5d0n

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of maize PDRP bound with AMP

Structural highlights

5d0n is a 1 chain structure with sequence from Zea mays. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.2Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PDRP1_MAIZE Bifunctional serine/threonine kinase and phosphorylase involved in the dark/light-mediated regulation of PPDK by catalyzing its phosphorylation/dephosphorylation. Dark/light-induced changes in stromal concentrations of the competing ADP and Pi substrates govern the direction of the reaction. In the dark, phosphorylates the catalytic intermediate of PPDK (PPDK-HisP), inactivating it. Light exposure induces the phosphorolysis reaction that reactivates PPDK. Phosphorylates PPDK at both Ser-528 and Thr-527 (PubMed:24710069). Can use ADP as a high specificity substrate and GDP as a lower affinity substrate, but has no activity with UDP (PubMed:21414960).^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

Pyruvate orthophosphate dikinase (PPDK) is one of the most important enzymes in C4 photosynthesis. PPDK regulatory protein (PDRP) regulates the inorganic phosphate-dependent activation and ADP-dependent inactivation of PPDK by reversible phosphorylation. PDRP shares no significant sequence similarity with other protein kinases or phosphatases. To investigate the molecular mechanism by which PDRP carries out its dual and competing activities, we determined the crystal structure of PDRP from maize (Zea mays). PDRP forms a compact homo-dimer in which each protomer contains two separate N-terminal (NTD) and C-terminal (CTD) domains. The CTD includes several key elements for performing both phosphorylation and dephosphorylation activities: the phosphate binding loop (P-loop) for binding the ADP and inorganic phosphate substrates, residues Lys-274 and Lys-299 for neutralizing the negative charge, and residue Asp-277 for protonating and deprotonating the target Thr residue of PPDK to promote nucleophilic attack. Surprisingly, the NTD shares the same protein fold as the CTD and also includes a putative P-loop with AMP bound but lacking enzymatic activities. Structural analysis indicated that this loop may participate in the interaction with and regulation of PPDK. The NTD has conserved intramolecular and intermolecular disulfide bonds for PDRP dimerization. Moreover, PDRP is the first structure of the domain of unknown function 299 enzyme family reported. This study provides a structural basis for understanding the catalytic mechanism of PDRP and offers a foundation for the development of selective activators or inhibitors that may regulate photosynthesis.

Structural Basis of Reversible Phosphorylation by Maize Pyruvate Orthophosphate Dikinase Regulatory Protein.,Jiang L, Chen YB, Zheng J, Chen Z, Liu Y, Tao Y, Wu W, Chen Z, Wang BC Plant Physiol. 2016 Feb;170(2):732-41. doi: 10.1104/pp.15.01709. Epub 2015 Nov, 30. PMID:26620526^[6]

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

References

↑ Chastain CJ, Botschner M, Harrington GE, Thompson BJ, Mills SE, Sarath G, Chollet R. Further analysis of maize C(4) pyruvate,orthophosphate dikinase phosphorylation by its bifunctional regulatory protein using selective substitutions of the regulatory Thr-456 and catalytic His-458 residues. Arch Biochem Biophys. 2000 Mar 1;375(1):165-70. PMID:10683263 doi:http://dx.doi.org/10.1006/abbi.1999.1651
↑ Chastain CJ, Failing CJ, Manandhar L, Zimmerman MA, Lakner MM, Nguyen TH. Functional evolution of C(4) pyruvate, orthophosphate dikinase. J Exp Bot. 2011 May;62(9):3083-91. doi: 10.1093/jxb/err058. Epub 2011 Mar 17. PMID:21414960 doi:http://dx.doi.org/10.1093/jxb/err058
↑ Chen YB, Lu TC, Wang HX, Shen J, Bu TT, Chao Q, Gao ZF, Zhu XG, Wang YF, Wang BC. Posttranslational Modification of Maize Chloroplast Pyruvate Orthophosphate Dikinase Reveals the Precise Regulatory Mechanism of Its Enzymatic Activity. Plant Physiol. 2014 Apr 7;165(2):534-549. PMID:24710069 doi:http://dx.doi.org/10.1104/pp.113.231993
↑ Roeske CA, Kutny RM, Budde RJ, Chollet R. Sequence of the phosphothreonyl regulatory site peptide from inactive maize leaf pyruvate, orthophosphate dikinase. J Biol Chem. 1988 May 15;263(14):6683-7. PMID:2834385
↑ Burnell JN, Hatch MD. Regulation of C4 photosynthesis: identification of a catalytically important histidine residue and its role in the regulation of pyruvate,Pi dikinase. Arch Biochem Biophys. 1984 May 15;231(1):175-82. PMID:6326674
↑ Jiang L, Chen YB, Zheng J, Chen Z, Liu Y, Tao Y, Wu W, Chen Z, Wang BC. Structural Basis of Reversible Phosphorylation by Maize Pyruvate Orthophosphate Dikinase Regulatory Protein. Plant Physiol. 2016 Feb;170(2):732-41. doi: 10.1104/pp.15.01709. Epub 2015 Nov, 30. PMID:26620526 doi:http://dx.doi.org/10.1104/pp.15.01709

