Team:NCHU Taichung/Basic Part

Basic Part

Part name Type Description Length
BBa_K3830008 protein Beta-xylanase 1860 bp
BBa_K3830013 protein Cellulose 1,4-beta-cellobiosidase 2688 bp
BBa_K3830014 protein Endoglucanase A 1434 bp
BBa_K3830015 protein Cellulosomal-scaffolding protein A 5565 bp
BBa_K3830004 protein Coenzyme PQQ synthesis protein A 83 bp
BBa_K3830003 Protein Coenzyme PQQ synthesis protein B 910 bp
BBa_K3830005 Protein Coenzyme PQQ synthesis protein C 717 bp
BBa_K3830006/td> Protein Coenzyme PQQ synthesis protein D 287 bp
BBa_K3830007 Protein Coenzyme PQQ synthesis protein E 1078 bp
BBa_K3830009 Plasmid backbone f1 ori 456 bp
BBa_K3830010 Terminator T7 terminator 48 bp
BBa_K3830011 Promoter pr promoter 148 bp

Introduction

  • Protein: Beta-xylanase
  • Part: xynC BBa_K3830008
  • Organism: Clostridium thermocellum
  • Short description: XynC is a xylanase.
  • Long description: XynC is endo-1,4-beta-xylanase,which can degrade hemicellulose at the non-reducing end.

The picture below shows the SDS-PAGE result.

The protein of those enzymes above can be quantified, but enzyme activity is more related to our project. So we focus on the effect of enzyme cooperation by using DNS to measure the amount of reducing sugars and confirm that enzymes can effectively decompose rice straws.

  • Protein: Cellulose 1,4-beta-cellobiosidase
  • Part: celK BBa_K3830013
  • Organism: Clostridium thermocellum
  • Short description: CelK is exoglycosidase.
  • Long description : After fiber has been hydrolyzed, exo-1,4-β-D-glucanase starts to hydrolyze the reducing or non-reducing end to xylan disaccharide Finally, β-glucosidase hydrolyze xylan disaccharide to glucose.

The picture below shows the SDS-PAGE result and the protein 3D structure.

The protein of those enzymes above can be quantified, but enzyme activity is more related to our project. So we focus on the effect of enzyme cooperation by using DNS to measure the amount of reducing sugars and confirm that enzymes can effectively decompose rice straws

  • Protein: Endoglucanase A
  • Part: celA BBa_K3830014
  • Organism: Clostridium thermocellum
  • Short description:celA is endoglycosidase.
  • Long description:(endo-1,4-β-D-glucanase) hydrolyze the β-1,4 bond by producing a new reduction end at the loosely arranged amorphous region then make the new reducing end at long chain molecules.

The picture below shows the SDS-PAGE result and the protein 3D structure.

The protein of those enzymes above can be quantified, but enzyme activity is more related to our project. So we focus on the effect of enzyme cooperation by using DNS to measure the amount of reducing sugars and confirm that enzymes can effectively decompose rice straws.

  • Protein: Cellulosomal-scaffolding protein A
  • Part: cipA BBa_K3830015
  • Organism: Clostridium thermocellum
  • Short description:Cip A acts as a scaffolding protein.
  • Long description: It promotes binding of cellulose to the catalytic domains of the cellulolytic enzymes.

The picture below shows how it work and the protein 3D structure.

The protein of those enzymes above can be quantified, but enzyme activity is more related to our project. So we focus on the effect of enzyme cooperation by using DNS to measure the amount of reducing sugars and confirm that enzymes can effectively decompose rice straws.

  • Protein: Coenzyme PQQ synthesis protein A
  • Part: pqqA BBa_K3830004
  • Organism:Gluconobacter oxydans
  • Short description: Pyrroloquinoline quinone (PQQ) is a peptide-derived redox cofactor produced by prokaryotes and it also plays beneficial roles in other organisms. we focusing on the mechanisms of PqqE,PqqA,PqqC,PqqD and PqqB.
  • Long description: The pqqA is translated into a short peptide that contains the fully conserved residues, glutamate, and tyrosine.

