6ZII

Structure of the isolated REC domain of RcsB from Salmonella enterica serovar Typhimurium in the presence of phosphomimetic BeF3-

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


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


Literature

Structure-based analyses of Salmonella RcsB variants unravel new features of the Rcs regulon.

Huesa, J., Giner-Lamia, J., Pucciarelli, M.G., Paredes-Martinez, F., Portillo, F.G., Marina, A., Casino, P.

(2021) Nucleic Acids Res 49: 2357-2374

  • DOI: https://doi.org/10.1093/nar/gkab060
  • Primary Citation of Related Structures:  
    6ZII, 6ZIL, 6ZIX, 6ZJ2

  • PubMed Abstract: 

    RcsB is a transcriptional regulator that controls expression of numerous genes in enteric bacteria. RcsB accomplishes this role alone or in combination with auxiliary transcriptional factors independently or dependently of phosphorylation. To understand the mechanisms by which RcsB regulates such large number of genes, we performed structural studies as well as in vitro and in vivo functional studies with different RcsB variants. Our structural data reveal that RcsB binds promoters of target genes such as rprA and flhDC in a dimeric active conformation. In this state, the RcsB homodimer docks the DNA-binding domains into the major groove of the DNA, facilitating an initial weak read-out of the target sequence. Interestingly, comparative structural analyses also show that DNA binding may stabilize an active conformation in unphosphorylated RcsB. Furthermore, RNAseq performed in strains expressing wild-type or several RcsB variants provided new insights into the contribution of phosphorylation to gene regulation and assign a potential role of RcsB in controlling iron metabolism. Finally, we delimited the RcsB box for homodimeric active binding to DNA as the sequence TN(G/A)GAN4TC(T/C)NA. This RcsB box was found in promoter, intergenic and intragenic regions, facilitating both increased or decreased gene transcription.

    • Organizational Affiliation: 