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5d0n"

Categories: Large Structures | Zea mays | Chen Z | Jiang L

@@ Line 1: / Line 1: @@
 ==Crystal structure of maize PDRP bound with AMP==
-<StructureSection load='5d0n' size='340' side='right' caption='[[5d0n]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
+<StructureSection load='5d0n' size='340' side='right'caption='[[5d0n]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5d0n]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D0N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D0N FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5d0n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Zea_mays Zea mays]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D0N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D0N FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 3.2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5d1f|5d1f]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=5d0n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d0n OCA], [http://pdbe.org/5d0n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d0n RCSB], [http://www.ebi.ac.uk/pdbsum/5d0n PDBsum]</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=5d0n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d0n OCA], [https://pdbe.org/5d0n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d0n RCSB], [https://www.ebi.ac.uk/pdbsum/5d0n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d0n ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PDRP1_MAIZE PDRP1_MAIZE]] Bifunctional serine/threonine kinase and phosphorylase involved in the dark/light-mediated regulation of PPDK by catalyzing its phosphorylation/dephosphorylation. Dark/light-induced changes in stromal concentrations of the competing ADP and Pi substrates govern the direction of the reaction. In the dark, phosphorylates the catalytic intermediate of PPDK (PPDK-HisP), inactivating it. Light exposure induces the phosphorolysis reaction that reactivates PPDK. Phosphorylates PPDK at both Ser-528 and Thr-527 (PubMed:24710069). Can use ADP as a high specificity substrate and GDP as a lower affinity substrate, but has no activity with UDP (PubMed:21414960).<ref>PMID:10683263</ref> <ref>PMID:21414960</ref> <ref>PMID:24710069</ref> <ref>PMID:2834385</ref> <ref>PMID:6326674</ref>
+[https://www.uniprot.org/uniprot/PDRP1_MAIZE PDRP1_MAIZE] Bifunctional serine/threonine kinase and phosphorylase involved in the dark/light-mediated regulation of PPDK by catalyzing its phosphorylation/dephosphorylation. Dark/light-induced changes in stromal concentrations of the competing ADP and Pi substrates govern the direction of the reaction. In the dark, phosphorylates the catalytic intermediate of PPDK (PPDK-HisP), inactivating it. Light exposure induces the phosphorolysis reaction that reactivates PPDK. Phosphorylates PPDK at both Ser-528 and Thr-527 (PubMed:24710069). Can use ADP as a high specificity substrate and GDP as a lower affinity substrate, but has no activity with UDP (PubMed:21414960).<ref>PMID:10683263</ref> <ref>PMID:21414960</ref> <ref>PMID:24710069</ref> <ref>PMID:2834385</ref> <ref>PMID:6326674</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Chen, Z]]
+[[Category: Large Structures]]
-[[Category: Jiang, L]]
+[[Category: Zea mays]]
-[[Category: Adp-dependent protein kinase/pi-dependent protein phosphatase]]
+[[Category: Chen Z]]
-[[Category: C4 photosynthesis]]
+[[Category: Jiang L]]
-[[Category: Pdrp]]
-[[Category: Reversible phosphorylation]]
-[[Category: Transferase]]

5d0n

From Proteopedia

Current revision

Crystal structure of maize PDRP bound with AMP

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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