7ZHM

Salmonella enterica Rhs1 C-terminal toxin TreTu complex with TriTu immunity protein

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Salmonella antibacterial Rhs polymorphic toxin inhibits translation through ADP-ribosylation of EF-Tu P-loop.

Jurenas, D., Rey, M., Byrne, D., Chamot-Rooke, J., Terradot, L., Cascales, E.

(2022) Nucleic Acids Res 50: 13114-13127

  • DOI: https://doi.org/10.1093/nar/gkac1162
  • Primary Citation of Related Structures:  
    7ZHL, 7ZHM

  • PubMed Abstract: 

    Rearrangement hot spot (Rhs) proteins are members of the broad family of polymorphic toxins. Polymorphic toxins are modular proteins composed of an N-terminal region that specifies their mode of secretion into the medium or into the target cell, a central delivery module, and a C-terminal domain that has toxic activity. Here, we structurally and functionally characterize the C-terminal toxic domain of the antibacterial Rhsmain protein, TreTu, which is delivered by the type VI secretion system of Salmonella enterica Typhimurium. We show that this domain adopts an ADP-ribosyltransferase fold and inhibits protein synthesis by transferring an ADP-ribose group from NAD+ to the elongation factor Tu (EF-Tu). This modification is specifically placed on the side chain of the conserved D21 residue located on the P-loop of the EF-Tu G-domain. Finally, we demonstrate that the TriTu immunity protein neutralizes TreTu activity by acting like a lid that closes the catalytic site and traps the NAD+.

    • Organizational Affiliation: 

    Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université, CNRS, UMR 7255, 13009 Marseille, France.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rhs1 protein
A, B
114Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: 
UniProt
Find proteins for Q8ZRL0 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q8ZRL0 
Go to UniProtKB:  Q8ZRL0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ZRL0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Immunity protein TriTu
C, D
87Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: 
A3104_21280, A3S30_24885, A3T81_18830, A3U32_23685, A3V03_03705, A3V89_26565, A3W57_07430, A3W75_17160, A3X15_18460, A3Y76_22790, A4N07_19890, A4O05_22095, A4O41_12545, A4R48_24810, A6D61_18845, AAA76_24645, AAB27_16245, AAB79_24185, AAC35_21755, ADQ28_19745, AGM99_21090, AIT36_18185, AKH62_23030, AL144_24155, AL168_20775, AL184_23325, AQ530_17415, AU613_26795, AVA38_22450, AVL16_21415, AWT30_20335, B1265_13470, B1642_20645, B1P38_21655, B2E31_16670, B4V59_16295, B4W90_20805, B6362_18775, B7Q27_21350, B8Y16_20415, B8Z46_24695, B9C90_17255, B9C96_11800, B9M14_21175, B9O84_21965, BG493_18250, BIC00_10565, BIC13_08285, BK110_20995, BKM50_05830, BMS46_06345, BZ203_05255, BZZ88_03145, C5W43_06445, CA117_20185, CAC59_18410, CB646_20565, CBM67_18245, CBM76_20015, CBZ90_02090, CC339_16850, CC453_18020, CC652_24350, CCP17_20025, CDZ72_05380, CE70_17375, CEQ70_05720, CFF58_06395, CFF59_23420, CHN22_22420, CIX60_10615, CPS79_21305, CQO33_21175, CSG22_15055, CVR97_23495, D4361_24780, D4387_21370, D5823_18210, D5N86_25720, D5N95_24415, D5X47_21300, D6422_21315, D6J79_20570, D8S24_24495, DD95_17770, DLB93_21650, DLR28_20680, DMI89_02275, DMO92_25405, DN165_21400, DNB97_10255, DNZ37_21745, DO533_23325, DP680_20880, DPB42_24965, DPD91_20640, DPF41_22985, DPS76_24805, DQD22_24730, DQR44_25750, DRT38_21835, DSF94_24595, DU071_23735, DU657_22350, DU793_24960, DWU22_23300, DY580_17115, DYM27_14260, E0935_15085, E1A11_24660, E6W45_19865, EBD14_21680, EBK21_05210, EC404_18500, ED463_24780, EER35_24745, EHB09_18595, EK388_24345, ELS01_16950, EPB30_20945, EVY71_17715, F0D96_10735, F2P00_21530, F3Q97_07515, F3R12_08905, F9G02_19695, F9O44_23175, FEM52_19775, FGZ46_23375, FQC24_21550, G0038_13780, G0040_20120, G0042_18040, G0045_14575, G0047_13425, G0048_23400, G0051_22050, G0052_21825, G0059_15490, G0061_22165, G0062_16025, G0063_14840, G0067_13555, G0069_22925, G0070_23015, G0071_21925, G0072_07235, G0074_16430, G0076_15445, G0077_22910, G0080_17120, G0084_21735, G0086_23605, G0087_16490, G0088_22725, G0089_23720, G0090_23715, G0094_19715, G0100_23135, G0101_12940, G0102_15580, G0111_13420, G0113_17090, G0117_16475, G0123_16485, G0124_22895, G0148_15150, G0157_15905, G0170_21030, G0A32_24610, G0A39_17590, G0A43_17095, G0A44_21085, G0A46_19240, G0A50_18180, G0A51_20520, G0A53_24605, G0A58_24565, G0A60_20185, G0A61_24205, G0A66_20235, G0A67_17800, G0A68_19685, G0A70_20300, G0A73_20560, G0A76_24590, G0A79_18405, G0A92_21395, G0A96_18505, G0A97_19250, G0B03_20850, G0B05_20705, G0B07_16840, G0B08_21360, G0B12_21550, G0B96_23080, G0C03_24060, G0C04_24220, G0E15_21920, G0J24_22230, G0J26_25045, G0J27_25740, G0J28_19390, G0J31_25020, G0J33_18415, G0J34_20270, G0J36_21375, G0J37_24850, G0J40_21210, G0J43_24590, G0J44_24385, G0J45_23050, G0J46_22870, G0J47_24120, G0J49_20830, G0J51_21340, G0J53_11145, G0J55_24390, G0J58_15270, G0J66_15690, G0J67_25385, G0J69_25180, G0J71_10030, G0J76_18575, G0J79_03375, G0J81_26215, G0J82_02110, G0J85_17250, G0J97_23130, G0K00_25630, G0K02_24765, G0K03_21950, G0K04_16625, G0K05_24660, G0K07_08180, G0K13_24505, G0K15_25490, G0K18_22600, G0K20_24440, G0K23_21730, G0K25_19165, G0K26_19795, G0K30_21835, G0K31_21125, G0K32_24960, G0K33_21675, G0K37_26455, G0K38_09335, G0K39_24415, G0K41_25485, G0K42_07385, G0K44_21165, G0K46_22525, G0K47_20865, G0K56_20360, G0K61_19885, G0K65_20230, G0K68_13530, G0K70_20080, G0K72_25870, G0K75_20250, G0K78_22450, G