2k29

From Proteopedia

(Difference between revisions)

Revision as of 08:39, 14 June 2023

Structure of the DBD domain of E. coli antitoxin RelB

Structural highlights

2k29 is a 2 chain structure with sequence from Escherichia coli. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RELB_ECOLI Antitoxin component of a toxin-antitoxin (TA) module. Counteracts the effect of RelE via direct protein-protein interaction, enabling the reversion of translation inhibition. Also acts as an autorepressor of relBE transcription. DNA-binding and repression is stronger when complexed with corepressor RelE. Increased transcription rate of relBE and activation of relE is consistent with a lower level of RelB in starved cells due to degradation of RelB by protease Lon.^[1] ^[2] ^[3] ^[4] ^[5] Seems to be a principal mediator of cell death in liquid media.^[6] ^[7] ^[8] ^[9] ^[10]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The Escherichia coli chromosomal relBE operon encodes a toxin-antitoxin system, which is autoregulated by its protein products, RelB and RelE. RelB acts as a transcriptional repressor and RelE functions as a cofactor to enhance the repressor activity of RelB. Here, we present the NMR-derived structure of a RelB dimer and show that a RelB dimer recognizes a hexad repeat in the palindromic operator region through a ribbon-helix-helix motif. Our biochemical data show that two weakly associated RelB dimers bind to the adjacent repeats in the 3'-site of the operator (O(R)) at a moderate affinity (K(d), approximately 10(-5) M). However, in the presence of RelE, a RelB tetramer binds two distinct binding sites within the operator region, each with an enhanced affinity (K(d), approximately 10(-6) M for the low-affinity site, O(L), and 10(-8) M for the high-affinity site, O(R)). We propose that the enhanced affinity for the operator element is mediated by a cooperative DNA binding by a pair of RelB dimers and that the interaction between RelB dimers is strongly augmented by the presence of the cognate toxin RelE.

Structural mechanism of transcriptional autorepression of the Escherichia coli RelB/RelE antitoxin/toxin module.,Li GY, Zhang Y, Inouye M, Ikura M J Mol Biol. 2008 Jun 27;380(1):107-19. Epub 2008 Apr 22. PMID:18501926^[11]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Gotfredsen M, Gerdes K. The Escherichia coli relBE genes belong to a new toxin-antitoxin gene family. Mol Microbiol. 1998 Aug;29(4):1065-76. PMID:9767574
↑ Galvani C, Terry J, Ishiguro EE. Purification of the RelB and RelE proteins of Escherichia coli: RelE binds to RelB and to ribosomes. J Bacteriol. 2001 Apr;183(8):2700-3. PMID:11274135 doi:http://dx.doi.org/10.1128/JB.183.8.2700-2703.2001
↑ Christensen SK, Mikkelsen M, Pedersen K, Gerdes K. RelE, a global inhibitor of translation, is activated during nutritional stress. Proc Natl Acad Sci U S A. 2001 Dec 4;98(25):14328-33. Epub 2001 Nov 20. PMID:11717402 doi:http://dx.doi.org/10.1073/pnas.251327898
↑ Pedersen K, Christensen SK, Gerdes K. Rapid induction and reversal of a bacteriostatic condition by controlled expression of toxins and antitoxins. Mol Microbiol. 2002 Jul;45(2):501-10. PMID:12123459
↑ Kolodkin-Gal I, Verdiger R, Shlosberg-Fedida A, Engelberg-Kulka H. A differential effect of E. coli toxin-antitoxin systems on cell death in liquid media and biofilm formation. PLoS One. 2009 Aug 26;4(8):e6785. doi: 10.1371/journal.pone.0006785. PMID:19707553 doi:10.1371/journal.pone.0006785
↑ Gotfredsen M, Gerdes K. The Escherichia coli relBE genes belong to a new toxin-antitoxin gene family. Mol Microbiol. 1998 Aug;29(4):1065-76. PMID:9767574
↑ Galvani C, Terry J, Ishiguro EE. Purification of the RelB and RelE proteins of Escherichia coli: RelE binds to RelB and to ribosomes. J Bacteriol. 2001 Apr;183(8):2700-3. PMID:11274135 doi:http://dx.doi.org/10.1128/JB.183.8.2700-2703.2001
↑ Christensen SK, Mikkelsen M, Pedersen K, Gerdes K. RelE, a global inhibitor of translation, is activated during nutritional stress. Proc Natl Acad Sci U S A. 2001 Dec 4;98(25):14328-33. Epub 2001 Nov 20. PMID:11717402 doi:http://dx.doi.org/10.1073/pnas.251327898
↑ Pedersen K, Christensen SK, Gerdes K. Rapid induction and reversal of a bacteriostatic condition by controlled expression of toxins and antitoxins. Mol Microbiol. 2002 Jul;45(2):501-10. PMID:12123459
↑ Kolodkin-Gal I, Verdiger R, Shlosberg-Fedida A, Engelberg-Kulka H. A differential effect of E. coli toxin-antitoxin systems on cell death in liquid media and biofilm formation. PLoS One. 2009 Aug 26;4(8):e6785. doi: 10.1371/journal.pone.0006785. PMID:19707553 doi:10.1371/journal.pone.0006785
↑ Li GY, Zhang Y, Inouye M, Ikura M. Structural mechanism of transcriptional autorepression of the Escherichia coli RelB/RelE antitoxin/toxin module. J Mol Biol. 2008 Jun 27;380(1):107-19. Epub 2008 Apr 22. PMID:18501926 doi:10.1016/j.jmb.2008.04.039

