1zg5: Difference between revisions
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==NarL complexed to narG-89 promoter palindromic tail-to-tail DNA site== | ==NarL complexed to narG-89 promoter palindromic tail-to-tail DNA site== | ||
<StructureSection load='1zg5' size='340' side='right' caption='[[1zg5]], [[Resolution|resolution]] 2.30Å' scene=''> | <StructureSection load='1zg5' size='340' side='right'caption='[[1zg5]], [[Resolution|resolution]] 2.30Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1zg5]] is a 8 chain structure with sequence from [ | <table><tr><td colspan='2'>[[1zg5]] is a 8 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=1ZG5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZG5 FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[ | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr> | ||
<tr><td class="sblockLbl"><b>[[ | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1zg5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zg5 OCA], [https://pdbe.org/1zg5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zg5 RCSB], [https://www.ebi.ac.uk/pdbsum/1zg5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zg5 ProSAT]</span></td></tr> | |||
<tr | </table> | ||
== Function == | |||
<table> | [https://www.uniprot.org/uniprot/NARL_ECOLI NARL_ECOLI] This protein activates the expression of the nitrate reductase (narGHJI) and formate dehydrogenase-N (fdnGHI) operons and represses the transcription of the fumarate reductase (frdABCD) operon in response to a nitrate/nitrite induction signal transmitted by either the NarX or NarQ proteins. | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zg/1zg5_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zg/1zg5_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/ | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </jmolCheckbox> | ||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/ | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1zg5 ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 1zg5" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Response regulator|Response regulator]] | *[[Response regulator 3D structure|Response regulator 3D structure]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
| Line 35: | Line 37: | ||
</StructureSection> | </StructureSection> | ||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Dickerson | [[Category: Large Structures]] | ||
[[Category: Gunsalus | [[Category: Dickerson RE]] | ||
[[Category: Kaczor-Grzeskowiak | [[Category: Gunsalus RP]] | ||
[[Category: Kopka | [[Category: Kaczor-Grzeskowiak M]] | ||
[[Category: Ma | [[Category: Kopka ML]] | ||
[[Category: Maris | [[Category: Ma Z]] | ||
[[Category: Maris AE]] | |||
Latest revision as of 10:32, 9 October 2024
NarL complexed to narG-89 promoter palindromic tail-to-tail DNA siteNarL complexed to narG-89 promoter palindromic tail-to-tail DNA site
Structural highlights
FunctionNARL_ECOLI This protein activates the expression of the nitrate reductase (narGHJI) and formate dehydrogenase-N (fdnGHI) operons and represses the transcription of the fumarate reductase (frdABCD) operon in response to a nitrate/nitrite induction signal transmitted by either the NarX or NarQ proteins. 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 PubMedNarL is a model response regulator for bacterial two-component signal transduction. The NarL C-terminal domain DNA binding domain alone (NarL(C)) contains all essential DNA binding determinants of the full-length NarL transcription factor. In the full-length NarL protein, the N-terminal regulatory domain must be phosphorylated to release the DNA binding determinants; however, the first NarL(C)-DNA cocrystal structure showed that dimerization of NarL(C) on DNA occurs in a manner independent of the regulatory domain [Maris, A. E., et al. (2002) Nat. Struct. Biol. 9, 771-778]. Dimerization via the NarL(C) C-terminal helix conferred high-affinity recognition of the tail-to-tail promoter site arrangement. Here, two new cocrystal structures are presented of NarL(C) complexed with additional 20mer oligonucleotides representative of other high-affinity tail-to-tail NarL binding sites found in upstream promoter regions. DNA structural recognition properties are described, such as backbone flexibility and groove width, that facilitate NarL(C) dimerization and high-affinity recognition. Lys 188 on the recognition helix accommodates DNA sequence variation between the three different cocomplexes by providing flexible specificity, recognizing the DNA major groove floor directly and/or via bridging waters. The highly conserved Val 189, which enforced significant DNA base distortion in the first cocrystal structure, enforces similar distortions in the two new cocrystal structures. Recognition also is conserved for Lys 192, which hydrogen bonds to guanines at regions of high DNA helical writhe. DNA affinity measurements for model NarL binding sites, including those that did not cocrystallize, suggest a framework for explaining the diversity of heptamer site arrangement and orientation. Primary and secondary modes of DNA recognition by the NarL two-component response regulator.,Maris AE, Kaczor-Grzeskowiak M, Ma Z, Kopka ML, Gunsalus RP, Dickerson RE Biochemistry. 2005 Nov 8;44(44):14538-52. PMID:16262254[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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