Difference between revisions of "Part:BBa K801090:Design"

Latest revision as of 12:07, 3 October 2012

phenylalanine ammonia lyase (PAL) + yeast consensus sequence

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
INCOMPATIBLE WITH RFC[21]
Illegal BglII site found at 2096
Illegal BamHI site found at 358
Illegal XhoI site found at 409
Illegal XhoI site found at 472
Illegal XhoI site found at 490
Illegal XhoI site found at 568
Illegal XhoI site found at 769
Illegal XhoI site found at 1012
Illegal XhoI site found at 1759
23
COMPATIBLE WITH RFC[23]
25
INCOMPATIBLE WITH RFC[25]
Illegal NgoMIV site found at 928
Illegal NgoMIV site found at 1174
Illegal NgoMIV site found at 1342
Illegal NgoMIV site found at 1485
Illegal NgoMIV site found at 1819
1000
INCOMPATIBLE WITH RFC[1000]
Illegal BsaI site found at 469
Illegal BsaI site found at 799
Illegal BsaI site found at 805
Illegal BsaI.rc site found at 1930
Illegal SapI site found at 759

Plasmid (template for PCR) provided by John A. Morgan, School of Chemical Engineering, Purdue University, West Lafayette, Indiana, USA

http://www.ncbi.nlm.nih.gov/nuccore/AX366866

PMID: 15932991

Keywords: Coumaryol-CoA, Coumaroyl-Coenzyme A, Xanthohumol, Biosynthesis, 4-coumarate-coenzyme A ligase

Abbreviations: PAL = Phenylalanine Ammonia Lyase

Design Notes

Related BioBrick:

Other versions: BBa_K801091: PAL coding region

Related BioBricks:

Cloning details:
Designed in RFC10

Quality control measures:
Part was totally sequenced

Backbone:

Backbone name: pSB1C3
Resistance: Cp
Copynumber: high

Protein coding:

Protein: Phenylalanine Ammonia Lyase
Tag: c-terminally fused Strep

Enzymatic activity: EC-number 4.3.1.25

Cytotoxicity:

Safety notes:

Intellectual property:

Corresponding part author/authors:

Source

Source:
Plasmid: pKS2µHyg-PAL-4CL-CHS, provided by John A. Morgan, Purdue University, USA

Organism:
Genesequence derived from Rhodosporidium toruloides'

References

Literature references:
[http://www.ncbi.nlm.nih.gov/pubmed/15932991 Pubmed : Jiang, H., Wood, K.V., Morgan, J.A., 2005. Metabolic Engineering of the Phenylpropanoid Pathway in Saccharomyces cerevisiae. Appl. Environ. Microbiol. 71, 2962–2969]

Database references:
[http://www.ncbi.nlm.nih.gov/nuccore/AX366866 GenBank: Sequence 18 from Patent WO0208402]

[http://www.uniprot.org/uniprot/P11544 Uniprot: Phenylalanine/tyrosine ammonia-lyase]

