9M14_07750, B9O84_03865, B9U29_16925, BBQ66_22400, BEL47_01700, BGP52_12050, BIC00_15290, BIC01_07585, BIC03_01705, BIC13_14715, BK110_14125, BKM50_18925, BLB03_06650, BMS46_01710, BMU56_14775, BSC80_10970, BSD55_23050, BZ203_07160, BZ210_05600, BZG47_12380, BZN20_21955, BZZ88_08275, C4E88_07135, C5U54_10255, C5W43_08440, CA117_06830, CB102_09095, CB161_12435, CB198_03550, CB383_17145, CB416_15020, CB570_03100, CB646_12990, CB657_13120, CBH20_16570, CBM40_09235, CBM67_08540, CBM76_05085, CBN77_16225, CBO42_07645, CBR08_06655, CBU32_08560, CBZ90_21900, CC339_11430, CC403_11750, CC453_16250, CC594_18870, CC652_15020, CC725_12230, CC886_21755, CC918_20825, CC971_08575, CCF93_09515, CCP17_01705, CCW27_10850, CD48_08120, CD977_03275, CDJ75_10025, CDT37_01705, CDZ72_15915, CE355_15790, CE615_11295, CE70_13735, CE806_06620, CE87_06570, CE896_03030, CEC46_13770, CEC56_15565, CED07_02450, CEQ70_07715, CER78_14360, CET98_15920, CEY64_08970, CFB16_04515, CFB28_08430, CFE76_15065, CFE79_07710, CFF58_07760, CFF59_21600, CFJ48_12970, CGG73_09310, CHN22_20115, CI444_09245, CIX60_06810, CJC42_18860, CPR79_08375, CPS79_04975, CPX68_11005, CQE35_09575, CQG18_10495, CQO33_23145, CR370_14620, CRB02_04225, CSG22_03755, CTJ81_14475, CVR97_08920, D3147_12900, D3174_12515, D3F31_17570, D3T68_19740, D3Y48_22090, D4361_13200, D4369_13900, D4380_15290, D4387_09200, D4422_08355, D4E62_18870, D4E68_11140, D4E74_16080, D4X64_22990, D4X79_14400, D4Y62_07960, D5823_02250, D5949_04945, D5B48_05985, D5C67_15220, D5C71_22800, D5N86_13570, D5N95_11065, D5O82_11210, D5P17_16875, D5X47_12835, D5Y28_14830, D6360_13875, D6367_01775, D6371_15020, D6373_22960, D6395_11270, D6421_22990, D6422_03940, D6J79_16000, D6K10_15800, D6P67_10040, D6S43_11565, D6T00_15005, D6T40_17210, D7F20_11850, D7H43_04840, D7N92_15415, D7O44_23205, D8S24_15275, DD95_21770, DJ388_06405, DJ702_21955, DK061_12005, DK631_22150, DK641_07990, DK642_14995, DK689_16610, DK696_10480, DK698_12575, DKJ10_03885, DKJ21_24750, DKR95_23780, DKS55_06660, DKU45_02600, DKU57_12910, DKU80_11870, DLB14_03640, DLB57_13375, DLB93_15590, DLR28_22750, DM322_08735, DMI89_21305, DMO92_15475, DMV40_10160, DMZ93_16755, DN165_12415, DN204_23180, DN359_15890, DNB97_07965, DNL62_06005, DNM27_06430, DNM63_04665, DNU59_12465, DNV08_16265, DNY92_12000, DNZ37_16420, DO350_13260, DO533_20155, DO585_14500, DO640_10995, DO698_21325, DO766_14485, DO960_10100, DOC60_13885, DOH72_08990, DOI32_07275, DOI53_16175, DOI92_01265, DOJ39_17870, DOJ91_20010, DOQ54_13620, DOQ88_14045, DOR12_12795, DOW25_08025, DP680_12770, DPB42_04135, DPB45_12875, DPB48_10435, DPB57_14405, DPD91_13890, DPD95_14660, DPD99_07790, DPF41_22715, DPF68_06930, DPK32_13610, DPK79_12210, DPL02_15330, DPP94_22985, DPS76_13310, DPU20_09230, DQ848_14045, DQ947_04090, DQ951_16680, DQC39_22985, DQC52_23140, DQD22_13225, DQE64_14105, DQE65_15845, DQK42_16030, DQR10_17820, DQR44_14445, DQS14_15905, DQY10_22630, DQZ46_12750, DQZ56_10175, DR982_12980, DRL45_09855, DRM14_10000, DRM16_13190, DRR75_21970, DRT38_11505, DRT61_02585, DRT65_12290, DRV05_13395, DRW84_10155, DRX66_11400, DS296_10255, DS453_14715, DS619_08355, DSF69_22565, DSF94_15310, DSM38_15030, DSN15_21865, DSR36_09395