The picture below shows how it work and the protein 3D structure.

  • Protein: Coenzyme PQQ synthesis protein B
  • Part: pqqB BBa_K3830003
  • Organism: Gluconobacter oxydans
  • Short description: Pyrroloquinoline quinone (PQQ) is a peptide-derived redox cofactor produced by prokaryotes and it also plays beneficial roles in other organisms. we focusing on the mechanisms of PqqE,PqqA,PqqC,PqqD and PqqB
  • Long description: PqqB(Figure A) belongs to the metallo-b-lactamase superfamily . Enzymes in this superfamily generally catalyze the hydrolysis of small molecules using metal centers(Figure B) that range from zinc to manganese, nickel, magnesium, and iron . PqqB serve as an oxygenase to modify the tyrosine side-chain within PqqA, and it can cross-over between the metallo-b-lactamase superfamily and the nonheme iron hydroxylases.

The picture below shows how it work and the protein 3D structure.

  • Protein: Coenzyme PQQ synthesis protein C
  • Part: pqqC BBa_K3830005
  • Organism: Gluconobacter oxydans
  • Short description: Pyrroloquinoline quinone (PQQ) is a peptide-derived redox cofactor produced by prokaryotes and it also plays beneficial roles in other organisms. we focusing on the mechanisms of PqqE,PqqA,PqqC,PqqD and PqqB.
  • Long description:PqqC catalyzes an eight-electron and eight-proton oxidation on AHQQ in the absence of organic metal cofactor, consuming three equivalents of O2. The utilization of O2 is accompanied by a progressive conformational change of PqqC, resulting in the reduction of product H2O2, rather than exogenous O2.
  • Protein: Coenzyme PQQ synthesis protein D
  • Part: pqqD BBa_K3830006
  • Organism: Gluconobacter oxydans
  • Short description :Pyrroloquinoline quinone (PQQ) is a peptide-derived redox cofactor produced by prokaryotes and it also plays beneficial roles in other organisms. we focusing on the mechanisms of PqqE,PqqA,PqqC,PqqD and PqqB.
  • Long description:PqqD, a peptide chaperone, forms a ternary complex with the radical SAM protein calls PqqE. And it can assist PqqE to do the modification on PqqA.
  • Protein: Coenzyme PQQ synthesis protein E
  • Part: pqqE BBa_K3830007
  • Organism: Gluconobacter oxydans
  • Short description: Pyrroloquinoline quinone (PQQ) is a peptide-derived redox cofactor produced by prokaryotes and it also plays beneficial roles in other organisms. we focusing on the mechanisms of PqqE,PqqA,PqqC,PqqD and PqqB.
  • Long description: In the structure of PqqE, a [2Fe-2S] cluster appeared in the AuxI site of the SPASM domain A [4Fe-4S] cluster within the AuxI site, and the Cys-to-His variant catalyzes reductive site.
  • Name: f1 ori BBa_K3830009
  • Part type: plasmid backbone
  • Organism name:f1 bacteriophage
  • Short description: origin of replication
  • Long description: F1 is a phage-derived ori that allows for the replication. The origin of DNA replication of bacteriophage f1 functions as a signal. It can enhance the synthesis of the downstream genes
  • Name:T7 terminator
  • Part type: terminator BBa_K3830010
  • Organism name: T7 bacteriophage
  • Short description: terminator.
  • Long description: The T7 terminator is a sequence from bacteriophage T7 which allows efficient transcription termination.The bacteriophage T7 terminator (T7-T phi) encodes an RNA sequence that can form a stable stem-loop structure followed by a run of six uridylate residues; termination occurs at a 3' G residue just downstream of the U run.
  • Name:pr promoter
  • Part type:promoter BBa_K3830011
  • Organism name:bacteriophage λ
  • Short description:promoter.
  • Long description: The promoter can enhance the expression of the plasmid that put PQQ gene.
  • nchutaichung2021@gmail.com
  • NCHU iGEM Team
  • igem_nchu_taichung
  • NCHU_Taichung
  • NCHU, Taichung, Taiwan