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1w15

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rat synaptotagmin 4 C2B domain in the presence of calcium

Structural highlights

1w15 is a 1 chain structure with sequence from Rattus norvegicus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.93Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SYT4_RAT Synaptotagmin family member which does not bind Ca(2+) (PubMed:7993622). Involved in neuronal dense core vesicles (DCVs) mobility through its interaction with KIF1A. Upon increased neuronal activity, phosphorylation by MAPK8/JNK1 destabilizes the interaction with KIF1A and captures DCVs to synapses (PubMed:29166604). Plays a role in dendrite formation by melanocytes (By similarity).[UniProtKB:Q9H2B2]^[1] ^[2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The neuronal protein synaptotagmin 1 functions as a Ca(2+) sensor in exocytosis via two Ca(2+)-binding C(2) domains. The very similar synaptotagmin 4, which includes all the predicted Ca(2+)-binding residues in the C(2)B domain but not in the C(2)A domain, is also thought to function as a neuronal Ca(2+) sensor. Here we show that, unexpectedly, both C(2) domains of fly synaptotagmin 4 exhibit Ca(2+)-dependent phospholipid binding, whereas neither C(2) domain of rat synaptotagmin 4 binds Ca(2+) or phospholipids efficiently. Crystallography reveals that changes in the orientations of critical Ca(2+) ligands, and perhaps their flexibility, render the rat synaptotagmin 4 C(2)B domain unable to form full Ca(2+)-binding sites. These results indicate that synaptotagmin 4 is a Ca(2+) sensor in the fly but not in the rat, that the Ca(2+)-binding properties of C(2) domains cannot be reliably predicted from sequence analyses, and that proteins clearly identified as orthologs may nevertheless have markedly different functional properties.

Structural basis for the evolutionary inactivation of Ca2+ binding to synaptotagmin 4.,Dai H, Shin OH, Machius M, Tomchick DR, Sudhof TC, Rizo J Nat Struct Mol Biol. 2004 Sep;11(9):844-9. Epub 2004 Aug 15. PMID:15311271^[3]

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

References

↑ Bharat V, Siebrecht M, Burk K, Ahmed S, Reissner C, Kohansal-Nodehi M, Steubler V, Zweckstetter M, Ting JT, Dean C. Capture of Dense Core Vesicles at Synapses by JNK-Dependent Phosphorylation of Synaptotagmin-4. Cell Rep. 2017 Nov 21;21(8):2118-2133. PMID:29166604 doi:10.1016/j.celrep.2017.10.084
↑ Ullrich B, Li C, Zhang JZ, McMahon H, Anderson RG, Geppert M, Südhof TC. Functional properties of multiple synaptotagmins in brain. Neuron. 1994 Dec;13(6):1281-91. PMID:7993622 doi:10.1016/0896-6273(94)90415-4
↑ Dai H, Shin OH, Machius M, Tomchick DR, Sudhof TC, Rizo J. Structural basis for the evolutionary inactivation of Ca2+ binding to synaptotagmin 4. Nat Struct Mol Biol. 2004 Sep;11(9):844-9. Epub 2004 Aug 15. PMID:15311271 doi:10.1038/nsmb817

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1w15"

@@ Line 3: / Line 3: @@
 <StructureSection load='1w15' size='340' side='right'caption='[[1w15]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1w15]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W15 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W15 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1w15]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W15 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W15 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.93&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1w16|1w16]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=1w15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w15 OCA], [https://pdbe.org/1w15 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w15 RCSB], [https://www.ebi.ac.uk/pdbsum/1w15 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w15 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/SYT4_RAT SYT4_RAT] Synaptotagmin family member which does not bind Ca(2+) (PubMed:7993622). Involved in neuronal dense core vesicles (DCVs) mobility through its interaction with KIF1A. Upon increased neuronal activity, phosphorylation by MAPK8/JNK1 destabilizes the interaction with KIF1A and captures DCVs to synapses (PubMed:29166604). Plays a role in dendrite formation by melanocytes (By similarity).[UniProtKB:Q9H2B2]<ref>PMID:29166604</ref> <ref>PMID:7993622</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 34: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Buffalo rat]]
 [[Category: Large Structures]]
-[[Category: Dai, H]]
+[[Category: Rattus norvegicus]]
-[[Category: Machius, M]]
+[[Category: Dai H]]
-[[Category: Rizo, J]]
+[[Category: Machius M]]
-[[Category: Shin, O H]]
+[[Category: Rizo J]]
-[[Category: Sudhof, T C]]
+[[Category: Shin O-H]]
-[[Category: Tomchick, D R]]
+[[Category: Sudhof TC]]
-[[Category: Endocytosis/exocytosis]]
+[[Category: Tomchick DR]]
-[[Category: Metal binding protein]]
-[[Category: Neurotransmitter release]]
-[[Category: Synaptotagmin]]
-[[Category: Transmembrane]]

1w15

From Proteopedia

Current revision

rat synaptotagmin 4 C2B domain in the presence of calcium

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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