4usj: Difference between revisions

Latest revision as of 10:35, 10 January 2024

N-acetylglutamate kinase from Arabidopsis thaliana in complex with PII from Chlamydomonas reinhardtii

Structural highlights

4usj is a 4 chain structure with sequence from Arabidopsis thaliana and Chlamydomonas reinhardtii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.85Å
Ligands:	ADP, ARG, ATP, GLN, MG, NLG, X2W
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NAGK_ARATH Involved in the arginine biosynthetic pathway via the intermediate compound ornithine.^[1] ^[2]

Publication Abstract from PubMed

Glutamine is the primary metabolite of nitrogen assimilation from inorganic nitrogen sources in microorganisms and plants. The ability to monitor cellular nitrogen status is pivotal for maintaining metabolic homeostasis and sustaining growth. The present study identifies a glutamine-sensing mechanism common in the entire plant kingdom except Brassicaceae. The plastid-localized PII signaling protein controls, in a glutamine-dependent manner, the key enzyme of the ornithine synthesis pathway, N-acetyl-l-glutamate kinase (NAGK), that leads to arginine and polyamine formation. Crystal structures reveal that the plant-specific C-terminal extension of PII, which we term the Q loop, forms a low-affinity glutamine-binding site. Glutamine binding alters PII conformation, promoting interaction and activation of NAGK. The binding motif is highly conserved in plants except Brassicaceae. A functional Q loop restores glutamine sensing in a recombinant Arabidopsis thaliana PII protein, demonstrating the modular concept of the glutamine-sensing mechanism adopted by PII proteins during the evolution of plant chloroplasts.

A widespread glutamine-sensing mechanism in the plant kingdom.,Chellamuthu VR, Ermilova E, Lapina T, Luddecke J, Minaeva E, Herrmann C, Hartmann MD, Forchhammer K Cell. 2014 Nov 20;159(5):1188-99. doi: 10.1016/j.cell.2014.10.015. PMID:25416954^[3]

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

References

↑ Chen YM, Ferrar TS, Lohmeier-Vogel EM, Morrice N, Mizuno Y, Berenger B, Ng KK, Muench DG, Moorhead GB. The PII signal transduction protein of Arabidopsis thaliana forms an arginine-regulated complex with plastid N-acetyl glutamate kinase. J Biol Chem. 2006 Mar 3;281(9):5726-33. Epub 2005 Dec 23. PMID:16377628 doi:https://dx.doi.org/10.1074/jbc.M510945200
↑ Ferrario-Mery S, Besin E, Pichon O, Meyer C, Hodges M. The regulatory PII protein controls arginine biosynthesis in Arabidopsis. FEBS Lett. 2006 Apr 3;580(8):2015-20. Epub 2006 Mar 10. PMID:16545809 doi:https://dx.doi.org/10.1016/j.febslet.2006.02.075
↑ Chellamuthu VR, Ermilova E, Lapina T, Luddecke J, Minaeva E, Herrmann C, Hartmann MD, Forchhammer K. A widespread glutamine-sensing mechanism in the plant kingdom. Cell. 2014 Nov 20;159(5):1188-99. doi: 10.1016/j.cell.2014.10.015. PMID:25416954 doi:https://dx.doi.org/10.1016/j.cell.2014.10.015

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Chen YM, Ferrar TS, Lohmeier-Vogel EM, Morrice N, Mizuno Y, Berenger B, Ng KK, Muench DG, Moorhead GB. The PII signal transduction protein of Arabidopsis thaliana forms an arginine-regulated complex with plastid N-acetyl glutamate kinase. J Biol Chem. 2006 Mar 3;281(9):5726-33. Epub 2005 Dec 23. PMID:16377628 doi:https://dx.doi.org/10.1074/jbc.M510945200

[2] Ferrario-Mery S, Besin E, Pichon O, Meyer C, Hodges M. The regulatory PII protein controls arginine biosynthesis in Arabidopsis. FEBS Lett. 2006 Apr 3;580(8):2015-20. Epub 2006 Mar 10. PMID:16545809 doi:https://dx.doi.org/10.1016/j.febslet.2006.02.075

[3] Chellamuthu VR, Ermilova E, Lapina T, Luddecke J, Minaeva E, Herrmann C, Hartmann MD, Forchhammer K. A widespread glutamine-sensing mechanism in the plant kingdom. Cell. 2014 Nov 20;159(5):1188-99. doi: 10.1016/j.cell.2014.10.015. PMID:25416954 doi:https://dx.doi.org/10.1016/j.cell.2014.10.015

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==N-acetylglutamate kinase from Arabidopsis thaliana in complex with PII from Chlamydomonas reinhardtii==
-<StructureSection load='4usj' size='340' side='right' caption='[[4usj]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
+<StructureSection load='4usj' size='340' side='right'caption='[[4usj]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4usj]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4USJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4USJ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4usj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] and [https://en.wikipedia.org/wiki/Chlamydomonas_reinhardtii Chlamydomonas reinhardtii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4USJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4USJ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=GLN:GLUTAMINE'>GLN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NLG:N-ACETYL-L-GLUTAMATE'>NLG</scene>, <scene name='pdbligand=X2W:N-ACETYL-L-GLUTAMYL+5-PHOSPHATE'>X2W</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]] 2.85&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ush|4ush]], [[4usi|4usi]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=GLN:GLUTAMINE'>GLN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NLG:N-ACETYL-L-GLUTAMATE'>NLG</scene>, <scene name='pdbligand=X2W:N-ACETYL-L-GLUTAMYL+5-PHOSPHATE'>X2W</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Acetylglutamate_kinase Acetylglutamate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.8 2.7.2.8] </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=4usj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4usj OCA], [https://pdbe.org/4usj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4usj RCSB], [https://www.ebi.ac.uk/pdbsum/4usj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4usj ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4usj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4usj OCA], [http://pdbe.org/4usj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4usj RCSB], [http://www.ebi.ac.uk/pdbsum/4usj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4usj ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NAGK_ARATH NAGK_ARATH]] Involved in the arginine biosynthetic pathway via the intermediate compound ornithine.<ref>PMID:16377628</ref> <ref>PMID:16545809</ref>
+[https://www.uniprot.org/uniprot/NAGK_ARATH NAGK_ARATH] Involved in the arginine biosynthetic pathway via the intermediate compound ornithine.<ref>PMID:16377628</ref> <ref>PMID:16545809</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Acetylglutamate kinase]]
+[[Category: Arabidopsis thaliana]]
-[[Category: Chellamuthu, V R]]
+[[Category: Chlamydomonas reinhardtii]]
-[[Category: Forchhammer, K]]
+[[Category: Large Structures]]
-[[Category: Hartmann, M D]]
+[[Category: Chellamuthu VR]]
-[[Category: C-terminal extension]]
+[[Category: Forchhammer K]]
-[[Category: Nagk]]
+[[Category: Hartmann MD]]
-[[Category: Nitrogen assimilation]]
-[[Category: Protein-protein complex]]
-[[Category: Q-loop]]
-[[Category: Regulation of arginine metabolism]]
-[[Category: Signaling protein]]
-[[Category: Transferase]]

4usj: Difference between revisions

Latest revision as of 10:35, 10 January 2024

N-acetylglutamate kinase from Arabidopsis thaliana in complex with PII from Chlamydomonas reinhardtii

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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