2R83,1TJM,1K5W


Conserved Protein Domain Family
C2B_Synaptotagmin-1

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cd08402: C2B_Synaptotagmin-1 
Click on image for an interactive view with Cn3D
C2 domain second repeat present in Synaptotagmin 1
Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. Synaptotagmin 1, a member of the class 1 synaptotagmins, is located in the brain and endocranium and localized to the synaptic vesicles and secretory granules. It functions as a Ca2+ sensor for fast exocytosis. It, like synaptotagmin-2, has an N-glycosylated N-terminus. Synaptotagmin 4, a member of class 4 synaptotagmins, is located in the brain. It functions are unknown. It, like synaptotagmin-11, has an Asp to Ser substitution in its C2A domain. 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: 176047
View PSSM: cd08402
Aligned: 19 rows
Threshold Bit Score: 228.825
Threshold Setting Gi: 196015773
Created: 21-Sep-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Ca2+ binding
Conserved site includes 5 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                                      #     #                                           
2R83_A       136 LGDICFSLRYVPTaGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQngKRLKKKKTTIKKNTLNPYYNESFSFEVPFEQI 215 human
XP_001623846 221 LGDICFSLRYVPSsGKLQITIVEAKSLKSMDLTGYSDPYVKIALVQegRKIKKKKTTVKKRTLNPYYNETFTFTVAFEKI 300 starlet sea ane...
BAA85622     254 LGDICFSLRYVPTsGKLTIVILEAKNLKKMDVGGLSDPYVKLSLMLngKRVKKKKTTIKKYTLNPYYNESFSFEVPFEQI 333 Dugesia japonica
EEC14452     213 LGDICFSLRYVPTaGKLTVVILEAKNLKKMDVGGLSDPYVKIALMMngKRLKKKKTSIKKCTLNPYYNESFTFEVPFEQI 292 black-legged tick
NP_001087607 237 LGDICFSLRYVPSnGKLTVIILEAKNLKRMDSDGFSDPFVKVHLALnrKKWKRKKTAVKPSTLKPYFNESFTFDVSLEQM 316 African clawed ...
ABR68850     279 LGDICFSLRYVPTaGKLTVVILEAKNLKKMDVGGLSDPYVKLSLMLngKRIKKKKTTIKKCTLNPYYNESFTFEVPFEQI 358 Dumeril's clam ...
AAB67801     278 LGDICFSLRYVPTaGKLTVVILEAKNLKKMDVGGLSDPYVKISLYMnnKRMKKKKTTIKKRTLNPYYNESFGFEVPFEQI 357 purple urchin
P21521       326 LGDICFSLRYVPTaGKLTVVILEAKNLKKMDVGGLSDPYVKIAIMQngKRLKKKKTSVKKCTLNPYYNESFSFEVPFEQM 405 fruit fly
XP_002595808 195 PGDICFSLRYVPTaGKLTIVILEAKNLKKCDVGGLSDPYVKMQLYSnnKRLKKKKTTIKKRTLNPYYNESFTFEVPFEQI 274 Florida lancelet
1K5W_A         4 LGDICFSLRYVPTaGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQngKRLKKKKTTIKKNTLNPYYNESFSFEVPFEQI 83  Norway rat
Feature 1                  # #     #                                     
2R83_A       216 QkvQVVVTVLDYDKIGKNDAIGKVFVGYnstgaELRHWSDMLANprRPIAQWHTLQ 271 human
XP_001623846 301 EqtSLIISVLDYDRVGKSEMIGKCVVGElssgaDLRHWADMLASprRSVAQWHTLH 356 starlet sea anemone
BAA85622     334 QkvNLIVTVVDYDRIGTSEPIGRIVLGCnatgaELRHWSDMLANprRPIAQWHTLQ 389 Dugesia japonica
EEC14452     293 QkvQLVVTVVDYDRIGTSEPIGKVVLGCnatgtELRHWMDMLASprRPIAQWHSLK 348 black-legged tick
NP_001087607 317 KnvDLIISVWDHDKVGKNEQIGKLFLGCrasgnALNHWSDMLAHprRPMAQWHKLQ 372 African clawed frog
ABR68850     359 QkvTLIITVVDYDRIGTSEPIGRVVLGCnatgtELRHWSDMLANprRPIAQWHTLQ 414 Dumeril's clam worm
AAB67801     358 QkvTLVVTVVDYDRMGSSEPIGKVVLGCnatgaGLRHWSDMLASprRPIAQWHTLQ 413 purple urchin
P21521       406 QkiCLVVTVVDYDRIGTSEPIGRCILGCmgtgtELRHWSDMLASprRPIAQWHTLK 461 fruit fly
XP_002595808 275 QrvELKLTVMDWDRTSKNDPIGELRLGPnaagaELRHWSDMLANprRPIAQWHTLT 330 Florida lancelet
1K5W_A        84 QkvQVVVTVLDYDKIGKNDAIGKVFVGYnstgaELRHWSDMLANprRPIAQWHTLQ 139 Norway rat

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