4fxp: Difference between revisions

Latest revision as of 08:20, 9 October 2024

Crystal structure of adenosine 5'-phosphosulfate kinase from Arabidopsis thaliana in Complex with Sulfate and APS

Structural highlights

4fxp is a 3 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 1.954Å
Ligands:	ADX, SO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

APK1_ARATH Catalyzes the synthesis of activated sulfate. Essential for plant reproduction and viability. Required for the production of glucosinolates.^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the ATP-dependent synthesis of adenosine 3'-phosphate 5'-phosphosulfate (PAPS), which is an essential metabolite for sulfur assimilation in prokaryotes and eukaryotes. Using APSK from Arabidopsis thaliana, we examine the energetics of nucleotide binary and ternary complex formation and probe active site features that coordinate the order of ligand addition. Calorimetric analysis shows that binding can occur first at either nucleotide site, but that initial interaction at the ATP/ADP site was favored and enhanced affinity for APS in the second site by 50-fold. The thermodynamics of the two possible binding models (i.e. ATP first versus APS first) differs and implies that active site structural changes guide the order of nucleotide addition. The ligand binding analysis also supports an earlier suggestion of intermolecular interactions in the dimeric APSK structure. Crystallographic, site-directed mutagenesis, and energetic analyses of oxyanion recognition by the P-loop in the ATP/ADP binding site and the role of Asp(136), which bridges the ATP/ADP and APS/PAPS binding sites, suggest how the ordered nucleotide binding sequence and structural changes are dynamically coordinated for catalysis.

Nucleotide binding site communication in Arabidopsis thaliana adenosine 5'-phosphosulfate kinase.,Ravilious GE, Jez JM J Biol Chem. 2012 Aug 31;287(36):30385-94. doi: 10.1074/jbc.M112.387001. Epub, 2012 Jul 18. PMID:22810229^[6]

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

References

↑ Lillig CH, Schiffmann S, Berndt C, Berken A, Tischka R, Schwenn JD. Molecular and catalytic properties of Arabidopsis thaliana adenylyl sulfate (APS)-kinase. Arch Biochem Biophys. 2001 Aug 15;392(2):303-10. PMID:11488606 doi:https://dx.doi.org/10.1006/abbi.2001.2453
↑ Mugford SG, Yoshimoto N, Reichelt M, Wirtz M, Hill L, Mugford ST, Nakazato Y, Noji M, Takahashi H, Kramell R, Gigolashvili T, Flugge UI, Wasternack C, Gershenzon J, Hell R, Saito K, Kopriva S. Disruption of adenosine-5'-phosphosulfate kinase in Arabidopsis reduces levels of sulfated secondary metabolites. Plant Cell. 2009 Mar;21(3):910-27. doi: 10.1105/tpc.109.065581. Epub 2009 Mar 20. PMID:19304933 doi:https://dx.doi.org/10.1105/tpc.109.065581
↑ Mugford SG, Matthewman CA, Hill L, Kopriva S. Adenosine-5'-phosphosulfate kinase is essential for Arabidopsis viability. FEBS Lett. 2010 Jan 4;584(1):119-23. doi: 10.1016/j.febslet.2009.11.014. Epub . PMID:19903478 doi:https://dx.doi.org/10.1016/j.febslet.2009.11.014
↑ Badenes-Perez FR, Reichelt M, Gershenzon J, Heckel DG. Interaction of glucosinolate content of Arabidopsis thaliana mutant lines and feeding and oviposition by generalist and specialist lepidopterans. Phytochemistry. 2013 Feb;86:36-43. doi: 10.1016/j.phytochem.2012.11.006. Epub, 2012 Dec 3. PMID:23218016 doi:https://dx.doi.org/10.1016/j.phytochem.2012.11.006
↑ Schiffmann S, Schwenn JD. APS-sulfotransferase activity is identical to higher plant APS-kinase (EC 2.7.1.25). FEBS Lett. 1994 Dec 5;355(3):229-32. PMID:7988678
↑ Ravilious GE, Jez JM. Nucleotide binding site communication in Arabidopsis thaliana adenosine 5'-phosphosulfate kinase. J Biol Chem. 2012 Aug 31;287(36):30385-94. doi: 10.1074/jbc.M112.387001. Epub, 2012 Jul 18. PMID:22810229 doi:https://dx.doi.org/10.1074/jbc.M112.387001

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OCA

[1] Lillig CH, Schiffmann S, Berndt C, Berken A, Tischka R, Schwenn JD. Molecular and catalytic properties of Arabidopsis thaliana adenylyl sulfate (APS)-kinase. Arch Biochem Biophys. 2001 Aug 15;392(2):303-10. PMID:11488606 doi:https://dx.doi.org/10.1006/abbi.2001.2453

[2] Mugford SG, Yoshimoto N, Reichelt M, Wirtz M, Hill L, Mugford ST, Nakazato Y, Noji M, Takahashi H, Kramell R, Gigolashvili T, Flugge UI, Wasternack C, Gershenzon J, Hell R, Saito K, Kopriva S. Disruption of adenosine-5'-phosphosulfate kinase in Arabidopsis reduces levels of sulfated secondary metabolites. Plant Cell. 2009 Mar;21(3):910-27. doi: 10.1105/tpc.109.065581. Epub 2009 Mar 20. PMID:19304933 doi:https://dx.doi.org/10.1105/tpc.109.065581

[3] Mugford SG, Matthewman CA, Hill L, Kopriva S. Adenosine-5'-phosphosulfate kinase is essential for Arabidopsis viability. FEBS Lett. 2010 Jan 4;584(1):119-23. doi: 10.1016/j.febslet.2009.11.014. Epub . PMID:19903478 doi:https://dx.doi.org/10.1016/j.febslet.2009.11.014

[4] Badenes-Perez FR, Reichelt M, Gershenzon J, Heckel DG. Interaction of glucosinolate content of Arabidopsis thaliana mutant lines and feeding and oviposition by generalist and specialist lepidopterans. Phytochemistry. 2013 Feb;86:36-43. doi: 10.1016/j.phytochem.2012.11.006. Epub, 2012 Dec 3. PMID:23218016 doi:https://dx.doi.org/10.1016/j.phytochem.2012.11.006

[5] Schiffmann S, Schwenn JD. APS-sulfotransferase activity is identical to higher plant APS-kinase (EC 2.7.1.25). FEBS Lett. 1994 Dec 5;355(3):229-32. PMID:7988678

[6] Ravilious GE, Jez JM. Nucleotide binding site communication in Arabidopsis thaliana adenosine 5'-phosphosulfate kinase. J Biol Chem. 2012 Aug 31;287(36):30385-94. doi: 10.1074/jbc.M112.387001. Epub, 2012 Jul 18. PMID:22810229 doi:https://dx.doi.org/10.1074/jbc.M112.387001

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 == Structural highlights ==
 <table><tr><td colspan='2'>[[4fxp]] is a 3 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=4FXP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FXP FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADX:ADENOSINE-5-PHOSPHOSULFATE'>ADX</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.954&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADX:ADENOSINE-5-PHOSPHOSULFATE'>ADX</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4fxp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fxp OCA], [https://pdbe.org/4fxp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fxp RCSB], [https://www.ebi.ac.uk/pdbsum/4fxp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fxp ProSAT]</span></td></tr>
 </table>

4fxp: Difference between revisions

Latest revision as of 08:20, 9 October 2024

Crystal structure of adenosine 5'-phosphosulfate kinase from Arabidopsis thaliana in Complex with Sulfate and APS

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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