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| | ==Structural basis for the regulation of N-acetylglutamate kinase by PII in Arabidopsis thaliana== | | ==Structural basis for the regulation of N-acetylglutamate kinase by PII in Arabidopsis thaliana== |
| - | <StructureSection load='2rd5' size='340' side='right' caption='[[2rd5]], [[Resolution|resolution]] 2.51Å' scene=''> | + | <StructureSection load='2rd5' size='340' side='right'caption='[[2rd5]], [[Resolution|resolution]] 2.51Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2rd5]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RD5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RD5 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2rd5]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RD5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RD5 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NLG:N-ACETYL-L-GLUTAMATE'>NLG</scene></td></tr> | + | </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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NLG:N-ACETYL-L-GLUTAMATE'>NLG</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2o66|2o66]], [[2o67|2o67]]</td></tr> | + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2o66|2o66]], [[2o67|2o67]]</div></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">T8H10.160 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH]), AT4g01900, T7B11.16 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr> | + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">T8H10.160 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH]), AT4g01900, T7B11.16 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Acetylglutamate_kinase Acetylglutamate kinase], with EC number [https://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rd5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rd5 OCA], [http://pdbe.org/2rd5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rd5 RCSB], [http://www.ebi.ac.uk/pdbsum/2rd5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rd5 ProSAT]</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=2rd5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rd5 OCA], [https://pdbe.org/2rd5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rd5 RCSB], [https://www.ebi.ac.uk/pdbsum/2rd5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rd5 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == 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> [[http://www.uniprot.org/uniprot/GLNB_ARATH GLNB_ARATH]] Participates in sensing carbon and organic nitrogen status and regulates some steps of primary carbon and nitrogen metabolism. Required for nitrite uptake in chloroplasts and regulates arginine biosynthesis through interaction with acetylglutamate kinase (NAGK) in chloroplasts. Regulates fatty acids synthesis in chloroplasts by interacting with the acetyl-CoA carboxylase complex and inhibiting acetyl-CoA carboxylase (ACCase) activity.<ref>PMID:16133214</ref> <ref>PMID:18325336</ref> <ref>PMID:9811909</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> [[https://www.uniprot.org/uniprot/GLNB_ARATH GLNB_ARATH]] Participates in sensing carbon and organic nitrogen status and regulates some steps of primary carbon and nitrogen metabolism. Required for nitrite uptake in chloroplasts and regulates arginine biosynthesis through interaction with acetylglutamate kinase (NAGK) in chloroplasts. Regulates fatty acids synthesis in chloroplasts by interacting with the acetyl-CoA carboxylase complex and inhibiting acetyl-CoA carboxylase (ACCase) activity.<ref>PMID:16133214</ref> <ref>PMID:18325336</ref> <ref>PMID:9811909</ref> |
| | == 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/rd/2rd5_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rd/2rd5_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
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| | [[Category: Acetylglutamate kinase]] | | [[Category: Acetylglutamate kinase]] |
| | [[Category: Arath]] | | [[Category: Arath]] |
| | + | [[Category: Large Structures]] |
| | [[Category: Mizuno, Y]] | | [[Category: Mizuno, Y]] |
| | [[Category: Moorhead, G B.G]] | | [[Category: Moorhead, G B.G]] |
| Structural highlights
2rd5 is a 4 chain structure with sequence from Arath. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Ligands: | , , , , |
| Related: | |
| Gene: | T8H10.160 (ARATH), AT4g01900, T7B11.16 (ARATH) |
| Activity: | Acetylglutamate kinase, with EC number 2.7.2.8 |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
[NAGK_ARATH] Involved in the arginine biosynthetic pathway via the intermediate compound ornithine.[1] [2] [GLNB_ARATH] Participates in sensing carbon and organic nitrogen status and regulates some steps of primary carbon and nitrogen metabolism. Required for nitrite uptake in chloroplasts and regulates arginine biosynthesis through interaction with acetylglutamate kinase (NAGK) in chloroplasts. Regulates fatty acids synthesis in chloroplasts by interacting with the acetyl-CoA carboxylase complex and inhibiting acetyl-CoA carboxylase (ACCase) activity.[3] [4] [5]
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
PII is a highly conserved regulatory protein found in organisms across the three domains of life. In cyanobacteria and plants, PII relieves the feedback inhibition of the rate-limiting step in arginine biosynthesis catalyzed by N-acetylglutamate kinase (NAGK). To understand the molecular structural basis of enzyme regulation by PII, we have determined a 2.5-A resolution crystal structure of a complex formed between two homotrimers of PII and a single hexamer of NAGK from Arabidopsis thaliana bound to the metabolites N-acetylglutamate, ADP, ATP, and arginine. In PII, the T-loop and Trp(22) at the start of the alpha1-helix, which are both adjacent to the ATP-binding site of PII, contact two beta-strands as well as the ends of two central helices (alphaE and alphaG) in NAGK, the opposing ends of which form major portions of the ATP and N-acetylglutamate substrate-binding sites. The binding of Mg(2+).ATP to PII stabilizes a conformation of the T-loop that favors interactions with both open and closed conformations of NAGK. Interactions between PII and NAGK appear to limit the degree of opening and closing of the active-site cleft in opposition to a domain-separating inhibitory effect exerted by arginine, thus explaining the stimulatory effect of PII on the kinetics of arginine-inhibited NAGK.
Structural basis for the regulation of N-acetylglutamate kinase by PII in Arabidopsis thaliana.,Mizuno Y, Moorhead GB, Ng KK J Biol Chem. 2007 Dec 7;282(49):35733-40. Epub 2007 Oct 3. PMID:17913711[6]
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:http://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:http://dx.doi.org/10.1016/j.febslet.2006.02.075
- ↑ Ferrario-Mery S, Bouvet M, Leleu O, Savino G, Hodges M, Meyer C. Physiological characterisation of Arabidopsis mutants affected in the expression of the putative regulatory protein PII. Planta. 2005 Dec;223(1):28-39. Epub 2005 Aug 16. PMID:16133214 doi:http://dx.doi.org/10.1007/s00425-005-0063-5
- ↑ Ferrario-Mery S, Meyer C, Hodges M. Chloroplast nitrite uptake is enhanced in Arabidopsis PII mutants. FEBS Lett. 2008 Apr 2;582(7):1061-6. doi: 10.1016/j.febslet.2008.02.056. Epub, 2008 Mar 4. PMID:18325336 doi:http://dx.doi.org/10.1016/j.febslet.2008.02.056
- ↑ Hsieh MH, Lam HM, van de Loo FJ, Coruzzi G. A PII-like protein in Arabidopsis: putative role in nitrogen sensing. Proc Natl Acad Sci U S A. 1998 Nov 10;95(23):13965-70. PMID:9811909
- ↑ Mizuno Y, Moorhead GB, Ng KK. Structural basis for the regulation of N-acetylglutamate kinase by PII in Arabidopsis thaliana. J Biol Chem. 2007 Dec 7;282(49):35733-40. Epub 2007 Oct 3. PMID:17913711 doi:10.1074/jbc.M707127200
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