7AK9

Structure of Salmonella TacT3 toxin bound to TacA3 antitoxin C-terminal peptide

• PDB DOI: https://doi.org/10.2210/pdb7AK9/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: 2.55 Å
• R-Value Free: 
  0.282 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

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 4-mer - A2B2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 47.75 kDa 
• Atom Count: 3,230 
• Modelled Residue Count: 397 
• Deposited Residue Count: 424 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyltransferase	A, B	176	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 1  Gene Names:  A2O69_14710, A3104_08525, A3111_02365, A3122_05715, A3146_07085, A3S30_20570, A3T81_15835, A3U32_19315, A3V03_13160, A3V89_13630, A3W57_15915, A3W75_13520, A3W86_09800, A3X15_14395, A3X55_09260, A3Y76_11330, A3Z96_17730, A4J27_06855, A4N07_06735, A4O05_06540, A4R48_05595, A6D61_06495, A9C21_11525, A9T39_06955, A9U46_17515, A9U64_03850, AAA76_13150, AAB27_19890, AAB39_07250, AAB79_09875, AAC08_00420, AAC35_15875, AAC42_08845, AAC44_05970, AAC95_11790, AAC98_08180, AAK29_13035, AAP89_06290, AAQ24_13230, AB424_06630, ABO94_10350, ABP87_20380, ADQ28_09230, ADQ45_03525, AE787_08375, AF480_02650, AF488_02445, AF489_05145, AF497_15340, AGC55_04185, AGM99_07505, AGQ32_07045, AH984_01035, AHN93_09010, AIC76_09285, AKH62_10520, AKH68_10580, AKI16_02015, AL144_10105, AL151_10950, AL166_11665, AL168_09635, AL170_09510, AL174_03655, AL184_10950, APY91_06225, AQ530_13930, AS118_08370, AT354_02285, AU613_08485, AU805_10975, AU830_04485, AU839_11895, AU951_07445, AU965_16560, AVA38_07605, AVB77_13980, AVB94_15035, AVC05_01920, AVC09_03465, AVD08_11675, AVD75_12175, AVD94_11625, AVL02_10280, AVL16_05965, AVM19_04730, AWT30_06955, AXM10_11690, AXM23_13930, AXR84_07880, AXU58_02150, AXX99_11930, B1265_07265, B1398_23385, B1642_13580, B1B86_06045, B1B89_02010, B1I91_06440, B1P38_03325, B1Q82_05910, B2E31_15360, B4V59_13460, B4W90_04250, B5A40_05340, B6362_07445, B6G98_04770, B6M25_12980, B6M43_01870, B7071_02280, B7890_10645, B7J30_02750, B7Q27_07260, B8Y16_10555, B8Y36_04530, B8Z46_07685, B9653_20405, B9C61_09950, B9C71_14620, B9C90_09640, B9C91_13400, B9C96_07470, B9M14_11835, B9O84_04625, B9U29_15940, BBQ66_03420, BEL47_20970, BGP52_08870, BIC00_01965, BIC01_05330, BIC03_09930, BIC13_10285, BK110_07455, BKM50_12355, BLB03_01740, BMS46_04300, BMU56_05250, BSC80_02300, BSD55_06335, BZ203_09215, BZ210_07060, BZG47_06310, BZN20_02445, BZZ88_18440, C4E88_02445, C5U54_02150, C5W43_12245, CA117_08410, CB102_08185, CB161_12015, CB198_02180, CB380_14500, CB383_01935, CB416_07355, CB530_05450, CB535_13640, CB570_08575, CB646_10705, CB657_09085, CBH20_06435, CBM40_20070, CBM67_16515, CBM76_14910, CBN77_16785, CBO42_11245, CBR08_04950, CBU32_07665, CBZ90_11485, CC403_06280, CC453_06265, CC594_15440, CC652_14675, CC725_04865, CC886_14180, CC918_07945, CC944_02215, CC971_01735, CCF93_10575, CCP17_12420, CCW27_01035, CD48_09215, CD977_05545, CDJ75_04635, CDT37_10325, CDZ72_03910, CE355_06180, CE615_05710, CE70_11930, CE806_07385, CE87_05355, CE896_10245, CEC46_10535, CEC56_05725, CED07_07405, CEQ70_02125, CER78_09050, CET98_05350, CEY64_12815, CFB16_10680, CFB28_09520, CFE76_07290, CFE79_02120, CFF58_10820, CFF59_05970, CFJ48_10970, CGG73_06885, CHN22_06165, CI444_05360, CIX60_02145, CJC42_03195, CPR79_16280, CPS79_11185, CPX68_05100, CQE35_07680, CQO33_16090, CR370_08455, CRB02_05340, CSG22_12020, CTJ81_12735, CVR97_12650, D3147_08940, D3174_07820, D3F31_20020, D3T68_17985, D3Y48_07440, D4361_09990, D4369_10995, D4380_01880, D4387_15140, D4422_12965, D4E62_16105, D4E68_14820, D4E74_13085, D4X64_15240, D4Y62_17435, D5823_15645, D5949_23340, D5B48_13110, D5C67_12005, D5C71_16355, D5N86_08970, D5N95_10230, D5O82_16440, D5P17_16530, D5X47_15185, D5Y28_18520, D6360_15430, D6367_13695, D6371_04230, D6373_15865, D6395_13525, D6421_15010, D6422_15625, D6J79_16905, D6K10_25570, D6P67_17865, D6Q64_15695, D6S43_13590, D6T00_01880, D6T40_09010, D7F20_20100, D7H43_13140, D7O44_15935, D8Q90_16805, D8S24_11150, D9O84_11660, DD95_05355, DJ388_12295, DJ702_05335, DK061_11060, DK631_03160, DK641_12245, DK642_13480, DK689_12875, DK696_12630, DK698_11875, DKJ10_12870, DKR95_21490, DKS55_05145, DKU45_05690, DKU57_07335, DKU80_06725, DLB14_13735, DLB57_11890, DLB93_11425, DLR28_16975, DM322_06960, DMI89_25655, DMO92_02670, DMV40_12195, DMZ93_26675, DN165_11055, DN204_16500, DN359_23735, DNB97_00775, DNL62_15760, DNM27_05590, DNU59_05715, DNV08_01875, DNV12_09940, DNV30_14235, DNY92_13980, DNZ37_15375, DO350_06855, DO533_06050, DO585_16180, DO640_14410, DO698_08950, DO766_06390, DO828_16965, DO960_09160, DOC60_02105, DOH72_07130, DOI32_13580, DOI92_13210, DOJ39_17520, DOJ91_12145, DOQ54_06625, DOQ88_13030, DOR12_06235, DOV43_10320, DOW25_12865, DP680_15120, DPB42_03780, DPB45_13780, DPB48_08570, DPB57_07290, DPD91_09220, DPD95_09935, DPD99_23550, DPF41_13030, DPF68_13810, DPJ93_05515, DPK32_07545, DPK79_14260, DPL02_04340, DPP94_15975, DPP97_15415, DPS76_00440, DPT18_14130, DPU20_13855, DPY58_11745, DQ848_11335, DQ947_01880, DQ951_13955, DQC39_17415, DQC52_23390, DQD03_08180, DQD22_04750, DQE65_01875, DQK42_05460, DQQ98_08490, DQR10_25350, DQR61_13365, DQS14_11730, DQY10_10410, DQZ46_12325, DQZ56_08295, DR982_12275, DRL45_08460, DRM14_13595, DRM16_12360, DRR75_02370, DRT38_02095, DRT61_15355, DRT65_10140, DRV05_05570, DRW84_08295, DRX66_12300, DS270_13440, DS296_06505, DS451_14735, DS453_11540, DS521_04860, DS619_14375, DSF69_15770, DSF94_01875, DSG41_06680, DSM38_13920, DSN15_14610, DSR36_07530, DTE73_08970, DTF68_01875, DTG22_06850, DTG27_07270, DTW13_15655, DTW14_17675, DTW26_10525, DU071_02620, DU223_03775, DU657_08025, DU821_15060