6Z4E

The structure of the C-terminal domain of RssB from E. coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

wwPDB Validation 3D Report Full Report



Literature

Insight into the RssB-Mediated Recognition and Delivery of sigmasto the AAA+ Protease, ClpXP.

Micevski, D.Zeth, K.Mulhern, T.D.Schuenemann, V.J.Zammit, J.E.Truscott, K.N.Dougan, D.A.

(2020) Biomolecules 10

  • DOI: 10.3390/biom10040615
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In Escherichia coli , SigmaS (σ S ) is the master regulator of the general stress response. The cellular levels of σ S are controlled by transcription, translation and protein stability. The turnover of σ S , ...

    In Escherichia coli , SigmaS (σ S ) is the master regulator of the general stress response. The cellular levels of σ S are controlled by transcription, translation and protein stability. The turnover of σ S , by the AAA+ protease (ClpXP), is tightly regulated by a dedicated adaptor protein, termed RssB (Regulator of Sigma S protein B)-which is an atypical member of the response regulator (RR) family. Currently however, the molecular mechanism of σ S recognition and delivery by RssB is only poorly understood. Here we describe the crystal structures of both RssB domains (RssB N and RssB C ) and the SAXS analysis of full-length RssB (both free and in complex with σ S ). Together with our biochemical analysis we propose a model for the recognition and delivery of σ S by this essential adaptor protein. Similar to most bacterial RRs, the N-terminal domain of RssB (RssB N ) comprises a typical mixed (βα) 5 -fold. Although phosphorylation of RssB N (at Asp58) is essential for high affinity binding of σ S , much of the direct binding to σ S occurs via the C-terminal effector domain of RssB (RssB C ). In contrast to most RRs the effector domain of RssB forms a β-sandwich fold composed of two sheets surrounded by α-helical protrusions and as such, shares structural homology with serine/threonine phosphatases that exhibit a PPM/PP2C fold. Our biochemical data demonstrate that this domain plays a key role in both substrate interaction and docking to the zinc binding domain (ZBD) of ClpX. We propose that RssB docking to the ZBD of ClpX overlaps with the docking site of another regulator of RssB, the anti-adaptor IraD. Hence, we speculate that docking to ClpX may trigger release of its substrate through activation of a "closed" state (as seen in the RssB-IraD complex), thereby coupling adaptor docking (to ClpX) with substrate release. This competitive docking to RssB would prevent futile interaction of ClpX with the IraD-RssB complex (which lacks a substrate). Finally, substrate recognition by RssB appears to be regulated by a key residue (Arg117) within the α5 helix of the N-terminal domain. Importantly, this residue is not directly involved in σ S interaction, as σ S binding to the R117A mutant can be restored by phosphorylation. Likewise, R117A retains the ability to interact with and activate ClpX for degradation of σ S , both in the presence and absence of acetyl phosphate. Therefore, we propose that this region of RssB (the α5 helix) plays a critical role in driving interaction with σ S at a distal site.


