Difference between revisions of "Part:BBa K801091:Design"
Line 12: Line 12:
 
PMID: 15932991  
 
PMID: 15932991  
 
<br>'''Keywords:'''
 
<br>'''Keywords:'''
−
<!--These keywords are necessary to find your part using a fulltext sarch.-->
+
Coumaryol-CoA, Coumaroyl-Coenzyme A, Xanthohumol, Biosynthesis, 4-coumarate-coenzyme A ligase
−
<!--keyword_1, keyword_2, keyword_3, keyword_4, keyword_5-->
+
  
 
<br>'''Abbreviations:'''
 
<br>'''Abbreviations:'''
 +
PAL = Phenylalanine Ammonia Lyase
 
<!--*used_abbreviation_1 = full_name_of_used_abbreviations_1-->
 
<!--*used_abbreviation_1 = full_name_of_used_abbreviations_1-->
 
<!--*used_abbreviation_2 = full_name_of_used_abbreviations_2-->
 
<!--*used_abbreviation_2 = full_name_of_used_abbreviations_2-->
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<!--*Test digestion using ?enzyme1? & ?enzyme2?/Not yet performed-->
 
<!--*Test digestion using ?enzyme1? & ?enzyme2?/Not yet performed-->
 
<!--*Sequencing using primer ?primer_name?/Not yet sequenced-->
 
<!--*Sequencing using primer ?primer_name?/Not yet sequenced-->
−
<!--*Part was partly sequenced/Part was totally sequenced-->
+
Part was totally sequenced
  
 
'''Backbone:'''<br>
 
'''Backbone:'''<br>
−
<!--*Backbone name: pSB1C3'/?backbone_name?-->
+
Backbone name: pSB1C3
−
<!--*Resistance: Amp/Cp/Kan/Tet-->
+
Resistance: Cp
 
<!--*Copynumber: low/medium/high-->
 
<!--*Copynumber: low/medium/high-->
  
 
'''Protein coding:'''<br>
 
'''Protein coding:'''<br>
−
<!--*Protein: ?Name_of_gene_product? [Nucleotide 1 to ???]-->
+
Protein: Phenylalanine Ammonia Lyase
 
<!--*The protein has the amino acid replacements ???99??? to ???99???.-->
 
<!--*The protein has the amino acid replacements ???99??? to ???99???.-->
 
<!--*The protein encoded is posttranslationally modified by ???.-->
 
<!--*The protein encoded is posttranslationally modified by ???.-->
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'''Enzymatic activity:'''
 
'''Enzymatic activity:'''
−
<!--none/EC-number ?.?.?.?-->
+
EC-number 4.3.1.25
  
 
'''Cytotoxicity:'''<br>
 
'''Cytotoxicity:'''<br>
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'''Source:'''<br>
 
'''Source:'''<br>
 
<!--*Commercial system: plasmid name, system name, company name-->
 
<!--*Commercial system: plasmid name, system name, company name-->
−
<!--*Plasmid: p???, provided by ?name_of_person?, ?institute/university?, ?country?-->
+
*Plasmid: pKS2µHyg-PAL-4CL-CHS, provided by John A. Morgan, Purdue University, USA
 
<!--*Preexisting BioBrick ?Bba_number?-->
 
<!--*Preexisting BioBrick ?Bba_number?-->
 
<!--*cDNA Clone: ?clone_name?, ?company_name?-->
 
<!--*cDNA Clone: ?clone_name?, ?company_name?-->
Line 76: Line 76:
  
 
'''Organism:'''<br>
 
'''Organism:'''<br>
−
<!--*Genesequence derived from ''?organism_name?''-->
+
*Genesequence derived from ''Rhodosporidium toruloides'
 
<!--*Codonoptimized for ''?organism_name?''-->
 
<!--*Codonoptimized for ''?organism_name?''-->
 
<!--*Designed for the following Chassis: ''?organism-name?''-->
 
<!--*Designed for the following Chassis: ''?organism-name?''-->
 
<!--*Statement about functionality in other chassis.-->
 
<!--*Statement about functionality in other chassis.-->
−
 
  
 
===References===
 
===References===
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'''Literature references:'''<br>
 
'''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>
 
'''Database references:'''<br>
−
<!--*[http://www.ncbi.nlm.nih.gov/nuccore/?accessNr? '''GenBank''': ?title?]-->
+
[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.ebi.ac.uk/interpro/IEntry?ac=?accessNr? '''Interpro''': ?title?]-->
−
<!--*[http://www.uniprot.org/uniprot/?accessNr? '''Uniprot''': ?title?]-->
+
 
 +
[http://www.uniprot.org/uniprot/P11544 '''Uniprot''': Phenylalanine/tyrosine ammonia-lyase]
 
<!--*[http://pfam.sanger.ac.uk/family/?accessNr? '''Pfam:''' ?title?]-->
 
<!--*[http://pfam.sanger.ac.uk/family/?accessNr? '''Pfam:''' ?title?]-->
 
<!--*[http://www.rcsb.org/pdb/explore/explore.do?structureId=?accessNR? '''PDB:''' ?tile?]-->
 
<!--*[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?]-->
 
<!--*[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=?accessNr? '''Branda:''' ?title?]-->

Revision as of 22:38, 26 September 2012

phenylalanine ammonia lyase (PAL) coding region


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 2090
    Illegal BamHI site found at 352
    Illegal XhoI site found at 403
    Illegal XhoI site found at 466
    Illegal XhoI site found at 484
    Illegal XhoI site found at 562
    Illegal XhoI site found at 763
    Illegal XhoI site found at 1006
    Illegal XhoI site found at 1753
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 922
    Illegal NgoMIV site found at 1168
    Illegal NgoMIV site found at 1336
    Illegal NgoMIV site found at 1479
    Illegal NgoMIV site found at 1813
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 463
    Illegal BsaI site found at 793
    Illegal BsaI site found at 799
    Illegal BsaI.rc site found at 1924
    Illegal SapI site found at 753


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:

Quality control measures:
Part was totally sequenced

Backbone:
Backbone name: pSB1C3 Resistance: Cp

Protein coding:
Protein: Phenylalanine Ammonia Lyase

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]