, DU879_12775, DU924_00430, DUQ28_15105, DUQ56_12120, DUQ92_16070, DUR36_05660, DUW10_17140, DUW48_07425, DVF14_10520, DVF88_05805, DVG01_14880, DVZ53_02690, DWU22_21650, DY580_03860, DYM27_25875, DYS82_16110, DZG11_12860, E0584_17725, E0595_12520, E0935_16805, E0989_11820, E0M34_00770, E0U75_12350, E0V94_13550, E1A11_13990, E1A20_08715, E5196_10530, E6W45_11290, EBB93_08225, EBC01_14215, EBD14_10775, EBD99_16245, EBK21_12495, EBL31_10765, EBO41_07985, EBP31_13400, EC404_10185, EC52_10650, ECA50_06355, ECC89_10360, ED424_12910, ED467_14455, EDL18_12335, EEK73_07615, EEQ30_03190, EER35_13455, EGL32_13215, EGN81_14320, EGU67_16280, EGU98_01815, EHB09_17685, EHB24_06860, EHB55_04625, EHC98_13055, EIE48_07335, EIW53_10865, EJI18_11855, EJO08_15295, EJO98_03745, EKA25_05275, EL822_10545, ELO47_06300, ELR28_12910, ELS01_13730, EM832_14630, EM840_15510, EMN66_11055, EMY79_07110, EO190_01820, EP115_08910, EP446_17725, EPB30_04875, EPH81_13125, EQG93_17545, EQG94_14990, ERM04_12360, EU349_14435, EU873_14810, EUB95_06180, EUQ56_12620, EUQ65_14085, EUQ74_12140, EUS13_11340, EVY71_02270, EW905_11445, EWB18_13125, EWE52_09515, EWJ47_12360, EWZ09_10265, EXA47_14060, EXB31_10305, EXB41_12245, EYA29_09815, EYJ91_01000, F0D96_04670, F2O93_06050, F2P00_05765, F3Q46_12455, F3Q59_03865, F3Q88_17410, F3Q97_01745, F3R12_04520, F3R61_14650, F3R63_08825, F9G02_11745, F9O44_07395, FE758_05780, FEM52_10645, FGZ46_12865, FJM64_15875, FL833_14220, FQC24_10790, FQD13_05150, GCH31_04025, GCQ81_09835, GCZ80_06975, GEZ01_15490, GW08_02135, JO10_05360, KP44_07640, LZ63_05160, NG02_08975, NG06_24275, NG18_05800, NU83_05230, QA89_10955, QB40_04985, R035_04270, RJ78_02450, SAMEA4398682_01021, SE14_03092, Y934_04800, YG50_06085, YT65_12255, Z700_09660, ZT09_11460, ZT28_14425, ZT74_12940, ZT89_06430, ZU86_13060, ZU92_03155, ZV33_12500, ZV34_13970, ZV38_09350, ZV58_11905, ZV70_14285, ZV78_10390, ZW74_09615, ZX03_03830, ZY23_09620, ZY27_14455, ZY40_09835, ZY51_10295, ZZ18_13325, ZZ43_10110, ZZ77_05435, ZZ79_07510 EC: 2.3.1
UniProt
Find proteins for A0A0F6B5X4 (Salmonella typhimurium (strain 14028s / SGSC 2262)) Explore A0A0F6B5X4  Go to UniProtKB:  A0A0F6B5X4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter	C, D	36	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: DD95_05360, SE14_03091, STMLT2P22_CBEKMEGD_03680
UniProt
Find proteins for A0A0F6B5X3 (Salmonella typhimurium (strain 14028s / SGSC 2262)) Explore A0A0F6B5X3  Go to UniProtKB:  A0A0F6B5X3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COD (Subject of Investigation/LOI)	E [auth A], F [auth B]	DEPHOSPHO COENZYME A C21 H35 N7 O13 P2 S KDTSHFARGAKYJN-IBOSZNHHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.282 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.671	α = 90
b = 76.633	β = 90
c = 119.655	γ = 90

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