0K83_20680, G0K84_08060, G0K88_004862, G0K89_004674, G0K90_004874, G0K94_004855, G0K95_004955, G0L00_004940, G0L02_004996, G0L03_24850, G0L06_24860, G0L07_26440, G0L10_24895, G0L14_15080, G0L15_24510, G0L18_24450, G0L19_24455, G0L20_20700, G0L24_22165, G0L25_20785, G0L29_20935, G0L31_20250, G0L32_18730, G0L34_19930, G0L35_16925, G0L36_21935, G0L37_20125, G0L38_12415, G0L48_24860, G0L49_24370, G0L51_18465, G0L52_23735, G0L55_21695, G0L59_24055, G0L62_23350, G0L63_24085, G0L65_24025, G0L67_19310, G0L68_17340, G0L73_23990, G0L76_23685, G0L78_24345, G0L79_23490, G0L83_23425, G0L86_004812, G0L89_24295, G0L91_24300, G0L96_18690, G0M05_22390, G0M06_004322, G0M13_004595, G0M14_21270, G0M16_23890, G0M18_004837, G0M21_22175, G0M22_004559, G0M25_004774, G0M26_24365, G0M29_004801, G0M30_21230, G0M33_24520, G0M35_09450, G0M38_22475, G0M39_24755, G0M41_21985, G0M45_21465, G0M46_004440, G0M48_004285, G0M53_23940, G0M55_19470, G0M56_19795, G0M58_20480, G0M63_26290, G0M65_19275, G0M67_19925, G0N45_07225, G0N48_21510, G0N51_19570, G0N53_23280, G0N55_14925, G0N57_23975, G0N58_12235, G0N59_12850, G0N60_07005, G0N61_11300, G0N62_19460, G0N64_21975, G0N65_17595, G0N66_06990, G0N67_21060, G0N71_13580, G0N75_12675, G0N78_12230, G0N82_24540, G0N84_21935, G0N85_09660, G0N86_06910, G0N88_19275, G0N89_17190, G0N90_13675, G0N94_23710, G0N95_20720, G0N98_19345, G0N99_14210, G0O00_10205, G0O10_08850, G0O14_23250, G0O19_21995, G0O20_19940, G0O22_07780, G0O25_02530, G0O27_12190, G0O31_13055, G0O32_20735, G0O37_05335, G0O39_11125, G0O40_07750, G0O41_22035, G0O42_21895, G0O43_14195, G0O47_22690, G0O52_15185, G0O55_24580, G0O57_14580, G0O58_14110, G0O59_02765, G0O60_13880, G0O63_14335, G0O68_16445, G0O70_16490, G0O71_22265, G0O74_11810, G0O75_22305, G0O77_14470, G0O78_16070, G0O80_13375, G0O81_17735, G0O82_14790, G0O84_15955, G0O85_22150, G0O87_15165, G0O89_22500, G0O92_22385, G0O93_21600, G0O97_23980, G0O99_21870, G0P00_11275, G0P01_09120, G0P02_11570, G0P06_15360, G0P08_23205, G0P12_21645, G0P13_14815, G0P17_08625, G0P18_23550, G0P19_15165, G0P24_23215, G0P26_16080, G0P28_15535, G0P30_18490, G0P31_16945, G0P36_17640, G0P37_03640, G0P41_08910, G0P44_05725, G0P45_20895, G0P48_14810, G0P49_24390, G0P52_16495, G0P53_25970, G0P56_15465, G0P57_22450, G0P58_07240, G0P65_09610, G0P69_15980, G0P73_20420, G0P75_21260, G0P76_06270, G1N61_22185, G1N64_16755, G1N66_16750, G1N68_16445, G1N71_16735, G1N72_16750, G1N86_17030, G1N87_16775, G1N91_02715, G1O00_17040, G1O02_17040, G1O04_16755, G1O05_16750, G1O08_22790, G1O10_20855, G1O12_17045, G1O16_17040, G1O17_16525, G1O18_17045, G1O20_17035, G1O23_16075, G1O25_17030, G1O26_17035, G1O27_21860, G1O28_16795, G1O29_21775, G1O32_17025, G1O34_17105, G1O38_22465, G1O40_23015, G1O43_17025, G1O46_16735, G1O48_16810, G1O49_16885, G1O51_17030, G1O53_17100, G1O62_17040, G1O63_17020, G1O65_21780, G1O67_16355, G1O68_22065, G1O69_16595, G1O71_16590, G1O72_22140, G1O76_17115, G1O77_17030, G1O80_17125, G1O81_16760, G1O83_17620, G1O84_17115, G1O87_17120, G1O88_22145, G1O89_17040, G1O90_17110, G1O93_17110, G1O94_17105, G1O96_17110, G1P02_17100, G1P03_17955, G1P06_22395, G1P09_16990, G1P10_17055, G1P12_17110, G1P14_23900, G1P15_17570, G1P17_17120, G1P19_17110, G1P23_17115, G1P24_22065, G1P25_18595, G1P26_22030, G1P29_17940, G1P31_17100, G1P35_17035, G1P36_17030, G1P37_20220, G1P40_22710, G1P44_17035, G1P45_17115, G1P47_16830, G1P48_17115, G1P51_17115, G1P52_17885, G1P53_17830, G1P54_17125, G1P55_16805, G1P56_17090, G1P57_16840, G1P58_17105, G1P59_17115, G1P61_17570, G1P64_16805, G1P67_21670, G1P69_17025, G1P72_20030, G1P75_16360, G1P76_16700, G1P78_17005, G1P83_20760, G1P84_17040, G1P87_17110, G1P90_16190, G1P91_17105, G1Q03_16720, G1Q08_21475, G1Q67_17115, G1Q78_19740, G1Q81_16595, G1Q83_17535, G1Q84_19165, G1Q85_16240, G1Q86_16210, G1Q88_20510, G1Q90_21735, G1Q91_22000, G1Q93_21400, G1Q96_25325, G1Q98_16260, G1Q99_20460, G1R01_17960, G1R02_17040, G1R03_22070, G1R04_17050, G1R08_14270, G1R13_21520, G1R