    Departamento de Bioquímica y Biología Molecular, Universitat de València. Dr Moliner 50, 46100 Burjassot, Spain.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulatory protein RcsBA [auth B],
B [auth A]		143Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: 
rcsB, A2O69_13765, A3042_19525, A3104_15245, A3111_09650, A3122_12425, A3146_09020, A3R41_09960, A3S30_08650, A3T21_09515, A3T81_14325, A3U32_14885, A3V03_11040, A3V89_10805, A3W57_14915, A3W75_12230, A3W86_06130, A3X15_13890, A3X55_20780, A3Y76_07040, A3Z96_14340, A4J27_11660, A4N07_14810, A4O05_20855, A4O41_07785, A4R48_08340, A6D61_15370, A9C21_06135, A9R92_21345, A9T39_16135, A9U46_10475, A9U64_21675, A9U69_21545, AAA76_10930, AAB27_22280, AAB39_09270, AAB79_16325, AAC08_11475, AAC35_11250, AAC42_16960, AAC44_14685, AAC95_13155, AAC98_10995, AAK29_10400, AAP89_11275, AAQ24_16295, AB424_18490, ABO94_17915, ABP11_15160, ABP87_18790, ABQ69_20575, ADQ28_04890, ADQ45_05825, AE787_14130, AF480_10895, AF488_12145, AF489_17255, AF497_17465, AGC55_06475, AGM99_13695, AGQ32_04375, AH984_14180, AHN93_10200, AIC76_12470, AKH62_06605, AKH68_10310, AKI16_13295, AL144_14225, AL151_13230, AL166_17425, AL168_14180, AL170_15835, AL174_14280, AL184_16885, APP08_20700, APY91_13970, AQ530_14880, AQ536_13855, AS118_05400, AT354_14865, AU613_13115, AU731_17745, AU805_14740, AU830_17945, AU839_16960, AU951_10785, AU965_14440, AVA38_10850, AVB77_17860, AVB94_12475, AVC05_13710, AVC09_15555, AVD08_14940, AVD75_10490, AVD94_16345, AVG17_17440, AVL02_06935, AVL16_12105, AVM19_11045, AWT30_16365, AXM10_15020, AXM23_15980, AXR84_09155, AXU58_12665, AXX99_08590, B1265_14695, B1398_15040, B1642_12470, B1B86_13860, B1B89_12995, B1I91_14010, B1P38_06210, B1Q82_08785, B2E31_12855, B4V59_14365, B4W90_11945, B5A40_18175, B6362_19530, B6G98_09840, B6M25_12470, B6M43_11445, B7071_09685, B7890_16815, B7J30_08950, B7Q27_13330, B8Y16_13920, B8Y36_10435, B8Z46_12215, B9653_08735, B9C61_09460, B9C71_10305, B9C90_09140, B9C91_11100, B9C96_06975, B9M14_15255, B9O84_06255, B9U29_20160, BBQ66_07980, BEL47_15520, BFE55_17500, BFE61_13600, BGP52_15605, BIC00_11775, BIC01_03425, BIC03_12465, BIC13_09510, BJP89_14935, BK110_11970, BKM50_13625, BLB03_12065, BMG85_01485, BMS46_14205, BMU56_10065, BSC80_16315, BSD55_15985, BZ203_13370, BZ210_08250, BZG47_14895, BZN20_13125, BZZ88_21635, C4E88_11520, C5U54_24325, C5W43_17645, CA117_14980, CB102_02675, CB119_10390, CB161_08930, CB198_19420, CB380_13295, CB383_12585, CB416_11695, CB530_12435, CB535_09465, CB570_05200, CB646_09025, CB657_11330, CBH20_11220, CBM40_08545, CBM67_14430, CBM76_12750, CBN77_20665, CBO42_14460, CBR08_08850, CBU15_19945, CBU32_00760, CBZ90_12320, CC339_03310, CC403_05060, CC453_12125, CC594_20855, CC652_11600, CC725_10110, CC886_11620, CC918_07450, CC944_09505, CC971_10010, CCF93_15515, CCP17_10715, CCW27_14410, CD48_15270, CD977_10835, CDJ75_08265, CDQ60_11320, CDT37_13185, CDZ72_16490, CE355_08040, CE615_16735, CE70_14835, CE806_10370, CE87_12900, CE896_01015, CEC46_09750, CEC56_04870, CED07_06500, CEL48_20705, CEL55_09205, CEQ70_15765, CER78_12570, CET98_13495, CEY64_16305, CFB16_15760, CFB28_17680, CFE76_19020, CFE79_15610, CFF58_13355, CFF59_13510, CFJ48_12690, CGG73_15810, CHN22_08020, CI444_12440, CIX60_15545, CJC42_16545, CPR79_14100, CPS79_08255, CPX68_07570, CQE35_07160, CQG18_09040, CQO33_12635, CR370_10310, CRB02_10290, CSG22_12970, CVR97_09845, D3147_17580, D3174_01810, D3F31_11215, D3T68_22780, D3Y48_14800, D4361_11425, D4369_10470, D4380_14255, D4387_10710, D4422_10715, D4E62_15595, D4E68_12645, D4E74_04805, D4X64_11635, D4X79_12705, D4Y62_12305, D5823_23275, D5949_13360, D5B48_08355, D5C67_13450, D5C71_13810, D5N86_08445, D5N95_12575, D5O82_10940, D5P17_11555, D5X47_11830, D5X51_21070, D5Y28_05580, D6360_11195, D6367_13185, D6371_12525, D6373_13850, D6395_09765, D6421_13000, D6422_12760, D6J79_14230, D6K10_23715, D6P67_11555, D6Q64_13765, D6S43_13075, D6T00_11290, D6T40_07430, D7F20_11320, D7H43_01075, D7N92_12075, D7O44_13065, D8Q90_09500, D8S24_13515, D9O84_14155, DD95_02420, DJ388_15095, DJ702_13640, DK061_07980, DK631_02345, DK641_19375, DK642_13375, DK689_12355, DK696_07780, DK698_07265, DKJ10_12345, DKR95_07440, DKS55_11340, DKU45_11320, DKU57_10630, DKU80_05405, DLB14_07805, DLB57_08870, DLB93_12855, DLR28_13470, DM322_20130, DM733_21940, DMI89_06860, DMO92_13710, DMV40_11670, DMZ93_22620, DN165_13395, DN204_13780, DN359_20245, DNB97_22830, DNL