1DQV,3HN8


Conserved Protein Domain Family
C2B_Synaptotagmin-3-5-6-9-10

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cd08403: C2B_Synaptotagmin-3-5-6-9-10 
Click on image for an interactive view with Cn3D
C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10
Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. Synaptotagmin 3, a member of class 3 synaptotagmins, is located in the brain and localized to the active zone and plasma membrane. It functions as a Ca2+ sensor for fast exocytosis. It, along with synaptotagmins 5,6, and 10, has disulfide bonds at its N-terminus. Synaptotagmin 9, a class 5 synaptotagmins, is located in the brain and localized to the synaptic vesicles. It is thought to be a Ca2+-sensor for dense-core vesicle exocytosis. Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium. Of the 17 identified synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10). The function of the two C2 domains that bind calcium are: regulating the fusion step of synaptic vesicle exocytosis (C2A) and binding to phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the absence of calcium ions and to phosphatidylinositol bisphosphate (PIP2) in their presence (C2B). C2B also regulates also the recycling step of synaptic vesicles. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the second C2 repeat, C2B, and has a type-I topology.
Statistics
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PSSM-Id: 176048
View PSSM: cd08403
Aligned: 8 rows
Threshold Bit Score: 225.08
Threshold Setting Gi: 215507951
Created: 30-Nov-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Ca2+ binding
Conserved site includes 6 residues -Click on image for an interactive view with Cn3D
Feature 1:Ca2+ binding site [ion binding site]
Evidence:

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                      #              #                       #           
1DQV_A        139 GELNFSLCYLPtaGLLTVTIIKASNLKAMDlt---------gFSDPYVKASLISegrRLKKRKTSIKKNtLNPTYNEALV 209  black rat
NP_001003985  359 GDLMFSLCYLPtaGRLTITIIKARNLKAMDit---------gASDPYVKVSLMCdgrRLKKRKTSTKRNtLNPVYNEAIV 429  zebrafish
XP_001187868 1262 GEVMFSLNYLPtaCRLTLTVIKARNLKAMDit---------gASDPYVKVSLMSqgkRIKKKKTTVKKNtLNPVYNEAMV 1332 purple urchin
XP_425830     355 GEIMFSLCYLPtaGRLTLTVIKCRNLKAMDit---------gYSDPYVKVSLLCdgrRLKKKKTTIKKNtLNPTYNEAII 425  chicken
AAI58239       11 GEINFSLCYLPtaGRLTATIIKATNLKAMDlt---------gFSDPYVKASLICegrRLKKRKTSIKKNtLNPTYNEALV 81   western clawe...
EEB19763      277 GELMLSLCYLPraGRLTLTVIKARNLKAKDii--------ngKSDPYVKVYLMCegkRIKKKKTTVKKStLFPIYNEALM 348  human body louse
EEC17405       88 GEVMLSLCYLPtaGRLTVTPHLSSDVTRYFlldevsaggavdGSDPYIKVILVCegkRIKKKKTSVKKStLNPVFNEALV 167  black-legged ...
3HN8_A        140 GELNFSLCYLPtaGLLTVTIIKASNLKAMDlt---------gFSDPYVKASLISegrRLKKRKTSIKKNtLNPTYNEALV 210  Norway rat
Feature 1                           # #     #                                     
1DQV_A        210 FDVApesvenvGLSIAVVDYDcigHNEVIGVCRVgpeaadpHGREHWAEMlanprkpVEHWHQL 273  black rat
NP_001003985  430 FDVPpenidqiSLLIAVMDYDrvgHNEVIGICHVgnr-apsLGRDHWNEMltyprkpIARWHQL 492  zebrafish
XP_001187868 1333 FDVApdsmeniCLIIAVVDYDwvgHSELIGVCEVgpn-apvQGAAHWADMltnprkpIAQWYQL 1395 purple urchin
XP_425830     426 FDIPpenmdqvSLLISVMDYDrvgHNEIIGVCRVgvn-aegLGRDHWNEMlayprkpIAHWHPL 488  chicken
AAI58239       82 FDIPnenmdhvSLTIAVMDYDcigHNEVIGMCRVgsd-admQGREHWNEMlanprkpIEHWHQL 144  western clawed frog
EEB19763      349 FDVPaenvedvSLIVNVVDHDiigVNELLGCIGIgnn-figIGRDHWLEMldnprkpVAQWYPL 411  human body louse
EEC17405      168 FDVPpenvddvNLAVKVVDYDrvgPNELMGCCAVgtl-aagVGREHWLAVmdnprkpTAQWYPL 230  black-legged tick
3HN8_A        211 FDVApesvenvGLSIAVVDYDcigHNEVIGVCRVgpeaadpHGREHWAEMlanprkpVEHWHQL 274  Norway rat

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