7acl

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of E. coli HTH-type transcriptional regulator RcdA at 2.05 A resolution

Structural highlights

7acl is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.049Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RCDA_ECOLI Regulates the expression of a number of genes involved in biofilm formation and stress response. Target genes include six stress-response transcriptional regulators: csgD, which is a master regulator of biofilm formation, appY, sxy, ycgF, fimB and rcdA itself. This indicates that a large number of genes must be regulated indirectly via these transcriptional regulators. Acts by binding to the upstream region of its target genes.^[1]

Publication Abstract from PubMed

RcdA is a helix-turn-helix (HTH) transcriptional regulator belonging to the TetR family. The protein regulates the transcription of curlin subunit gene D, the master regulator of biofilm formation. Moreover, it was predicted that it might be involved in the regulation of up to 27 different genes. However, an effector of RcdA and the environmental conditions which trigger RcdA action remain unknown. Herein, we report the first crystal structures of RcdA in complexes with ligands, trimethylamine N-oxide (TMAO) and tris(hydroxymethyl)aminomethane (Tris), which might serve as RcdA effectors. Based on these structures, the ligand-binding pocket of RcdA was characterized in detail. The conservation of the amino acid residues forming the ligand-binding cavity was analyzed and the comprehensive search for RcdA structural homologs was performed. This analysis indicated that RcdA is structurally similar to multidrug-binding TetR family members, however, its ligand-binding cavity differs significantly from the pockets of its structural homologs. The interaction of RcdA with TMAO and Tris indicates that the protein might be involved in alkaline stress response.

Structures of the TetR-like transcription regulator RcdA alone and in complexes with ligands.,Pietrzyk-Brzezinska AJ, Cociurovscaia A Proteins. 2021 Jul 20. doi: 10.1002/prot.26183. PMID:34288132^[2]

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

References

↑ Shimada T, Katayama Y, Kawakita S, Ogasawara H, Nakano M, Yamamoto K, Ishihama A. A novel regulator RcdA of the csgD gene encoding the master regulator of biofilm formation in Escherichia coli. Microbiologyopen. 2012 Dec;1(4):381-94. doi: 10.1002/mbo3.42. Epub 2012 Oct 8. PMID:23233451 doi:http://dx.doi.org/10.1002/mbo3.42
↑ Pietrzyk-Brzezinska AJ, Cociurovscaia A. Structures of the TetR-like transcription regulator RcdA alone and in complexes with ligands. Proteins. 2021 Jul 20. doi: 10.1002/prot.26183. PMID:34288132 doi:http://dx.doi.org/10.1002/prot.26183

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/7acl"

Categories: Escherichia coli | Large Structures | Cociurovscaia A | Pietrzyk-Brzezinska AJ

@@ Line 3: / Line 3: @@
 <StructureSection load='7acl' size='340' side='right'caption='[[7acl]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7acl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ACL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ACL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7acl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ACL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ACL FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.049&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rcdA, ybjK, b0846, JW5114 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></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=7acl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7acl OCA], [https://pdbe.org/7acl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7acl RCSB], [https://www.ebi.ac.uk/pdbsum/7acl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7acl ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RCDA_ECOLI RCDA_ECOLI]] Regulates the expression of a number of genes involved in biofilm formation and stress response. Target genes include six stress-response transcriptional regulators: csgD, which is a master regulator of biofilm formation, appY, sxy, ycgF, fimB and rcdA itself. This indicates that a large number of genes must be regulated indirectly via these transcriptional regulators. Acts by binding to the upstream region of its target genes.<ref>PMID:23233451</ref>
+[https://www.uniprot.org/uniprot/RCDA_ECOLI RCDA_ECOLI] Regulates the expression of a number of genes involved in biofilm formation and stress response. Target genes include six stress-response transcriptional regulators: csgD, which is a master regulator of biofilm formation, appY, sxy, ycgF, fimB and rcdA itself. This indicates that a large number of genes must be regulated indirectly via these transcriptional regulators. Acts by binding to the upstream region of its target genes.<ref>PMID:23233451</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 7acl" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[RcdA|RcdA]]
+*[[Tetracycline repressor protein 3D structures|Tetracycline repressor protein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Cociurovscaia, A]]
+[[Category: Cociurovscaia A]]
-[[Category: Pietrzyk-Brzezinska, A J]]
+[[Category: Pietrzyk-Brzezinska AJ]]
-[[Category: Dna-binding protein]]
-[[Category: Gene regulation]]
-[[Category: Hth motif]]
-[[Category: Transcription factor]]

7acl

From Proteopedia

Current revision

Crystal structure of E. coli HTH-type transcriptional regulator RcdA at 2.05 A resolution

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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