5kdi

From Proteopedia

(Difference between revisions)

Current revision

How FAPP2 Selects Simple Glycosphingolipids Using the GLTP-fold

Structural highlights

5kdi 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.
Method:	X-ray diffraction, Resolution 1.45Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PKHA8_HUMAN Cargo transport protein that is required for apical transport from the Golgi complex. Transports AQP2 from the trans-Golgi network (TGN) to sites of AQP2 phosphorylation. Mediates the non-vesicular transport of glucosylceramide (GlcCer) from the trans-Golgi network (TGN) to the plasma membrane and plays a pivotal role in the synthesis of complex glycosphingolipids. Binding of both phosphatidylinositol 4-phosphate (PIP) and ARF1 are essential for the GlcCer transfer ability. Also required for primary cilium formation, possibly by being involved in the transport of raft lipids to the apical membrane, and for membrane tubulation.^[1] ^[2] ^[3]

Publication Abstract from PubMed

The glycolipid transfer protein (GLTP) fold defines a superfamily of eukaryotic proteins that selectively transport sphingolipids (SLs) between membranes. However, the mechanisms determining the protein selectivity for specific glycosphingolipids (GSLs) are unclear. Here, we report the crystal structure of the GLTP homology (GLTPH) domain of human 4-phosphate adaptor protein 2 (FAPP2) bound with N-oleoyl-galactosylceramide. Using this domain, FAPP2 transports glucosylceramide from its cis-Golgi synthesis site to the trans-Golgi for conversion into complex GSLs. The FAPP2-GLTPH structure revealed an element, termed the ID loop, that controls specificity in the GLTP family. We found that, in accordance with FAPP2 preference for simple GSLs, the ID loop protrudes from behind the SL headgroup-recognition center to mitigate binding by complex GSLs. Mutational analyses including GLTP and FAPP2 chimeras with swapped ID loops supported the proposed restrictive role of the FAPP2 ID loop in GSL selectivity. Comparative analysis revealed distinctly designed ID loops in each GLTP family member. This analysis also disclosed a conserved H-bond triplet that "clasps" both ID-loop ends together to promote structural autonomy and rigidity. The findings indicated that various ID loops work in concert with conserved recognition centers to create different specificities among family members. We also observed four bulky, conserved hydrophobic residues involved in "sensor-like" interactions with lipid chains in protein hydrophobic pockets and FF motifs in GLTP and FAPP2, well-positioned to provide acyl chain-dependent SL selectivity for the hydrophobic pockets. In summary, our study provides mechanistic insights into sphingolipid recognition by the GLTP fold and uncovers the elements involved in this recognition.

Structural analyses of 4-phosphate adaptor protein 2 yield mechanistic insights into sphingolipid recognition by the glycolipid transfer protein family.,Ochoa-Lizarralde B, Gao YG, Popov AN, Samygina VR, Zhai X, Mishra SK, Boldyrev IA, Molotkovsky JG, Simanshu DK, Patel DJ, Brown RE, Malinina L J Biol Chem. 2018 Oct 26;293(43):16709-16723. doi: 10.1074/jbc.RA117.000733. Epub, 2018 Sep 11. PMID:30206120^[4]

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

References

↑ Godi A, Di Campli A, Konstantakopoulos A, Di Tullio G, Alessi DR, Kular GS, Daniele T, Marra P, Lucocq JM, De Matteis MA. FAPPs control Golgi-to-cell-surface membrane traffic by binding to ARF and PtdIns(4)P. Nat Cell Biol. 2004 May;6(5):393-404. Epub 2004 Apr 25. PMID:15107860 doi:10.1038/ncb1119
↑ Vieira OV, Verkade P, Manninen A, Simons K. FAPP2 is involved in the transport of apical cargo in polarized MDCK cells. J Cell Biol. 2005 Aug 15;170(4):521-6. doi: 10.1083/jcb.200503078. PMID:16103222 doi:http://dx.doi.org/10.1083/jcb.200503078
↑ D'Angelo G, Polishchuk E, Di Tullio G, Santoro M, Di Campli A, Godi A, West G, Bielawski J, Chuang CC, van der Spoel AC, Platt FM, Hannun YA, Polishchuk R, Mattjus P, De Matteis MA. Glycosphingolipid synthesis requires FAPP2 transfer of glucosylceramide. Nature. 2007 Sep 6;449(7158):62-7. doi: 10.1038/nature06097. Epub 2007 Aug 8. PMID:17687330 doi:http://dx.doi.org/10.1038/nature06097
↑ Ochoa-Lizarralde B, Gao YG, Popov AN, Samygina VR, Zhai X, Mishra SK, Boldyrev IA, Molotkovsky JG, Simanshu DK, Patel DJ, Brown RE, Malinina L. Structural analyses of 4-phosphate adaptor protein 2 yield mechanistic insights into sphingolipid recognition by the glycolipid transfer protein family. J Biol Chem. 2018 Oct 26;293(43):16709-16723. doi: 10.1074/jbc.RA117.000733. Epub, 2018 Sep 11. PMID:30206120 doi:http://dx.doi.org/10.1074/jbc.RA117.000733

