2rd5: Difference between revisions

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New page: left|200px<br /><applet load="2rd5" size="350" color="white" frame="true" align="right" spinBox="true" caption="2rd5, resolution 2.51Å" /> '''Structural basis for...
 
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[[Image:2rd5.jpg|left|200px]]<br /><applet load="2rd5" size="350" color="white" frame="true" align="right" spinBox="true"
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'''Structural basis for the regulation of N-acetylglutamate kinase by PII in Arabidopsis thaliana'''<br />


==Overview==
==Structural basis for the regulation of N-acetylglutamate kinase by PII in Arabidopsis thaliana==
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.
<StructureSection load='2rd5' size='340' side='right'caption='[[2rd5]], [[Resolution|resolution]] 2.51&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2rd5]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. 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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.51&#8491;</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='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>
== Function ==
[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>
== 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/rd/2rd5_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=2rd5 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== 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.


==About this Structure==
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<ref>PMID:17913711</ref>
2RD5 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=ARG:'>ARG</scene>, <scene name='pdbligand=ADP:'>ADP</scene>, <scene name='pdbligand=NLG:'>NLG</scene> and <scene name='pdbligand=ATP:'>ATP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RD5 OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17913711 17913711]
</div>
[[Category: Acetylglutamate kinase]]
<div class="pdbe-citations 2rd5" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Arabidopsis thaliana]]
[[Category: Arabidopsis thaliana]]
[[Category: Protein complex]]
[[Category: Large Structures]]
[[Category: Mizuno, Y.]]
[[Category: Mizuno Y]]
[[Category: Moorhead, G.B.G.]]
[[Category: Moorhead GBG]]
[[Category: Ng, K.K.S.]]
[[Category: Ng KKS]]
[[Category: ADP]]
[[Category: ARG]]
[[Category: ATP]]
[[Category: MG]]
[[Category: NLG]]
[[Category: kinase]]
[[Category: nitrogen metabolism]]
[[Category: protein binding]]
[[Category: protein-protein complex]]
[[Category: regulation of arginine biosynthesis]]
[[Category: transcription]]
[[Category: transcription regulation]]
[[Category: transferase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 11:32:00 2008''

Latest revision as of 14:54, 30 August 2023

Structural basis for the regulation of N-acetylglutamate kinase by PII in Arabidopsis thalianaStructural basis for the regulation of N-acetylglutamate kinase by PII in Arabidopsis thaliana

Structural highlights

2rd5 is a 4 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.51Å
Ligands:, , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NAGK_ARATH Involved in the arginine biosynthetic pathway via the intermediate compound ornithine.[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

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[3]

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

References

  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:http://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:http://dx.doi.org/10.1016/j.febslet.2006.02.075
  3. ↑ 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

2rd5, resolution 2.51Å

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