, DTE73_12195, DTF68_14150, DTG22_17535, DTG27_04610, DTW13_22385, DTW14_23350, DTW26_13730, DU071_20480, DU657_04180, DU821_12055, DU879_07280, DUQ28_08770, DUQ56_13065, DUQ92_07010, DUW48_13490, DVF14_14365, DVF88_13730, DVG01_02530, DVZ53_14165, DWU22_16775, DY580_18915, DYM27_17260, DYS82_07805, DZG11_07810, E0584_10585, E0595_22380, E0935_09175, E0989_14220, E0M34_08655, E0U75_14625, E0V94_12675, E1A11_12010, E1A20_04620, E5196_12370, E6W45_15425, EBC01_12685, EBD14_13830, EBK21_16645, EBL31_13785, EBO41_10395, EBP31_14040, EC404_21670, EC52_04050, ECA50_08690, ECC89_13490, ED424_13845, ED467_22615, EDL18_14745, EEK73_21530, EEQ30_21815, EER35_15285, EGN81_10220, EGU67_22475, EGU98_12825, EHB09_19975, EHB24_13180, EHC98_15145, EIE48_12945, EIW53_11885, EJI18_16640, EJO08_22445, EJO98_07025, EKA25_12110, EL822_14500, ELO47_13850, ELR28_11565, ELS01_18370, EM832_22795, EM840_14640, EMN66_15280, EMY79_10355, EO190_06835, EP446_01035, EPB30_15215, EPH81_09830, EQG93_09760, EQG94_22450, ERM04_13190, EU306_14230, EU349_22150, EUB95_22555, EUQ56_14705, EUQ65_01755, EUQ74_15275, EUS13_12180, EVY71_07900, EWB18_00620, EWE52_06800, EWJ47_13005, EWZ09_12070, EXA47_13190, EXB31_11140, EXB41_13600, EYA29_12720, EYJ91_14485, F0D96_14075, F2O93_10970, F2P00_16200, F3Q46_00300, F3Q58_05940, F3Q59_00435, F3Q88_05750, F3Q97_09865, F3R12_05235, F3R61_00300, F3R63_13825, F9G02_11140, F9O44_17815, FEM52_15655, FGZ46_10920, FQC24_13065, FQD13_16090, GCH31_09085, GCZ80_05985, GEZ01_14635, GW08_08845, JO10_09985, KP44_01710, LZ63_09660, NCTC13348_02288, NG02_17950, NG06_07905, NG18_21940, NU83_23015, QA89_21480, QB40_12820, QD15_12985, R035_20165, RJ78_05095, SAMEA4398682_04321, SE14_04558, Y934_12485, YG50_21405, YR17_04665, Z700_13205, ZB89_15140, ZC54_11150, ZT09_03135, ZT28_02460, ZT74_07710, ZT89_07650, ZU86_06785, ZU92_08685, ZV06_04225, ZV33_08630, ZV34_09010, ZV38_21720, ZV58_02460, ZV70_03190, ZV78_02855, ZV90_19040, ZW74_08020, ZX03_01895, ZY00_12875, ZY23_10425, ZY27_08590, ZY40_08385, ZY51_00615, ZZ18_04390, ZZ43_06690, ZZ77_04740, ZZ79_20260
UniProt
Find proteins for Q8ZKC7 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZKC7  Go to UniProtKB:  Q8ZKC7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACO (Subject of Investigation/LOI)	G [auth A], H [auth B]	ACETYL COENZYME *A C23 H38 N7 O17 P3 S ZSLZBFCDCINBPY-ZSJPKINUSA-N
CL	I [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.263 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.491	α = 100.57
b = 54.452	β = 97.73
c = 76.9	γ = 117

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-08-18 
Deposition Author(s): Grabe, G.J., Morgan, R.M.L., Hare, S.A., Helaine, S.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/M009629/1
European Research Council (ERC)	United Kingdom	757369
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/D524840/1
Wellcome Trust	United Kingdom	202926/Z/16/Z

Revision History  

• Version 1.0: 2021-08-18
  Type: Initial release
  
• Version 1.1: 2021-10-06
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2021-12-01
  Changes: Data collection, Database references
• Version 1.3: 2024-01-31
  Changes: Data collection, Refinement description