    Organizational Affiliation

    Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Victoria, Australia.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Regulator of RpoSA337Escherichia coliMutation(s): 0 
Gene Names: 
rssBhnrhnr_1mprAA6592_12285A9819_08910A9P13_11755A9R57_00160A9X72_14735AC067_21430AC789_1c13280ACN002_1789ACN81_08095ACU57_17620ACU90_08885AM446_12740AM464_24190AMK83_01205AML35_06845APT94_15840ARC77_27795AU473_15945AUQ13_16200AW059_17300AWB10_14700AWG90_009190AWP75_04025AZZ83_000992B7C53_18050B9M99_24180B9T59_25180BANRA_01040BANRA_01808BANRA_04363BB545_17980BE963_20595BEN53_11945BER14_03290BHF46_19570BHS81_07890BHS87_06485BIQ87_08370BIU72_22630BJJ90_10855BK248_11085BK292_03160BK296_14330BK334_26025BK373_11990BK375_23175BK383_02950BMA87_22030BMT49_09055BMT91_09245BN17_10821BOH76_13050BON66_13145BON72_24405BON75_08375BON76_11355BON83_18640BON86_11210BON87_22805BON92_24370BON94_22865BON95_24035BON96_12105BTQ04_24715BUE81_18980BvCms12BK_02484BvCms2454_02833BvCms28BK_02803BvCms35BK_05038BvCmsC61A_02256BvCmsHHP001_02186BvCmsHHP019_01301BvCmsHHP056_05034BvCmsKKP036_04672BvCmsKKP061_04975BvCmsKSNP120_02192BvCmsKSP011_00462BvCmsKSP024_02476BvCmsKSP026_01332BvCmsKSP045_03694BvCmsKSP067_03440BvCmsKSP076_03541BvCmsNSP006_02213BvCmsNSP047_02978BvCmsNSP072_02109BvCmsOUP014_03751BvCmsSINP011_00253BvCmsSINP022_03769BvCmsSIP019_02784BvCmsSIP044_03844BW690_18240BWI89_07875BWP17_16430BXT93_09825BZL31_06510BZL69_22380C2M16_23935C4M78_06805C5715_26490C5N07_14815C5P01_10130C6B13_24695C7B08_19445C7B18_10400C9098_20715C9114_03490C9162_19930C9E25_09535C9E67_16735C9Z28_09575C9Z37_18675C9Z39_16170C9Z43_21850C9Z68_04975C9Z70_10925C9Z78_19580CDL37_21850CG692_16970CI641_022095CI693_21315CI694_02515CIG45_18955CJU63_07225CJU64_07205CMR93_08290CO706_02245CQP61_12380CR538_14935CR539_10900CRD98_02710CRE06_20400CRM83_08195CSB64_26365CVH05_11605CWM24_25125CWS33_12195D0X26_16310D2184_21845D2185_04660D2188_06515D3821_18960D3822_25725D3O91_15125D3P01_18245D3Y67_03705D4011_19390D4074_18420D4628_24790D4638_16915D4660_17800D4718_17015D4L91_18070D4M06_18325D4U49_02375D4U85_24170D4V08_24465D5I97_16070D6C36_19015D6D43_18990D6T98_15825D6W00_04815D6X36_08455D6X63_10260D6X76_19735D7K33_16565D7K63_19625D7K66_17590D7Y10_04695D8Y65_17330D9C99_06000D9D20_02685D9D31_11935D9D43_15965D9D44_20665D9E34_23220D9E73_15920D9F17_15425D9F32_14445D9F87_03430D9G11_13315D9G29_18360D9G42_02925D9G48_18310D9G69_04710D9G95_14555D9H36_14670D9H53_02790D9H68_05330D9H94_13155D9I18_20435D9I20_17620D9I87_18935D9I88_16720D9I97_10925D9J03_02525D9J11_07315D9J44_04270D9J52_04145D9J58_07860D9J60_06710D9J78_06745D9K02_11490D9K54_27670D9L89_18585D9L99_03780D9X77_22665D9X97_16420D9Z28_16200DAH18_05280DAH26_19015DAH34_18750DAH37_10860DAH43_21690DB359_24230DBQ99_14635DD762_14095DEN86_06655DJ503_14225DL257_23010DL326_10420DL455_24225DL479_22750DL545_14110DL705_22810DLT82_22375DLU50_18730DLU67_16595DLW88_23395DLY44_17335DM102_21135DM129_24100DM267_12650DM272_05300DM280_22885DM296_17140DM382_21020DM962_21285DMI04_17380DMI53_17620DMO02_18740DN703_16890DN808_10315DNB37_20075DNC98_05100DND16_23550DNJ62_18255DNK12_16330DNQ45_05955DNX19_14700DNX30_19735DOE35_17195DOM23_04930DOS18_17410DOT81_18245DOU81_17165DOY22_23715DOY56_17830DP265_16525DP277_16630DQE83_20590DQF57_24990DQF72_16360DQG35_18210DQP61_23770DRP48_23545DS721_23135DS732_11210DT034_21255DTL43_10840DTM10_08180DTM45_18755DTZ20_17555DU309