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4lv7

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Revision as of 10:33, 21 December 2022

Crystal structure of inositol 1,3,4,5,6-pentakisphosphate 2-kinase E82C/S142C

Structural highlights

4lv7 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.
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 1,3,4,5,6-pentakisphosphate 2-kinase (IPK1) converts inositol 1,3,4,5,6-pentakisphosphate(IP5) to inositol hexakisphosphate (IP6). IPK1 shares structural similarity with protein kinases and is suspected to employ a similar mechanism of activation. Previous studies revealed roles for the 1- and 3-phosphates of IP5 in IPK1 activation and revealed that the N-lobe of IPK1 is unstable in the absence of inositol phosphate (IP). Here, we demonstrate the link between IPK1 substrate specificity and the stability of its N-lobe. Limited proteolysis of IPK1 revealed that N-lobe stability is dependent on the presence of the 1-phosphate of the substrate, whereas overall stability of IPK1 was increased in ternary complexes with nucleotide and IPs possessing 1- and 3-phosphates that engage the N-lobe of IPK1. Thus, the 1- and 3-phosphates possess dual roles in both IPK1 activation and IPK1 stability. To test whether kinase stability directly contributed to substrate selectivity of the kinase, we engineered IPK1 mutants with disulfide bonds that artificially stabilized the N-lobe in an IP-independent manner thereby mimicking its substrate-bound state in the absence of IP. IPK1 E82C/S142C exhibited a DTT-sensitive 5-fold increase in kcat for 3,4,5,6-inositol tetrakisphosphate (3,4,5,6-IP4) as compared with wild-type IPK1. The crystal structure of the IPK1 E82C/S142C mutant confirmed the presence of the disulfide bond and revealed a small shift in the N-lobe. Finally, we determined that IPK1 E82C/S142C is substantially more stable than wild-type IPK1 under nonreducing conditions, revealing that increased stability of IPK1 E82C/S142C correlates with changes in substrate specificity by allowing IPs lacking the stabilizing 1-phosphate to be used. Taken together, our results show that IPK1 substrate selection is linked to the ability of each potential substrate to stabilize IPK1.

Conformational stability of inositol 1,3,4,5,6-pentakisphosphate 2-kinase (IPK1) dictates its substrate selectivity.,Gosein V, Miller GJ J Biol Chem. 2013 Dec 27;288(52):36788-95. doi: 10.1074/jbc.M113.512731. Epub, 2013 Oct 28. PMID:24165122^[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, Miller GJ. Conformational stability of inositol 1,3,4,5,6-pentakisphosphate 2-kinase (IPK1) dictates its substrate selectivity. J Biol Chem. 2013 Dec 27;288(52):36788-95. doi: 10.1074/jbc.M113.512731. Epub, 2013 Oct 28. PMID:24165122 doi:http://dx.doi.org/10.1074/jbc.M113.512731

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/4lv7"

Categories: Arabidopsis thaliana | Large Structures | Gosein V | Miller GJ

@@ Line 3: / Line 3: @@
 <StructureSection load='4lv7' size='340' side='right'caption='[[4lv7]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4lv7]] is a 2 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=4LV7 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=4LV7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4lv7]] 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=4LV7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LV7 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>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3udz|3udz]]</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=4lv7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lv7 OCA], [https://pdbe.org/4lv7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lv7 RCSB], [https://www.ebi.ac.uk/pdbsum/4lv7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lv7 ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">At5g42810, IPK1, MJB21.19 ([http://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/Inositol-pentakisphosphate_2-kinase Inositol-pentakisphosphate 2-kinase], with EC number [http://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'>[http://proteopedia.org/fgij/fg.htm?mol=4lv7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lv7 OCA], [http://pdbe.org/4lv7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4lv7 RCSB], [http://www.ebi.ac.uk/pdbsum/4lv7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4lv7 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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 25: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
-[[Category: Inositol-pentakisphosphate 2-kinase]]
 [[Category: Large Structures]]
-[[Category: Gosein, V]]
+[[Category: Gosein V]]
-[[Category: Miller, G J]]
+[[Category: Miller GJ]]
-[[Category: Atipk1]]
-[[Category: Inositol phosphorylation]]
-[[Category: Ins5p 2-k]]
-[[Category: Ip5 2-k]]
-[[Category: Ipk]]
-[[Category: Transferase]]

4lv7

From Proteopedia

Revision as of 10:33, 21 December 2022

Crystal structure of inositol 1,3,4,5,6-pentakisphosphate 2-kinase E82C/S142C

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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