5c46: Difference between revisions

Revision as of 06:19, 7 June 2023

Crystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta in complex with GTP gamma S loaded Rab11

Structural highlights

5c46 is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	GSP, MG, SO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PI4KB_HUMAN Phosphorylates phosphatidylinositol (PI) in the first committed step in the production of the second messenger inositol-1,4,5,-trisphosphate (PIP). May regulate Golgi disintegration/reorganization during mitosis, possibly via its phosphorylation. Involved in Golgi-to-plasma membrane trafficking (By similarity).^[1] ^[2] ^[3]

Publication Abstract from PubMed

The ability of proteins to bind and interact with protein partners plays fundamental roles in many cellular contexts. X-ray crystallography has been a powerful approach to understand protein-protein interactions, however, a challenge in the crystallization of proteins and their complexes is the presence of intrinsically disordered regions. In this article we describe an application of hydrogen deuterium exchange mass spectrometry (HDX-MS) to identify dynamic regions within type III phosphatidylinositol 4 kinase beta (PI4KIIIbeta) in complex with the GTPase Rab11. This information was then used to design deletions that allowed for the production of diffraction quality crystals. Importantly we also used HDX-MS to verify that the new construct was properly folded, consistent with it being catalytically and functionally active. Structures of PI4KIIIbeta in an Apo state and bound to the potent inhibitor BQR695 in complex with both GTPgammaS and GDP loaded Rab11 were determined. This hybrid HDX-MS/crystallographic strategy revealed novel aspects of the PI4KIIIbeta-Rab11 complex, as well as the molecular mechanism of potency of a PI4K specific inhibitor (BQR695). This approach is widely applicable to protein-protein complexes, and is an excellent strategy to optimize constructs for high-resolution structural approaches. This article is protected by copyright. All rights reserved.

Using hydrogen deuterium exchange mass spectrometry to engineer optimized constructs for crystallization of protein complexes: Case study of PI4KIIIbeta with Rab11.,Fowler ML, McPhail JA, Jenkins ML, Masson GR, Rutaganira FU, Shokat KM, Williams RL, Burke JE Protein Sci. 2016 Jan 12. doi: 10.1002/pro.2879. PMID:26756197^[4]

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

References

↑ Suzuki K, Hirano H, Okutomi K, Suzuki M, Kuga Y, Fujiwara T, Kanemoto N, Isono K, Horie M. Identification and characterization of a novel human phosphatidylinositol 4-kinase. DNA Res. 1997 Aug 31;4(4):273-80. PMID:9405935
↑ Godi A, Pertile P, Meyers R, Marra P, Di Tullio G, Iurisci C, Luini A, Corda D, De Matteis MA. ARF mediates recruitment of PtdIns-4-OH kinase-beta and stimulates synthesis of PtdIns(4,5)P2 on the Golgi complex. Nat Cell Biol. 1999 Sep;1(5):280-7. PMID:10559940 doi:https://dx.doi.org/10.1038/12993
↑ Heilmeyer LM Jr, Vereb G Jr, Vereb G, Kakuk A, Szivak I. Mammalian phosphatidylinositol 4-kinases. IUBMB Life. 2003 Feb;55(2):59-65. PMID:12749687 doi:https://dx.doi.org/10.1002/tbmb.718540873
↑ Fowler ML, McPhail JA, Jenkins ML, Masson GR, Rutaganira FU, Shokat KM, Williams RL, Burke JE. Using hydrogen deuterium exchange mass spectrometry to engineer optimized constructs for crystallization of protein complexes: Case study of PI4KIIIbeta with Rab11. Protein Sci. 2016 Jan 12. doi: 10.1002/pro.2879. PMID:26756197 doi:https://dx.doi.org/10.1002/pro.2879

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Suzuki K, Hirano H, Okutomi K, Suzuki M, Kuga Y, Fujiwara T, Kanemoto N, Isono K, Horie M. Identification and characterization of a novel human phosphatidylinositol 4-kinase. DNA Res. 1997 Aug 31;4(4):273-80. PMID:9405935

[2] Godi A, Pertile P, Meyers R, Marra P, Di Tullio G, Iurisci C, Luini A, Corda D, De Matteis MA. ARF mediates recruitment of PtdIns-4-OH kinase-beta and stimulates synthesis of PtdIns(4,5)P2 on the Golgi complex. Nat Cell Biol. 1999 Sep;1(5):280-7. PMID:10559940 doi:https://dx.doi.org/10.1038/12993

[3] Heilmeyer LM Jr, Vereb G Jr, Vereb G, Kakuk A, Szivak I. Mammalian phosphatidylinositol 4-kinases. IUBMB Life. 2003 Feb;55(2):59-65. PMID:12749687 doi:https://dx.doi.org/10.1002/tbmb.718540873

