Difference between revisions of "Part:BBa K3765014"
 
(One intermediate revision by the same user not shown)
Line 6: Line 6:
  
 
===Usage and Biology===
 
===Usage and Biology===
−
The fusion protein encoded by this CDS part is the same as that for [https://parts.igem.org/Part:BBa_K3765013 OpdA-SpyTag002-sfGFP] excluding the sfGFP module, which was removed by digestion with KpnI followed by ligation. As a result, this fusion protein is less bulky than its previous version.
+
This CDS part is the same as [https://parts.igem.org/Part:BBa_K3765013 OpdA-SpyTag002-sfGFP] excluding the sfGFP module, which was removed by digestion with KpnI followed by ligation. As a result, the fusion protein encoded by this CDS is less bulky than its previous version.
 
[[File:T--IISc-Bangalore--images--Map_C2(2.0).png|thumb|center|900px|Fig 1. Feature Map]]
 
[[File:T--IISc-Bangalore--images--Map_C2(2.0).png|thumb|center|900px|Fig 1. Feature Map]]
  
 
A tertiary structure for this fusion protein was predicted using [https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb AlphaFold]. The OpdA module folds as in its native state, while the other stretches of amino acids exist as intrinsically disordered regions (IDRs). This also implies that the SpyTag002 module is far away from the core enzyme and can reliably form an isopeptide bond with SpyCatcher/SpyCatcher002, and this binding is not expected to hamper the enzymatic activity of OpdA.  
 
A tertiary structure for this fusion protein was predicted using [https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb AlphaFold]. The OpdA module folds as in its native state, while the other stretches of amino acids exist as intrinsically disordered regions (IDRs). This also implies that the SpyTag002 module is far away from the core enzyme and can reliably form an isopeptide bond with SpyCatcher/SpyCatcher002, and this binding is not expected to hamper the enzymatic activity of OpdA.  
 
[[File:T--IISc-Bangalore--images--C2(2.0)_CartoonModel.png|thumb|center|400px|Fig 2. Predicted cartoon model [N- to C- direction is blue to red]]]
 
[[File:T--IISc-Bangalore--images--C2(2.0)_CartoonModel.png|thumb|center|400px|Fig 2. Predicted cartoon model [N- to C- direction is blue to red]]]
 +
----
  
 
<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>

Latest revision as of 18:27, 20 October 2021


OpdA_Signal+OpdA+22aaL+SpyTag002+10xHis

CDS of fusion protein consisting of SpyTag002 linked to OpdA (phosphotriesterase), which can covalently bind to SpyCatcher/SpyCatcher002. In our project, the protein encoded by this part is designed to get anchored to a SpyCatcher002-dCBD fusion protein.

Usage and Biology

This CDS part is the same as OpdA-SpyTag002-sfGFP excluding the sfGFP module, which was removed by digestion with KpnI followed by ligation. As a result, the fusion protein encoded by this CDS is less bulky than its previous version.

Fig 1. Feature Map

A tertiary structure for this fusion protein was predicted using AlphaFold. The OpdA module folds as in its native state, while the other stretches of amino acids exist as intrinsically disordered regions (IDRs). This also implies that the SpyTag002 module is far away from the core enzyme and can reliably form an isopeptide bond with SpyCatcher/SpyCatcher002, and this binding is not expected to hamper the enzymatic activity of OpdA.

Fig 2. Predicted cartoon model [N- to C- direction is blue to red]

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 1219
    Illegal AgeI site found at 1282
  • 1000
    COMPATIBLE WITH RFC[1000]