15_20520, G1R20_02785, G1R21_15830, G1R22_16790, G1R23_14625, G1R27_16360, G1R28_16555, G1R29_17120, G1R30_16810, G1R31_16595, G1R36_18045, G1R38_16005, G1R40_16640, G1R42_25245, G1R44_22230, G1R45_21135, G1R47_16330, G1R48_19405, G1R51_16745, G1R53_18050, G1R63_22140, G1R69_20835, G1R87_17240, G1R93_16715, G1S02_16830, G2203_21425, G2212_15325, G2218_13260, G2279_08735, G2290_16920, G2793_20235, G2951_19065, G3221_004811, G3230_001780, G3231_003879, G3247_004837, G3248_001209, G3254_003730, G3270_004034, G3275_004813, G3336_003433, G3357_000489, G3369_004805, G3433_001837, G3464_004195, G3593_004828, G3A35_20820, G3V06_004100, G3V14_003903, G3V17_004533, G3V56_003854, G3V57_003910, G3X03_003938, G4189_003906, G4190_003784, G4192_004102, G4198_004153, G4201_001080, G4202_004362, G4A01_004238, G4A73_004743, G4A83_005114, G4A87_000956, G4B68_004665, G4B72_003508, G4B74_004047, G4C74_004222, G4D46_003776, G4F88_05850, G4F89_18520, G4F91_18175, G4F92_05850, G4G62_004887, G4G67_004167, G4G68_004801, G4G75_004042, G4G76_004048, G4G97_002755, G4H00_004444, G4H04_005144, G4H08_004806, G4H18_004810, G4H21_004803, G4H24_004341, G4H63_002715, G4I66_000598, G4J08_004555, G4J11_001980, G4J12_003329, G4J18_004322, G4J37_003944, G4J39_003448, G4J41_004178, G4J45_003829, G4J90_001468, G4K02_001147, G4K03_003353, G4O54_004070, G4O56_003838, G4O59_004025, G4O60_004234, G4O67_004414, G4O69_004025, G4P83_003986, G4P85_004251, G4P91_004016, G4P93_004472, G4Q12_004823, G4Q28_004358, G4Q31_004334, G4Q50_003968, G4Q52_003922, G4Q59_002007, G4Q60_003792, G4Q63_001067, G4Q94_004834, G4R01_003770, G4R02_004438, G4R15_004098, G4R16_004319, G4W68_004926, G4W73_004895, G4W86_004198, G4W87_004002, G4W88_004801, G4W91_004805, G4Y10_002409, G9269_004199, G9302_002703, G9305_004856, G9309_005009, G9313_003833, G9314_004703, G9367_004346, G9381_004732, G9C41_003972, G9C46_003916, G9C47_004060, G9C49_003732, G9C57_004803, G9C64_004472, G9G03_003957, G9G04_001247, G9G36_005129, G9G45_004558, G9G50_004372, G9G62_001322, G9W28_004171, G9W45_003984, G9W63_004617, G9W65_003987, G9W79_004270, G9W95_004378, G9W96_004800, GB021_10965, GB055_04415, GB076_17045, GB120_12265, GB131_19950, GB139_22990, GB171_14405, GB238_02775, GB280_14665, GB321_14460, GB331_23540, GB339_17310, GB342_18675, GB368_16270, GB372_23665, GB416_05155, GB452_17995, GB551_15365, GB567_23270, GBS44_20470, GBS58_20685, GBV53_19000, GBV54_05600, GBV60_14260, GBW44_24125, GBW52_14355, GBX12_18915, GBX20_18780, GBX46_21740, GBX55_16600, GBX64_17400, GBY13_08040, GBY23_19195, GBY73_04995, GBZ51_12855, GBZ55_24160, GCZ80_16680, GEZ01_12860, GJE27_26390, GJE28_08005, GNB28_004372, GNB36_003911, GNB86_003798, GNC11_003866, GNC19_004178, GNC45_003899, GNC75_003847, GTH60_08285, GTH62_23985, GTH63_21380, GTH68_16350, GTH70_24020, GTH73_18915, GTH75_20565, GTH77_04125, GTH78_21700, GTH79_06145, GTH81_12470, GTH85_15115, GTH87_15270, GTH89_25265, GTH90_24705, GTH91_24140, GTH93_17950, GTH94_22025, GTH99_25265, GXC51_12215, GXC56_23790, GXG40_14360, GYI62_004095, GYI77_06055, GYJ04_10830, GYJ27_02810, GYJ28_003616, GYJ30_21530, GYJ32_17670, GYJ53_17120, GYJ59_23540, GYJ60_22120, H8S97_01475, JJB80_01480, JJB81_01480, KP44_21460, NG06_24890, R035_03375, SEL4126_35730, STMLT2P22_CBEKMEGD_01031, Z700_16310, ZV17_24660, ZV33_19520, ZX03_23930, ZY40_12970

UniProt
Find proteins for A0A0H3TET1 (Salmonella typhimurium)
Explore A0A0H3TET1 
Go to UniProtKB:  A0A0H3TET1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3TET1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.645α = 90
b = 94.036β = 110.069
c = 61.305γ = 90
Software Package:
Software NamePurpose
PDB-REDOrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-17-CE11-0039
Agence Nationale de la Recherche (ANR)FranceANR-20-CE11-0017

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release
  • Version 1.1: 2022-12-28
    Changes: Database references
  • Version 1.2: 2023-01-18
    Changes: Database references