[4] Fowler ML, McPhail JA, Jenkins ML, Masson GR, Rutaganira FU, Shokat KM, Williams RL, Burke JE. Using hydrogen deuterium exchange mass spectrometry to engineer optimized constructs for crystallization of protein complexes: Case study of PI4KIIIbeta with Rab11. Protein Sci. 2016 Jan 12. doi: 10.1002/pro.2879. PMID:26756197 doi:https://dx.doi.org/10.1002/pro.2879

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[2]

[3]

[4]

@@ Line 3: / Line 3: @@
 <StructureSection load='5c46' size='340' side='right'caption='[[5c46]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5c46]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C46 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C46 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5c46]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C46 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C46 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GSP:5-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE'>GSP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GSP:5-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE'>GSP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PI4KB, PIK4CB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), RAB11A, RAB11 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5c46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c46 OCA], [https://pdbe.org/5c46 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c46 RCSB], [https://www.ebi.ac.uk/pdbsum/5c46 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c46 ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1-phosphatidylinositol_4-kinase 1-phosphatidylinositol 4-kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.67 2.7.1.67] </span></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=5c46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c46 OCA], [http://pdbe.org/5c46 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c46 RCSB], [http://www.ebi.ac.uk/pdbsum/5c46 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5c46 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PI4KB_HUMAN PI4KB_HUMAN]] Phosphorylates phosphatidylinositol (PI) in the first committed step in the production of the second messenger inositol-1,4,5,-trisphosphate (PIP). May regulate Golgi disintegration/reorganization during mitosis, possibly via its phosphorylation. Involved in Golgi-to-plasma membrane trafficking (By similarity).<ref>PMID:9405935</ref> <ref>PMID:10559940</ref> <ref>PMID:12749687</ref>  [[http://www.uniprot.org/uniprot/RB11A_HUMAN RB11A_HUMAN]] The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes. Rabs cycle between an inactive GDP-bound form and an active GTP-bound form that is able to recruit to membranes different set of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion. That Rab regulates endocytic recycling. Acts as a major regulator of membrane delivery during cytokinesis. Together with MYO5B and RAB8A participates in epithelial cell polarization. Together with RAB3IP, RAB8A, the exocyst complex, PARD3, PRKCI, ANXA2, CDC42 and DNMBP promotes transcytosis of PODXL to the apical membrane initiation sites (AMIS), apical surface formation and lumenogenesis. Together with MYO5B participates in CFTR trafficking to the plasma membrane and TF (Transferrin) recycling in nonpolarized cells. Required in a complex with MYO5B and RAB11FIP2 for the transport of NPC1L1 to the plasma membrane. Participates in the sorting and basolateral transport of CDH1 from the Golgi apparatus to the plasma membrane. Regulates the recycling of FCGRT (receptor of Fc region of monomeric Ig G) to basolateral membranes. May also play a role in melanosome transport and release from melanocytes.<ref>PMID:15601896</ref> <ref>PMID:15689490</ref> <ref>PMID:17462998</ref> <ref>PMID:19542231</ref> <ref>PMID:20890297</ref> <ref>PMID:21282656</ref>
+[https://www.uniprot.org/uniprot/PI4KB_HUMAN PI4KB_HUMAN] Phosphorylates phosphatidylinositol (PI) in the first committed step in the production of the second messenger inositol-1,4,5,-trisphosphate (PIP). May regulate Golgi disintegration/reorganization during mitosis, possibly via its phosphorylation. Involved in Golgi-to-plasma membrane trafficking (By similarity).<ref>PMID:9405935</ref> <ref>PMID:10559940</ref> <ref>PMID:12749687</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 20: @@
 ==See Also==
-*[[Ras-related protein Rab|Ras-related protein Rab]]
+*[[Phosphatidylinositol 4-kinase|Phosphatidylinositol 4-kinase]]
+*[[Ras-related protein Rab 3D structures|Ras-related protein Rab 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: 1-phosphatidylinositol 4-kinase]]
+[[Category: Homo sapiens]]
-[[Category: Human]]
 [[Category: Large Structures]]
-[[Category: Burke, J E]]
+[[Category: Burke JE]]
-[[Category: Fowler, M L]]
+[[Category: Fowler ML]]
-[[Category: Gtpase complex]]
-[[Category: Lipid kinase]]
-[[Category: Protein-protein complex]]
-[[Category: Transferase-signaling protein complex]]

5c46: Difference between revisions

Revision as of 06:19, 7 June 2023

Crystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta in complex with GTP gamma S loaded Rab11

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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