_09895DU321_13755DWB25_10945DXT71_06715DXT73_23015DXX80_001800E0K84_08575E0L12_11290E2114_19485E2115_17895E2119_11270E2127_03150E2128_00695E2129_00615E2134_01855E2135_14125E2148_22680E4K55_12025E5P28_11910E5P37_05250E5S46_13055E5S58_07175E5S61_08040EA213_10060EA214_18925EA218_20425EA223_17475EA225_16145EA233_22945EAI42_22930EAI46_14000EAI52_18695EAN77_11025EAX79_03880EB476_02540EB509_22450EB510_13060EB515_18140EBA46_08625EBA84_20095EBJ06_17920EC1094V2_2584EC3234A_230c00200EC3426_02205EC382_13645ECONIH1_07535ECs1737ECTO6_02736ED225_17390ED307_00720ED607_14200ED611_18575ED903_05620ED944_19555EEA45_13325EEP23_09200EF082_15380EF173_20100EG796_16015EG808_13125EGC26_05775EGU87_14985EHD45_15345EHD63_15135EHD79_19600EHJ66_19635EHV81_21430EHV90_16075EHW09_14885EHX09_17035EI021_07435EI028_11465EI032_01895EI041_13575EIA08_21525EIZ86_03715EJ366_12035EL75_2532EL79_2537EL80_2538ELT20_12120ELT23_11540ELT58_14860ELU85_13030ELV08_05005ELY05_04790EPS91_14965EPT01_10820EPU41_06515EQ823_18775EQ825_00975EQ830_20830ERL57_09830ERS085365_01743ERS085366_03233ERS085374_04259ERS085379_03047ERS085386_04518ERS085416_00026ERS139211_03176ERS150873_03092EST51_14450EVY14_23735ExPECSC019_00040ExPECSC038_03617EXX13_01755EXX24_08715EXX71_05755EYD11_13005EYX82_04675EYY27_02655EYY34_17095EYY78_13800F1E13_06985F1E19_10610F7F11_15235F7F18_21485F7F29_12065F7G01_19090F7G03_12390F9059_23885F9Z74_19590FAF34_015415FE846_20005FNJ69_03755FNJ83_09180FORC82_2685FQ022_16345FQ915_07375FRV13_08100FTV90_15170FTV92_07355FTV93_07630FV293_13565FV438_12175FVB16_13470FWK02_05620FY127_06520GII91_22080GIY13_08440GJ11_07635GJD97_15685GKE15_16485GKE22_17540GKE24_17870GKE26_17520GKE29_16140GKE31_18415GKE39_17505GKE46_17825GKE58_16120GKE60_16420GKE64_18180GKE77_18175GKE87_24075GKE93_22065GKF03_14165GKF28_17130GKF34_17325GKF47_16885GKF74_11940GKF86_14100GKF89_00950GKG12_03700GN312_21280GNZ00_18580GNZ02_14165GNZ03_13750GP654_03565GP689_02970GP700_11105GP712_15645GP720_20035GP727_10930GP912_15560GP950_08230GQE22_17090GQE34_03950GQE64_00365GQE68_18270GQE88_12505GQM06_08320GQM17_08750GRW42_04950GRW80_13665HmCms184_02215HmCmsJML074_03291HmCmsJML204_01220HMPREF3040_00025HW43_09890MJ49_00040MS6198_13920NCTC10082_00435NCTC10090_00811NCTC10764_02469NCTC10766_00432NCTC10963_02922NCTC10974_03222NCTC11181_04669NCTC11341_05061NCTC13148_00433NCTC13216_03820NCTC13846_02173NCTC7922_01688NCTC7927_03158NCTC7928_00223NCTC8179_03170NCTC8500_03154NCTC8622_05643NCTC9036_03009NCTC9044_04544NCTC9045_03320NCTC9050_05503NCTC9058_04083NCTC9062_00871NCTC9073_01776NCTC9077_03581NCTC9111_02898NCTC9117_03685NCTC9701_03123NCTC9702_03416NCTC9703_02100NCTC9706_00228NCTC9777_03824NCTC9962_06125PGD_02019RK56_003900RX35_02955SAMEA3472043_03611SAMEA3472047_00899SAMEA3472055_01216SAMEA3472070_03354SAMEA3472080_01194SAMEA3472090_03299SAMEA3472108_02818SAMEA3472110_01008SAMEA3472112_01334SAMEA3472114_00123SAMEA3484427_01683SAMEA3484429_01548SAMEA3484434_02232SAMEA3485113_00260SAMEA3752372_01438SAMEA3752553_01775SAMEA3752557_04723SAMEA3753064_00121SAMEA3753290_01115SAMEA3753300_01534SK85_01369UC41_16245UN86_12285WR15_17665YDC107_4543

Find proteins for C3TCP2 (Escherichia coli)
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Go to UniProtKB:  C3TCP2
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.239α = 90
b = 56.239β = 90
c = 294.462γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-07-29
    Type: Initial release