9gui: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

~~The entry~~ 9gui is ~~ON HOLD until Paper~~ Publication

==Crystal structure of transcription factor NtcA from Synechococcus elongatus in complex with its target DNA.==

== Structural highlights ==

<table><tr><td colspan='2'>[[9gui]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechococcus_elongatus_PCC_7942_=_FACHB-805 Synechococcus elongatus PCC 7942 = FACHB-805]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9GUI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9GUI 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]] 3Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</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=9gui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9gui OCA], [https://pdbe.org/9gui PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9gui RCSB], [https://www.ebi.ac.uk/pdbsum/9gui PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9gui ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/NTCA_SYNE7 NTCA_SYNE7]

== Publication Abstract from PubMed ==

The CRP-FNR (cAMP receptor protein-fumarate/nitrate reductase regulator) superfamily of transcriptional regulators includes the cyanobacterial master regulator NtcA, which orchestrates large responses of cyanobacteria to nitrogen scarcity. NtcA uses as allosteric activator 2-oxoglutarate (2OG), a signal of nitrogen poorness and carbon richness, and binds a co-activating protein (PipX) that shuttles between the signaling protein PII and NtcA depending on nitrogen richness, thus connecting PII signaling and gene expression regulation. Here, combining structural (X-ray crystallography of six types of crystals including NtcA complexes with DNA, 2OG, and PipX), modeling, and functional [electrophoretic mobility shift assays and bacterial two-hybrid (BACTH)] studies, we clarify the reasons for the exquisite specificity for the binding of NtcA to its target DNA, its mechanisms of activation by 2OG, and its co-activation by PipX. Our crystal structures of PipX-NtcA-DNA complexes prove that PipX does not interact with DNA, although it increases NtcA-DNA contacts, and that it stabilizes the active, DNA-binding-competent conformation of NtcA. Superimposition of this complex on a very recently reported cryo-electron microscopy structure of NtcA in a transcription activity complex with RNA polymerase (RNAP), shows that PipX binding helps recruit RNAP by PipX interaction with RNAP, particularly with its gamma and sigma (region 4) subunits, a structural prediction supported here by BACTH experiments.

~~Authors~~:

Structures of the cyanobacterial nitrogen regulators NtcA and PipX complexed to DNA shed light on DNA binding by NtcA and implicate PipX in the recruitment of RNA polymerase.,Forcada-Nadal A, Bibak S, Salinas P, Contreras A, Rubio V, Llacer JL Nucleic Acids Res. 2025 Feb 8;53(4):gkaf096. doi: 10.1093/nar/gkaf096. PMID:39995039<ref>PMID:39995039</ref>

~~Description~~:

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

[[Category: ~~Unreleased~~ Structures]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Synechococcus elongatus PCC 7942 = FACHB-805]]

[[Category: Forcada-Nadal A]]

[[Category: Llacer JL]]

[[Category: Rubio V]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9gui is ON HOLD  until Paper Publication
+==Crystal structure of transcription factor NtcA from Synechococcus elongatus in complex with its target DNA.==
+<StructureSection load='9gui' size='340' side='right'caption='[[9gui]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9gui]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechococcus_elongatus_PCC_7942_=_FACHB-805 Synechococcus elongatus PCC 7942 = FACHB-805]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9GUI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9GUI 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]] 3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</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=9gui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9gui OCA], [https://pdbe.org/9gui PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9gui RCSB], [https://www.ebi.ac.uk/pdbsum/9gui PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9gui ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NTCA_SYNE7 NTCA_SYNE7]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The CRP-FNR (cAMP receptor protein-fumarate/nitrate reductase regulator) superfamily of transcriptional regulators includes the cyanobacterial master regulator NtcA, which orchestrates large responses of cyanobacteria to nitrogen scarcity. NtcA uses as allosteric activator 2-oxoglutarate (2OG), a signal of nitrogen poorness and carbon richness, and binds a co-activating protein (PipX) that shuttles between the signaling protein PII and NtcA depending on nitrogen richness, thus connecting PII signaling and gene expression regulation. Here, combining structural (X-ray crystallography of six types of crystals including NtcA complexes with DNA, 2OG, and PipX), modeling, and functional [electrophoretic mobility shift assays and bacterial two-hybrid (BACTH)] studies, we clarify the reasons for the exquisite specificity for the binding of NtcA to its target DNA, its mechanisms of activation by 2OG, and its co-activation by PipX. Our crystal structures of PipX-NtcA-DNA complexes prove that PipX does not interact with DNA, although it increases NtcA-DNA contacts, and that it stabilizes the active, DNA-binding-competent conformation of NtcA. Superimposition of this complex on a very recently reported cryo-electron microscopy structure of NtcA in a transcription activity complex with RNA polymerase (RNAP), shows that PipX binding helps recruit RNAP by PipX interaction with RNAP, particularly with its gamma and sigma (region 4) subunits, a structural prediction supported here by BACTH experiments.
-Authors:
+Structures of the cyanobacterial nitrogen regulators NtcA and PipX complexed to DNA shed light on DNA binding by NtcA and implicate PipX in the recruitment of RNA polymerase.,Forcada-Nadal A, Bibak S, Salinas P, Contreras A, Rubio V, Llacer JL Nucleic Acids Res. 2025 Feb 8;53(4):gkaf096. doi: 10.1093/nar/gkaf096. PMID:39995039<ref>PMID:39995039</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 9gui" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Synechococcus elongatus PCC 7942 = FACHB-805]]
+[[Category: Forcada-Nadal A]]
+[[Category: Llacer JL]]
+[[Category: Rubio V]]