1k6x

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Nmra, a negative transcriptional regulator in complex with NAD at 1.5 A resolution (Trigonal form)

Structural highlights

1k6x is a 1 chain structure with sequence from Aspergillus nidulans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.5Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NMRA_EMENI May be a redox sensor protein. Has much higher affinity for NAD(P) than for NAD(P)H. Has similar affinity for NAD and NADP. Negative transcriptional regulator involved in the post-transcriptional modulation of the GATA-type transcription factor areA, forming part of a system controlling nitrogen metabolite repression (By similarity). Interferes with the interaction between areA and target DNA. Overexpression leads to areA inhibition.^[1] ^[2] ^[3] ^[4]

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

NmrA is a negative transcriptional regulator involved in the post-translational modulation of the GATA-type transcription factor AreA, forming part of a system controlling nitrogen metabolite repression in various fungi. X-ray structures of two NmrA crystal forms, both to 1.8 A resolution, show NmrA consists of two domains, including a Rossmann fold. NmrA shows an unexpected similarity to the short-chain dehydrogenase/reductase (SDR) family, with the closest relationship to UDP-galactose 4-epimerase. We show that NAD binds to NmrA, a previously unreported nucleotide binding property for this protein. NmrA is unlikely to be an active dehydrogenase, however, as the conserved catalytic tyrosine in SDRs is absent in NmrA, and thus the nucleotide binding to NmrA could have a regulatory function. Our results suggest that other transcription factors possess the SDR fold with functions including RNA binding. The SDR fold appears to have been adapted for other roles including non-enzymatic control functions such as transcriptional regulation and is likely to be more widespread than previously recognized.

The structure of the negative transcriptional regulator NmrA reveals a structural superfamily which includes the short-chain dehydrogenase/reductases.,Stammers DK, Ren J, Leslie K, Nichols CE, Lamb HK, Cocklin S, Dodds A, Hawkins AR EMBO J. 2001 Dec 3;20(23):6619-26. PMID:11726498^[5]

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

References

↑ Wong KH, Hynes MJ, Todd RB, Davis MA. Transcriptional control of nmrA by the bZIP transcription factor MeaB reveals a new level of nitrogen regulation in Aspergillus nidulans. Mol Microbiol. 2007 Oct;66(2):534-51. Epub 2007 Sep 10. PMID:17854403 doi:http://dx.doi.org/10.1111/j.1365-2958.2007.05940.x
↑ Lamb HK, Leslie K, Dodds AL, Nutley M, Cooper A, Johnson C, Thompson P, Stammers DK, Hawkins AR. The negative transcriptional regulator NmrA discriminates between oxidized and reduced dinucleotides. J Biol Chem. 2003 Aug 22;278(34):32107-14. Epub 2003 May 22. PMID:12764138 doi:10.1074/jbc.M304104200
↑ Lamb HK, Ren J, Park A, Johnson C, Leslie K, Cocklin S, Thompson P, Mee C, Cooper A, Stammers DK, Hawkins AR. Modulation of the ligand binding properties of the transcription repressor NmrA by GATA-containing DNA and site-directed mutagenesis. Protein Sci. 2004 Dec;13(12):3127-38. Epub 2004 Nov 10. PMID:15537757 doi:10.1110/ps.04958904
↑ Kotaka M, Johnson C, Lamb HK, Hawkins AR, Ren J, Stammers DK. Structural analysis of the recognition of the negative regulator NmrA and DNA by the zinc finger from the GATA-type transcription factor AreA. J Mol Biol. 2008 Aug 29;381(2):373-82. Epub 2008 Jun 5. PMID:18602114 doi:http://dx.doi.org/10.1016/j.jmb.2008.05.077
↑ Stammers DK, Ren J, Leslie K, Nichols CE, Lamb HK, Cocklin S, Dodds A, Hawkins AR. The structure of the negative transcriptional regulator NmrA reveals a structural superfamily which includes the short-chain dehydrogenase/reductases. EMBO J. 2001 Dec 3;20(23):6619-26. PMID:11726498 doi:10.1093/emboj/20.23.6619

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/1k6x"