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2k29"

@@ Line 1: / Line 1: @@
 ==Structure of the DBD domain of E. coli antitoxin RelB==
-<StructureSection load='2k29' size='340' side='right'caption='[[2k29]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2k29' size='340' side='right'caption='[[2k29]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2k29]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K29 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2K29 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2k29]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K29 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2K29 FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">relB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
+</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=2k29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k29 OCA], [https://pdbe.org/2k29 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2k29 RCSB], [https://www.ebi.ac.uk/pdbsum/2k29 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2k29 ProSAT]</span></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=2k29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k29 OCA], [https://pdbe.org/2k29 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2k29 RCSB], [https://www.ebi.ac.uk/pdbsum/2k29 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2k29 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RELB_ECOLI RELB_ECOLI]] Antitoxin component of a toxin-antitoxin (TA) module. Counteracts the effect of RelE via direct protein-protein interaction, enabling the reversion of translation inhibition. Also acts as an autorepressor of relBE transcription. DNA-binding and repression is stronger when complexed with corepressor RelE. Increased transcription rate of relBE and activation of relE is consistent with a lower level of RelB in starved cells due to degradation of RelB by protease Lon.<ref>PMID:9767574</ref> <ref>PMID:11274135</ref> <ref>PMID:11717402</ref> <ref>PMID:12123459</ref> <ref>PMID:19707553</ref>   Seems to be a principal mediator of cell death in liquid media.<ref>PMID:9767574</ref> <ref>PMID:11274135</ref> <ref>PMID:11717402</ref> <ref>PMID:12123459</ref> <ref>PMID:19707553</ref>
+[https://www.uniprot.org/uniprot/RELB_ECOLI RELB_ECOLI] Antitoxin component of a toxin-antitoxin (TA) module. Counteracts the effect of RelE via direct protein-protein interaction, enabling the reversion of translation inhibition. Also acts as an autorepressor of relBE transcription. DNA-binding and repression is stronger when complexed with corepressor RelE. Increased transcription rate of relBE and activation of relE is consistent with a lower level of RelB in starved cells due to degradation of RelB by protease Lon.<ref>PMID:9767574</ref> <ref>PMID:11274135</ref> <ref>PMID:11717402</ref> <ref>PMID:12123459</ref> <ref>PMID:19707553</ref>   Seems to be a principal mediator of cell death in liquid media.<ref>PMID:9767574</ref> <ref>PMID:11274135</ref> <ref>PMID:11717402</ref> <ref>PMID:12123459</ref> <ref>PMID:19707553</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 31: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Ikura, M]]
+[[Category: Ikura M]]
-[[Category: Inouye, M]]
+[[Category: Inouye M]]
-[[Category: Li, G]]
+[[Category: Li G]]
-[[Category: Zhang, Y]]
+[[Category: Zhang Y]]
-[[Category: Antitoxin]]
-[[Category: Relb]]
-[[Category: Repressor]]
-[[Category: Ribbon-helix-helix]]
-[[Category: Stress response]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]

2k29

From Proteopedia

Revision as of 08:39, 14 June 2023

Structure of the DBD domain of E. coli antitoxin RelB

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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