1nxt

From Proteopedia

(Difference between revisions)

Current revision

MicArec pH 4.0

Structural highlights

1nxt is a 1 chain structure with sequence from Streptococcus pneumoniae TIGR4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.34Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

WALR_STRPN Member of the two-component regulatory system WalK/WalR that regulates genes involved in cell wall metabolism (By similarity). Binds to the promoter region of the transcription factor fabT gene in the fabTH-acp operon in vitro (PubMed:27610104). Inhibits transcription of fabT, probably acting in an unphosphorylated form, thereby playing a role in the regulation of fatty acid biosynthesis (PubMed:15774879, PubMed:27610104). Essential for normal growth in vitro (By similarity). Required for maintaining normal cellular morphology, acting, at least in part, by regulating peptidoglycan hydrolase pcsB (By similarity). Involved in maintaining expression of WalRK regulon genes in exponentially growing cells (By similarity).[UniProtKB:A0A0H2ZN37][UniProtKB:P37478][UniProtKB:Q8DPL7]^[1] ^[2]

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

A variety of bacterial cellular responses to environmental signals are mediated by two-component signal transduction systems comprising a membrane-associated histidine protein kinase and a cytoplasmic response regulator (RR), which interpret specific stimuli and produce a measured physiological response. In RR activation, transient phosphorylation of a highly conserved aspartic acid residue drives the conformation changes needed for full activation of the protein. Sequence homology reveals that RR02 from Streptococcus pneumoniae belongs to the OmpR subfamily of RRs. The structures of the receiver domains from four members of this family, DrrB and DrrD from Thermotoga maritima, PhoB from Escherichia coli, and PhoP from Bacillus subtilis, have been elucidated. These domains are globally very similar in that they are composed of a doubly wound alpha(5)beta(5); however, they differ remarkably in the fine detail of the beta4-alpha4 and alpha4 regions. The structures presented here reveal a further difference of the geometry in this region. RR02 is has been shown to be the essential RR in the gram-positive bacterium S. pneumoniae R. Lange, C. Wagner, A. de Saizieu, N. Flint, J. Molnos, M. Stieger, P. Caspers, M. Kamber, W. Keck, and K. E. Amrein, Gene 237:223-234, 1999; J. P. Throup, K. K. Koretke, A. P. Bryant, K. A. Ingraham, A. F. Chalker, Y. Ge, A. Marra, N. G. Wallis, J. R. Brown, D. J. Holmes, M. Rosenberg, and M. K. Burnham, Mol. Microbiol. 35:566-576, 2000). RR02 functions as part of a phosphotransfer system that ultimately controls the levels of competence within the bacteria. Here we report the native structure of the receiver domain of RR02 from serotype 4 S. pneumoniae (as well as acetate- and phosphate-bound forms) at different pH levels. Two native structures at 2.3 A, phased by single-wavelength anomalous diffraction (xenon SAD), and 1.85 A and a third structure at pH 5.9 revealed the presence of a phosphate ion outside the active site. The fourth structure revealed the presence of an acetate molecule in the active site.

Crystal structure of the response regulator 02 receiver domain, the essential YycF two-component system of Streptococcus pneumoniae in both complexed and native states.,Bent CJ, Isaacs NW, Mitchell TJ, Riboldi-Tunnicliffe A J Bacteriol. 2004 May;186(9):2872-9. PMID:15090529^[3]

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

References

↑ Mohedano ML, Overweg K, de la Fuente A, Reuter M, Altabe S, Mulholland F, de Mendoza D, López P, Wells JM. Evidence that the essential response regulator YycF in Streptococcus pneumoniae modulates expression of fatty acid biosynthesis genes and alters membrane composition. J Bacteriol. 2005 Apr;187(7):2357-67. PMID:15774879 doi:10.1128/JB.187.7.2357-2367.2005
↑ Mohedano ML, Amblar M, de la Fuente A, Wells JM, López P. The Response Regulator YycF Inhibits Expression of the Fatty Acid Biosynthesis Repressor FabT in Streptococcus pneumoniae. Front Microbiol. 2016 Aug 25;7:1326. PMID:27610104 doi:10.3389/fmicb.2016.01326
↑ Bent CJ, Isaacs NW, Mitchell TJ, Riboldi-Tunnicliffe A. Crystal structure of the response regulator 02 receiver domain, the essential YycF two-component system of Streptococcus pneumoniae in both complexed and native states. J Bacteriol. 2004 May;186(9):2872-9. PMID:15090529

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1nxt"

@@ Line 1: / Line 1: @@
 ==MicArec pH 4.0==
-<StructureSection load='1nxt' size='340' side='right' caption='[[1nxt]], [[Resolution|resolution]] 2.34&Aring;' scene=''>
+<StructureSection load='1nxt' size='340' side='right'caption='[[1nxt]], [[Resolution|resolution]] 2.34&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1nxt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptococcus_pneumoniae_tigr4 Streptococcus pneumoniae tigr4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NXT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NXT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1nxt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_TIGR4 Streptococcus pneumoniae TIGR4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NXT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NXT FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XE:XENON'>XE</scene><br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.34&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PHD:ASPARTYL+PHOSPHATE'>PHD</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PHD:ASPARTYL+PHOSPHATE'>PHD</scene>, <scene name='pdbligand=XE:XENON'>XE</scene></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nxt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nxt RCSB], [http://www.ebi.ac.uk/pdbsum/1nxt PDBsum]</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=1nxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nxt OCA], [https://pdbe.org/1nxt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nxt RCSB], [https://www.ebi.ac.uk/pdbsum/1nxt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nxt ProSAT]</span></td></tr>
-<table>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/WALR_STRPN WALR_STRPN] Member of the two-component regulatory system WalK/WalR that regulates genes involved in cell wall metabolism (By similarity). Binds to the promoter region of the transcription factor fabT gene in the fabTH-acp operon in vitro (PubMed:27610104). Inhibits transcription of fabT, probably acting in an unphosphorylated form, thereby playing a role in the regulation of fatty acid biosynthesis (PubMed:15774879, PubMed:27610104). Essential for normal growth in vitro (By similarity). Required for maintaining normal cellular morphology, acting, at least in part, by regulating peptidoglycan hydrolase pcsB (By similarity). Involved in maintaining expression of WalRK regulon genes in exponentially growing cells (By similarity).[UniProtKB:A0A0H2ZN37][UniProtKB:P37478][UniProtKB:Q8DPL7]<ref>PMID:15774879</ref> <ref>PMID:27610104</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nx/1nxt_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nx/1nxt_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1nxt ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 25: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1nxt" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Response regulator|Response regulator]]
+*[[Response regulator 3D structure|Response regulator 3D structure]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Streptococcus pneumoniae tigr4]]
+[[Category: Large Structures]]
-[[Category: Bent, C J.]]
+[[Category: Streptococcus pneumoniae TIGR4]]
-[[Category: Isaacs, N W.]]
+[[Category: Bent CJ]]
-[[Category: Mitchell, T J.]]
+[[Category: Isaacs NW]]
-[[Category: Riboldi-Tunnicliffe, A.]]
+[[Category: Mitchell TJ]]
-[[Category: 5 beta fold]]
+[[Category: Riboldi-Tunnicliffe A]]
-[[Category: Doubly wound 5 alpha]]
-[[Category: Signaling protein]]

1nxt

From Proteopedia

Current revision

MicArec pH 4.0

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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