3udz

From Proteopedia

(Difference between revisions)

Current revision

Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with ADP and IP6.

Structural highlights

3udz is a 2 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 2.5Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

IPPK_ARATH Phosphorylates Ins(1,3,4,5,6)P5 at position 2 to form Ins(1,2,3,4,5,6)P6 (InsP6 or phytate). Phytate is a regulator of intracellular signaling, a highly abundant animal antinutrient, and a phosphate store in plant seeds. Also phosphorylates Ins(1,3,4,6)P4 and Ins(1,4,5,6)P4 to produce Ins(1,2,3,4,6)P5 and Ins(1,2,4,5,6)P5.^[1] ^[2]

Publication Abstract from PubMed

Inositol phosphate kinases (IPKs) sequentially phosphorylate inositol phosphates (IPs) on their inositol rings to yield an array of signaling molecules. IPKs must possess the ability to recognize their physiological substrates from among a pool of over 30 cellular IPs that differ in numbers and positions of phosphates. Crystal structures from IPK subfamilies have revealed structural determinants for IP discrimination, which vary considerably between IPKs. However, recent structures of inositol 1,3,4,5,6-pentakisphosphate 2-kinase (IPK1) did not reveal how IPK1 selectively recognizes its physiological substrate, IP5, while excluding others. Here, we report that limited proteolysis has revealed the presence of multiple conformational states in the IPK1 catalytic cycle, with notable protection from protease only in the presence of IP. Further, a 3.1 A crystal structure of IPK1 bound to ADP in the absence of IP revealed decreased order in residues 110-140 within the N-lobe of the kinase compared to structures in which IP is bound. Using this solution and crystallographic data, we propose a model for recognition of IP substrate by IPK1 wherein phosphate groups at the 4-, 5- and 6-positions are recognized initially by the C-lobe with subsequent interaction of the 1-position phosphate by Arg130 that stabilizes this residue and the N-lobe. This model explains how IPK1 can be highly specific for a single IP substrate by linking its interactions with substrate phosphate groups to the stabilization of the N- and C-lobes and kinase activation.

Inositol phosphate-induced stabilization of inositol 1,3,4,5,6-pentakisphosphate 2-kinase and its role in substrate specificity.,Gosein V, Leung TF, Krajden O, Miller GJ Protein Sci. 2012 Feb 23. doi: 10.1002/pro.2049. PMID:22362712^[3]

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

References

↑ Stevenson-Paulik J, Bastidas RJ, Chiou ST, Frye RA, York JD. Generation of phytate-free seeds in Arabidopsis through disruption of inositol polyphosphate kinases. Proc Natl Acad Sci U S A. 2005 Aug 30;102(35):12612-7. Epub 2005 Aug 17. PMID:16107538 doi:10.1073/pnas.0504172102
↑ Sweetman D, Johnson S, Caddick SE, Hanke DE, Brearley CA. Characterization of an Arabidopsis inositol 1,3,4,5,6-pentakisphosphate 2-kinase (AtIPK1). Biochem J. 2006 Feb 15;394(Pt 1):95-103. PMID:16223361 doi:BJ20051331
↑ Gosein V, Leung TF, Krajden O, Miller GJ. Inositol phosphate-induced stabilization of inositol 1,3,4,5,6-pentakisphosphate 2-kinase and its role in substrate specificity. Protein Sci. 2012 Feb 23. doi: 10.1002/pro.2049. PMID:22362712 doi:10.1002/pro.2049

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/3udz"

@@ Line 3: / Line 3: @@
 <StructureSection load='3udz' size='340' side='right'caption='[[3udz]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3udz]] is a 2 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=3UDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UDZ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3udz]] is a 2 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=3UDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UDZ FirstGlance]. <br>
-</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=IHP:INOSITOL+HEXAKISPHOSPHATE'>IHP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.5&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=IHP:INOSITOL+HEXAKISPHOSPHATE'>IHP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3uds|3uds]], [[3udt|3udt]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">At5g42810, IPK1, MJB21.19 ([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'>[https://en.wikipedia.org/wiki/Inositol-pentakisphosphate_2-kinase Inositol-pentakisphosphate 2-kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.158 2.7.1.158] </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=3udz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3udz OCA], [https://pdbe.org/3udz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3udz RCSB], [https://www.ebi.ac.uk/pdbsum/3udz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3udz ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/IPPK_ARATH IPPK_ARATH]] Phosphorylates Ins(1,3,4,5,6)P5 at position 2 to form Ins(1,2,3,4,5,6)P6 (InsP6 or phytate). Phytate is a regulator of intracellular signaling, a highly abundant animal antinutrient, and a phosphate store in plant seeds. Also phosphorylates Ins(1,3,4,6)P4 and Ins(1,4,5,6)P4 to produce Ins(1,2,3,4,6)P5 and Ins(1,2,4,5,6)P5.<ref>PMID:16107538</ref> <ref>PMID:16223361</ref>
+[https://www.uniprot.org/uniprot/IPPK_ARATH IPPK_ARATH] Phosphorylates Ins(1,3,4,5,6)P5 at position 2 to form Ins(1,2,3,4,5,6)P6 (InsP6 or phytate). Phytate is a regulator of intracellular signaling, a highly abundant animal antinutrient, and a phosphate store in plant seeds. Also phosphorylates Ins(1,3,4,6)P4 and Ins(1,4,5,6)P4 to produce Ins(1,2,3,4,6)P5 and Ins(1,2,4,5,6)P5.<ref>PMID:16107538</ref> <ref>PMID:16223361</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
-[[Category: Inositol-pentakisphosphate 2-kinase]]
 [[Category: Large Structures]]
-[[Category: Gosein, V]]
+[[Category: Gosein V]]
-[[Category: Krajden, O]]
+[[Category: Krajden O]]
-[[Category: Leung, T F]]
+[[Category: Leung T-F]]
-[[Category: Miller, G J]]
+[[Category: Miller GJ]]
-[[Category: Atipk1]]
-[[Category: Inositol]]
-[[Category: Ins5p 2-k]]
-[[Category: Ip5 2-k]]
-[[Category: Ipk]]
-[[Category: Polyphosphate kinase]]
-[[Category: Transferase]]

3udz

From Proteopedia

Current revision

Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with ADP and IP6.

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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