@@ Line 1: / Line 1: @@
-[[Image:1k6x.gif|left|200px]]<br /><applet load="1k6x" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1k6x, resolution 1.50&Aring;" />
-'''Crystal structure of Nmra, a negative transcriptional regulator in complex with NAD at 1.5 A resolution (Trigonal form)'''<br />
-==Overview==
+==Crystal structure of Nmra, a negative transcriptional regulator in complex with NAD at 1.5 A resolution (Trigonal form)==
-NmrA is a negative transcriptional regulator involved in the, post-translational modulation of the GATA-type transcription factor AreA, forming part of a system controlling nitrogen metabolite repression in, various fungi. X-ray structures of two NmrA crystal forms, both to 1.8 A, resolution, show NmrA consists of two domains, including a Rossmann fold., NmrA shows an unexpected similarity to the short-chain, dehydrogenase/reductase (SDR) family, with the closest relationship to, UDP-galactose 4-epimerase. We show that NAD binds to NmrA, a previously, unreported nucleotide binding property for this protein. NmrA is unlikely, to be an active dehydrogenase, however, as the conserved catalytic, tyrosine in SDRs is absent in NmrA, and thus the nucleotide binding to, NmrA could have a regulatory function. Our results suggest that other, transcription factors possess the SDR fold with functions including RNA, binding. The SDR fold appears to have been adapted for other roles, including non-enzymatic control functions such as transcriptional, regulation and is likely to be more widespread than previously recognized.
+<StructureSection load='1k6x' size='340' side='right'caption='[[1k6x]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1k6x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_nidulans Aspergillus nidulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K6X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K6X FirstGlance]. <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]] 1.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=1k6x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k6x OCA], [https://pdbe.org/1k6x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k6x RCSB], [https://www.ebi.ac.uk/pdbsum/1k6x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k6x ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NMRA_EMENI NMRA_EMENI] May be a redox sensor protein. Has much higher affinity for NAD(P) than for NAD(P)H. Has similar affinity for NAD and NADP. Negative transcriptional regulator involved in the post-transcriptional modulation of the GATA-type transcription factor areA, forming part of a system controlling nitrogen metabolite repression (By similarity). Interferes with the interaction between areA and target DNA. Overexpression leads to areA inhibition.<ref>PMID:17854403</ref> <ref>PMID:12764138</ref> <ref>PMID:15537757</ref> <ref>PMID:18602114</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/k6/1k6x_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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/main_output.php?pdb_ID=1k6x ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+NmrA is a negative transcriptional regulator involved in the post-translational modulation of the GATA-type transcription factor AreA, forming part of a system controlling nitrogen metabolite repression in various fungi. X-ray structures of two NmrA crystal forms, both to 1.8 A resolution, show NmrA consists of two domains, including a Rossmann fold. NmrA shows an unexpected similarity to the short-chain dehydrogenase/reductase (SDR) family, with the closest relationship to UDP-galactose 4-epimerase. We show that NAD binds to NmrA, a previously unreported nucleotide binding property for this protein. NmrA is unlikely to be an active dehydrogenase, however, as the conserved catalytic tyrosine in SDRs is absent in NmrA, and thus the nucleotide binding to NmrA could have a regulatory function. Our results suggest that other transcription factors possess the SDR fold with functions including RNA binding. The SDR fold appears to have been adapted for other roles including non-enzymatic control functions such as transcriptional regulation and is likely to be more widespread than previously recognized.
-==About this Structure==
+The structure of the negative transcriptional regulator NmrA reveals a structural superfamily which includes the short-chain dehydrogenase/reductases.,Stammers DK, Ren J, Leslie K, Nichols CE, Lamb HK, Cocklin S, Dodds A, Hawkins AR EMBO J. 2001 Dec 3;20(23):6619-26. PMID:11726498<ref>PMID:11726498</ref>
-K6X is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Emericella_nidulans Emericella nidulans] with CL and NAD as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1K6X OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-The structure of the negative transcriptional regulator NmrA reveals a structural superfamily which includes the short-chain dehydrogenase/reductases., Stammers DK, Ren J, Leslie K, Nichols CE, Lamb HK, Cocklin S, Dodds A, Hawkins AR, EMBO J. 2001 Dec 3;20(23):6619-26. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11726498 11726498]
+</div>
-[[Category: Emericella nidulans]]
+<div class="pdbe-citations 1k6x" style="background-color:#fffaf0;"></div>
-[[Category: Single protein]]
+== References ==
-[[Category: Cocklin, S.]]
+<references/>
-[[Category: Dodds, A.]]
+__TOC__
-[[Category: Hawkins, A.R.]]
+</StructureSection>
-[[Category: Lamb, H.K.]]
+[[Category: Aspergillus nidulans]]
-[[Category: Leslie, K.]]
+[[Category: Large Structures]]
-[[Category: Nichols, C.E.]]
+[[Category: Cocklin S]]
-[[Category: Ren, J.]]
+[[Category: Dodds A]]
-[[Category: Stammers, D.K.]]
+[[Category: Hawkins AR]]
-[[Category: CL]]
+[[Category: Lamb HK]]
-[[Category: NAD]]
+[[Category: Leslie K]]
-[[Category: rossmann fold transcriptional regulation short chain dehydrogenase reductase nadh binding]]
+[[Category: Nichols CE]]
+[[Category: Ren J]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 00:52:07 2007''
+[[Category: Stammers DK]]

1k6x

From Proteopedia

Current revision

Crystal structure of Nmra, a negative transcriptional regulator in complex with NAD at 1.5 A resolution (Trigonal form)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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