jakub pas structure prediction and evolution of chase domain
TRANSCRIPT
![Page 1: Jakub pas structure prediction and evolution of chase domain](https://reader035.vdocument.in/reader035/viewer/2022071907/55c9da12bb61ebac388b45a9/html5/thumbnails/1.jpg)
Structure prediction and evolution of CHASE domain
Jakub Pas1,2, Jan Barciszewski1 1. Institute of Bioorganic Chemistry Polish Academy of Science,
Poznan, Poland 2. Bioinfobank Institute, Poznan, Poland
![Page 2: Jakub pas structure prediction and evolution of chase domain](https://reader035.vdocument.in/reader035/viewer/2022071907/55c9da12bb61ebac388b45a9/html5/thumbnails/2.jpg)
Characteristics of CRE1 cytokinin receptor
1000 aa long N terminal ligand binding domain ( 300 aa) Histidine kinase domain at the C terminus
followed by two receiver domains T 278 mutation causes the loss of function A part of the two component system
![Page 3: Jakub pas structure prediction and evolution of chase domain](https://reader035.vdocument.in/reader035/viewer/2022071907/55c9da12bb61ebac388b45a9/html5/thumbnails/3.jpg)
CHASE
200 – 230 aa Present in bacteria, lower eukaryotes and
plants Bound at the C terminus Binds cytokinins and peptides Helices at the both ends Two internal helices divided by strands (a + b
fold) Mechanism of ligand binding and evolutional
relationships are unknown.
![Page 4: Jakub pas structure prediction and evolution of chase domain](https://reader035.vdocument.in/reader035/viewer/2022071907/55c9da12bb61ebac388b45a9/html5/thumbnails/4.jpg)
Modelling ProcesMetaserver
3D Jury
Modeller Verrify 3D
Domain Split
Domain selection
Structure Prediction
(Profile)
Structure Evaluation
Molecular modelling Quality check
Alignment corection
Query sequence (CRE1)
Final Model
![Page 5: Jakub pas structure prediction and evolution of chase domain](https://reader035.vdocument.in/reader035/viewer/2022071907/55c9da12bb61ebac388b45a9/html5/thumbnails/5.jpg)
Profile - profile fold recognition method
1st pass: Query sequence vs Sequence Database
2nd pass: Query Profile vs Profile Database
alignment
alignment
![Page 6: Jakub pas structure prediction and evolution of chase domain](https://reader035.vdocument.in/reader035/viewer/2022071907/55c9da12bb61ebac388b45a9/html5/thumbnails/6.jpg)
Evolutionary relationships to CHASE domain
(GRDB-Gene Related Data Base)
1jogA - sensory domain of the membraneous two-component fumarate - sensor Dcus from E. coli, 1p0zA - sensor kinase cita. 1e4eA, 1ehiA - D-Alanine-D-lactate ligase.
![Page 7: Jakub pas structure prediction and evolution of chase domain](https://reader035.vdocument.in/reader035/viewer/2022071907/55c9da12bb61ebac388b45a9/html5/thumbnails/7.jpg)
Structures of receptor domains selected by 3DHit as related to 1joga.
Domain 3d-hit score
PDB code
Function Organism Ligand
CACHE 84.3 1p0z Ca2+ channels and chemotaxis receptors
K.pneumoniae Citrate Anion
GAF 55.6 1mc0 cGMP phosphodiesterase, adenyl cyclase, FhlA domain
M.musculus Cyclic guanosine monophosphate
PAS/PYP 47.2 1f98 Periodic clock protein, aryl hydrocarbon receptor and single-minded protein/Photoactive Yellow Protein
E. halophila 4'-Hydroxycinnamic Acid
Profiln 46.2 1g5u monomeric actin binding H. brasiliensis Actin ACT - 1psdA1 Aspartate kinase –
chorismate mutase – TyrA E.coli Nicotinamide-
Adenine-Dinucleotide
![Page 8: Jakub pas structure prediction and evolution of chase domain](https://reader035.vdocument.in/reader035/viewer/2022071907/55c9da12bb61ebac388b45a9/html5/thumbnails/8.jpg)
Topological representation and evolution of PYP family
![Page 9: Jakub pas structure prediction and evolution of chase domain](https://reader035.vdocument.in/reader035/viewer/2022071907/55c9da12bb61ebac388b45a9/html5/thumbnails/9.jpg)
Molecular model of CRE1a receptor from A. thaliana with trans-zeatin.
![Page 10: Jakub pas structure prediction and evolution of chase domain](https://reader035.vdocument.in/reader035/viewer/2022071907/55c9da12bb61ebac388b45a9/html5/thumbnails/10.jpg)
Conclusions
CRE1 and 1mc0 are located on the same clade and may have common origin
Cre1 is lacking a strand they are structurally much more similar to each other then to other members of PAS/PYP superfamily
The ligands bound by both domains are also structurally similar
CACHE, PAS/PYP and Profilin form a separate branch. These two groups separated very early in evolution.
Most of the protein-ligand interaction fulfiled by closely related receptors which are diverse in primary structure but share a common structure.