62_12910, DNM27_08910, DNM63_11945, DNU59_10640, DNV08_13515, DNV12_21330, DNV30_09985, DNY92_08010, DNZ37_12590, DO350_10650, DO533_09745, DO585_12725, DO640_13295, DO698_21090, DO766_09590, DO828_16445, DO960_04625, DOC60_14865, DOH72_12230, DOI32_09640, DOI53_11380, DOI92_10015, DOJ39_13330, DOJ91_15905, DOQ54_10850, DOQ88_19075, DOR12_10695, DOV43_19010, DOW25_10390, DP680_11760, DPB42_06345, DPB45_09375, DPB48_12795, DPB57_11855, DPD91_07890, DPD95_08365, DPD99_18580, DPF41_10345, DPF68_09290, DPJ93_06885, DPK32_10835, DPK79_10855, DPL02_08725, DPP13_16840, DPP94_12530, DPP97_14020, DPS76_08870, DPT18_10485, DPU20_11590, DPY58_18740, DQ848_10815, DQ947_12275, DQ951_12780, DQC39_14690, DQC52_17465, DQD03_12025, DQD22_14205, DQE64_12330, DQE65_13455, DQK42_17635, DQQ98_14965, DQR10_20350, DQR44_12005, DQR61_11120, DQS14_10375, DQY10_09140, DQZ46_08550, DQZ56_12760, DR982_22020, DRL45_07940, DRM14_11520, DRM16_14710, DRR75_23095, DRT38_13015, DRT61_23690, DRT65_15310, DRV05_08945, DRW84_11665, DRX36_22780, DRX66_07345, DS270_18375, DS296_03655, DS451_17430, DS453_12950, DS521_10015, DS619_11600, DSF69_12145, DSF94_10460, DSG41_14570, DSM38_11155, DSN15_12590, DSR36_10905, DTE73_10415, DTF68_07740, DTG22_22525, DTG27_16445, DTW13_10745, DTW14_14950, DTW26_11965, DU071_21905, DU223_06195, DU657_07745, DU821_10140, DU879_10520, DU924_08500, DUQ28_11140, DUQ56_08490, DUQ92_13185, DUR36_14185, DUV75_15260, DUW10_15950, DUW48_09895, DVF14_11920, DVF88_08270, DVG01_14360, DVZ53_05935, DWU22_23860, DWU62_21645, DY580_21440, DYM27_06865, DYS82_09690, DZG11_20930, E0584_16370, E0595_14185, E0600_21890, E0935_14485, E0989_09310, E0M34_15895, E0S07_16310, E0U75_13640, E0V94_09045, E1336_08925, E1A11_13485, E1A20_12000, E5196_05695, E6W45_14470, EBB93_17635, EBC01_10965, EBD14_12205, EBD99_18850, EBK21_14930, EBL31_09840, EBO41_09410, EBP31_06115, EC404_15850, EC52_15480, ECA50_20460, ECC89_11785, ED424_08285, ED467_11830, EDL18_13765, EEK73_13190, EEQ30_16240, EER35_07340, EGL32_12130, EGN81_07495, EGU67_13655, EGU98_14315, EHB09_14460, EHB24_11945, EHB55_22345, EHC98_05345, EIE48_10505, EIW53_04795, EJI18_11350, EJO08_13340, EJO98_13625, EKA25_12980, EL822_07390, ELO47_09560, ELR28_08900, ELS01_12400, EM832_12680, EM840_06380, EMN66_07620, EMY79_09360, EO190_08315, EP115_18440, EP446_20135, EPB30_13505, EPH81_08120, EQG93_05510, EQG94_13030, ERM04_09810, EU306_11875, EU349_11640, EU873_21965, EUB95_05675, EUQ56_12115, EUQ65_09175, EUQ74_13570, EUS13_08790, EVT69_22445, EVY71_04215, EW905_06135, EWB18_06485, EWE52_05820, EWJ47_09340, EWZ09_13550, EXA47_07665, EXB31_05300, EXB41_09095, EYA29_15940, EYJ91_08825, F0D96_14965, F2O93_14305, F2P00_11865, F3Q46_16675, F3Q58_07850, F3Q59_15070, F3Q88_00720, F3Q97_16025, F3R12_18690, F3R61_10195, F3R63_13520, F9G02_06435, F9O44_04025, FE758_13940, FEM52_13990, FGZ46_08850, FJM64_14760, FL833_11895, FQC24_10010, FQD13_04095, FQX78_02535, GCH31_06840, GCQ81_17295, GCZ80_15980, GEZ01_10265, GW08_14750, JO10_24665, KP44_13855, LZ63_14980, NCTC13348_05301, NG02_14230, NG06_18895, NG18_08765, NU83_17610, QA89_08030, QB40_11485, QD15_11360, R035_06990, RJ78_11590, SAMEA4398682_01637, SE14_02481, Y934_23370, YG50_16765, YR17_10960, YT65_22010, Z700_22650, Z705_18140, ZB89_19920, ZC54_19680, ZT09_16805, ZT28_13365, ZT74_18075, ZT89_18160, ZU86_17815, ZU92_16805, ZV06_14780, ZV17_16185, ZV33_17250, ZV34_18355, ZV38_13400, ZV58_19590, ZV70_18315, ZV76_14470, ZV78_21800, ZV90_21250, ZW74_16110, ZX03_15750, ZY23_11835, ZY27_17660, ZY40_02770, ZY51_16230, ZZ18_15945, ZZ43_13745, ZZ77_13130, ZZ79_15595

UniProt
Find proteins for P58663 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P58663 
Go to UniProtKB:  P58663
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58663
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
BFD
Query on BFD		A [auth B],
B [auth A]		L-PEPTIDE LINKINGC4 H6 Be F3 N O4ASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.144α = 90
b = 64.4β = 100.14
c = 47.131γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBFU2016-78606-P
Spanish Ministry of Economy and CompetitivenessSpainBIO2016-78571-P
Spanish Ministry of Economy and CompetitivenessSpainBIO2016-77639-P
Spanish Ministry of Economy and CompetitivenessSpainRYC-2014-16490

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-17
    Type: Initial release
  • Version 1.1: 2021-03-10
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description