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==Structure of the isolated REC domain of RcsB from Salmonella enterica serovar Typhimurium in the presence of phosphomimetic BeF3-== | ==Structure of the isolated REC domain of RcsB from Salmonella enterica serovar Typhimurium in the presence of phosphomimetic BeF3-== | ||
<StructureSection load='6zii' size='340' side='right'caption='[[6zii]]' scene=''> | <StructureSection load='6zii' size='340' side='right'caption='[[6zii]], [[Resolution|resolution]] 2.50Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZII OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZII FirstGlance]. <br> | <table><tr><td colspan='2'>[[6zii]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZII OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZII FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6zii FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zii OCA], [https://pdbe.org/6zii PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zii RCSB], [https://www.ebi.ac.uk/pdbsum/6zii PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zii ProSAT]</span></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | ||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BFD:ASPARTATE+BERYLLIUM+TRIFLUORIDE'>BFD</scene></td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">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 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892])</td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6zii FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zii OCA], [https://pdbe.org/6zii PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zii RCSB], [https://www.ebi.ac.uk/pdbsum/6zii PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zii ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[[https://www.uniprot.org/uniprot/C4PCU2_SALTM C4PCU2_SALTM]] Component of the Rcs signaling system, which controls transcription of numerous genes. RcsB is the response regulator that binds to regulatory DNA regions. Can function both in an RcsA-dependent or RcsA-independent manner.[HAMAP-Rule:MF_00981] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
Structure-based analyses of Salmonella RcsB variants unravel new features of the Rcs regulon.,Huesa J, Giner-Lamia J, Pucciarelli MG, Paredes-Martinez F, Garcia-del Portillo F, Marina A, Casino P Nucleic Acids Res. 2021 Feb 26;49(4):2357-2374. doi: 10.1093/nar/gkab060. PMID:33638994<ref>PMID:33638994</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6zii" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Bacillus typhimurium loeffler 1892]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Casino P]] | [[Category: Casino, P]] | ||
[[Category: Huesa J]] | [[Category: Huesa, J]] | ||
[[Category: Marina A]] | [[Category: Marina, A]] | ||
[[Category: Dna binding protein]] | |||
[[Category: Phosphorylation]] | |||
[[Category: Response regulator]] | |||
[[Category: Transcriptional factor]] | |||
[[Category: Two-component system]] | |||
Revision as of 20:53, 10 March 2021
Structure of the isolated REC domain of RcsB from Salmonella enterica serovar Typhimurium in the presence of phosphomimetic BeF3-Structure of the isolated REC domain of RcsB from Salmonella enterica serovar Typhimurium in the presence of phosphomimetic BeF3-
Structural highlights
Function[C4PCU2_SALTM] Component of the Rcs signaling system, which controls transcription of numerous genes. RcsB is the response regulator that binds to regulatory DNA regions. Can function both in an RcsA-dependent or RcsA-independent manner.[HAMAP-Rule:MF_00981] Publication Abstract from PubMedRcsB 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. Structure-based analyses of Salmonella RcsB variants unravel new features of the Rcs regulon.,Huesa J, Giner-Lamia J, Pucciarelli MG, Paredes-Martinez F, Garcia-del Portillo F, Marina A, Casino P Nucleic Acids Res. 2021 Feb 26;49(4):2357-2374. doi: 10.1093/nar/gkab060. PMID:33638994[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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