@@ Line 24: / Line 24: @@
 '''Related BioBrick:'''
-<!--*Other versions:[https://parts.igem.org/wiki/index.php?title=Part:BBa_?????? BBa_??????: Name_of_part] -->
-<!--*Related BioBricks:[https://parts.igem.org/wiki/index.php?title=Part:BBa_?????? BBa_??????: Name_of_part]
+Other versions: [https://parts.igem.org/Part:BBa_K801091 BBa_K801091: PAL coding region]
+Related BioBricks:
+* [https://parts.igem.org/Part:BBa_K801091 BBa_K801091: phenylalanine ammonia lyase (PAL) coding region]
+* [https://parts.igem.org/Part:BBa_K801092 BBa_K801092: 4-coumarate - coenzym A ligase (4CL) + yeast consensus sequence]
+* [https://parts.igem.org/Part:BBa_K801093 BBa_K801093: 4-coumarate--coenzyme A ligase (4CL) coding region]
+* [https://parts.igem.org/Part:BBa_K801094 BBa_K801094: Naringenin - chalcone synthase (CHS) + yeast consensus sequence]
+* [https://parts.igem.org/Part:BBa_K801095 BBa_K801095: Naringenin - chalcone synthase (CHS) coding region]
+* [https://parts.igem.org/Part:BBa_K801096 BBa_K801096: Aromatic prenyltransferase (APT) coding region]
+* [https://parts.igem.org/Part:BBa_K801097 BBa_K801097: Chalcone O-methyltransferase (OMT1) + yeast consensus sequence]
+* [https://parts.igem.org/Part:BBa_K801098 BBa_K801098: O-methyltransferase 1 (OMT1) coding region]
 '''Cloning details:'''<br>
-<!--*Designed in RFC10/RFC23/RFC25/RFC25_N-part-->
+Designed in RFC10
 <!--*Mutation C889G to delete XbaI restriction site-->
 <!--*Truncation upstream/downstream compared to template, ?explanation?-->
@@ Line 38: / Line 48: @@
 '''Backbone:'''<br>
-Backbone name: pSB1C3
+*Backbone name: pSB1C3
-Resistance: Cp
+*Resistance: Cp
-<!--*Copynumber: low/medium/high-->
+*Copynumber: high
 '''Protein coding:'''<br>
-Protein: Phenylalanine Ammonia Lyase
+*Protein: Phenylalanine Ammonia Lyase
 <!--*The protein has the amino acid replacements ???99??? to ???99???.-->
 <!--*The protein encoded is posttranslationally modified by ???.-->
-<!--*Tag: n-terminally fused/c-terminally fused His5/His6/Strep/Flag/other-->
+*Tag: c-terminally fused Strep
 '''Enzymatic activity:'''
@@ Line 69: / Line 79: @@
 '''Source:'''<br>
 <!--*Commercial system: plasmid name, system name, company name-->
-*Plasmid: pKS2µHyg-PAL-4CL-CHS, provided by John A. Morgan, Purdue University, USA
+Plasmid: pKS2µHyg-PAL-4CL-CHS, provided by John A. Morgan, Purdue University, USA
 <!--*Preexisting BioBrick ?Bba_number?-->
 <!--*cDNA Clone: ?clone_name?, ?company_name?-->
@@ Line 78: / Line 88: @@
 '''Organism:'''<br>
-*Genesequence derived from ''Rhodosporidium toruloides''-->
+Genesequence derived from ''Rhodosporidium toruloides'
 <!--*Codonoptimized for ''?organism_name?''-->
 <!--*Designed for the following Chassis: ''?organism-name?''-->
@@ Line 87: / Line 97: @@
 '''Literature references:'''<br>
-<!--*[http://www.ncbi.nlm.nih.gov/pubmed/?PMID? '''Pubmed:''' ?Author(s)?, ?year?: ?title?]-->
+[http://www.ncbi.nlm.nih.gov/pubmed/15932991 '''Pubmed''' : Jiang, H., Wood, K.V., Morgan, J.A., 2005. Metabolic Engineering of the Phenylpropanoid Pathway in Saccharomyces cerevisiae. Appl. Environ. Microbiol. 71, 2962–2969]
 '''Database references:'''<br>
 [http://www.ncbi.nlm.nih.gov/nuccore/AX366866 '''GenBank''': Sequence 18 from Patent WO0208402]
 <!--*[http://www.ebi.ac.uk/interpro/IEntry?ac=?accessNr? '''Interpro''': ?title?]-->
 [http://www.uniprot.org/uniprot/P11544 '''Uniprot''': Phenylalanine/tyrosine ammonia-lyase]
 <!--*[http://pfam.sanger.ac.uk/family/?accessNr? '''Pfam:''' ?title?]-->
 <!--*[http://www.rcsb.org/pdb/explore/explore.do?structureId=?accessNR? '''PDB:''' ?tile?]-->
 <!--*[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=?accessNr? '''Branda:''' ?title?]-->