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/5kdi"

@@ Line 3: / Line 3: @@
 <StructureSection load='5kdi' size='340' side='right'caption='[[5kdi]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5kdi]] 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=5KDI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KDI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5kdi]] 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=5KDI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KDI FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6S8:(~{Z})-~{N}-[(~{E},2~{S},3~{R})-1-[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-octadec-4-en-2-yl]octadec-9-enamide'>6S8</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]] 1.45&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PLEKHA8, FAPP2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6S8:(~{Z})-~{N}-[(~{E},2~{S},3~{R})-1-[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-octadec-4-en-2-yl]octadec-9-enamide'>6S8</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=5kdi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kdi OCA], [http://pdbe.org/5kdi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kdi RCSB], [http://www.ebi.ac.uk/pdbsum/5kdi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kdi ProSAT]</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=5kdi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kdi OCA], [https://pdbe.org/5kdi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kdi RCSB], [https://www.ebi.ac.uk/pdbsum/5kdi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kdi ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PKHA8_HUMAN PKHA8_HUMAN]] Cargo transport protein that is required for apical transport from the Golgi complex. Transports AQP2 from the trans-Golgi network (TGN) to sites of AQP2 phosphorylation. Mediates the non-vesicular transport of glucosylceramide (GlcCer) from the trans-Golgi network (TGN) to the plasma membrane and plays a pivotal role in the synthesis of complex glycosphingolipids. Binding of both phosphatidylinositol 4-phosphate (PIP) and ARF1 are essential for the GlcCer transfer ability. Also required for primary cilium formation, possibly by being involved in the transport of raft lipids to the apical membrane, and for membrane tubulation.<ref>PMID:15107860</ref> <ref>PMID:16103222</ref> <ref>PMID:17687330</ref>
+[https://www.uniprot.org/uniprot/PKHA8_HUMAN PKHA8_HUMAN] Cargo transport protein that is required for apical transport from the Golgi complex. Transports AQP2 from the trans-Golgi network (TGN) to sites of AQP2 phosphorylation. Mediates the non-vesicular transport of glucosylceramide (GlcCer) from the trans-Golgi network (TGN) to the plasma membrane and plays a pivotal role in the synthesis of complex glycosphingolipids. Binding of both phosphatidylinositol 4-phosphate (PIP) and ARF1 are essential for the GlcCer transfer ability. Also required for primary cilium formation, possibly by being involved in the transport of raft lipids to the apical membrane, and for membrane tubulation.<ref>PMID:15107860</ref> <ref>PMID:16103222</ref> <ref>PMID:17687330</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Brown, R E]]
+[[Category: Brown RE]]
-[[Category: Malinina, L]]
+[[Category: Malinina L]]
-[[Category: Ochoa-Lizarralde, B]]
+[[Category: Ochoa-Lizarralde B]]
-[[Category: Patel, D J]]
+[[Category: Patel DJ]]
-[[Category: Popov, A N]]
+[[Category: Popov AN]]
-[[Category: Samygina, V R]]
+[[Category: Samygina VR]]
-[[Category: Gltp-fold]]
-[[Category: Lipid transfer]]
-[[Category: Lipid transport]]

5kdi

From Proteopedia

Current revision

How FAPP2 Selects Simple Glycosphingolipids Using the GLTP-fold

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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