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cyt b5 and P450 Reduc

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P450 ESTs

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Click here for lists of Arabidopsis P450s, sorted by number, family, and type.

About

Cytochrome P450s were first identified in 1958 (Klingenberg 1958 and Garfinkel 1958) from their spectral properties. At this time they have been found in all living organisms, from bacteria to animals and plants. They are involved in a vast array of reactions (eg. hydroxylation, isomerization, epoxydation, N-dealkylation, cyclization) in many different pathways (eg. hormone metabolism, secondary metabolism, biopolymers). They are hemoproteins, and require a Cytochrome P450 Reductase to transfer electrons from NADPH to their substrate. Please see the reaction mechanism below.


(Click for a larger image.)

In Eukaryotes, P450s are membrane-bound and primarily located in the Endoplasmic Reticulum. They often catalyze a specific reaction on valuable products, and are becoming more and more attractive for biotechnologies. Due to their crucial role in drug metabolism, they are well-studied in humans.

Our FASTA files, used in creating our BLAST databases, multiple sequence alignments, and phylogenetic trees, are now available for download.
• Click here for the Arabidopsis P450 protein sequence file.
• Click here for the Arabidopsis P450 genomic sequence file (includes GenBank genomic sequences as well as unspliced, BAC/chromosomal genomic sequences).
• Click here for the Arabidopsis P450 cDNA sequence file (includes GenBank cDNA sequences as well as annotations based on GenBank genomic sequences).

Chr 1 Genetic ~ Base Pair

Chr 2 Genetic ~ Base Pair

Chr 3 Genetic ~ Base Pair

Chr 4 Genetic ~ Base Pair

Chr 5 Genetic ~ Base Pair


All Five Chromosomes. (270k, JPG, Landscape)

All Five Chromosomes. (270k, JPG, A4-portrait)

Please read the introduction to the PDF-file alignments for information on alignment parameters and specifics.
The alignment presented in Paquette et al., with intron phases marked. (330k, PDF)
A more recent alignment of 246 Arabidopsis cytochrome P450 sequences. (506k, PDF)
An alignment of 153 A-type Arabidopsis P450 sequences. (280k, PDF)
An alignment of 93 non-A type Arabidopsis P450 sequences. (138k, PDF)

This multiple alignment was made with ClustalX 1.83 for Windows.
An alignment of 157 P450s from different organisms.
A table listing the non-Arabidopsis P450s and their sources.

All phylogenetic trees were made with ClustalX 1.83 for Windows (1000 boostrap trials) or MEGA 3.1 for Windows.
A phylogenetic tree of the A-type alignment presented above.
An unrooted phylogenetic tree of the A-type alignment presented above.
A phylogenetic tree of the non-A type alignment presented above.
An unrooted phylogenetic tree of the non-A type alignment presented above.
A phylogenetic tree of all of the P450s in the complete 246-member alignment.

This phylogenetic tree was made with ClustalX 1.83 for Windows32 (1000 bootstrap trials).
A multi-organism tree of the alignment presented above.

Logos were made using weblogo.berkeley.edu.
A logo of the heme-binding region of all full-length Arabidopsis P450s.
A logo of the I-helix region of all full-length Arabidopsis P450s.
A logo of the K-helix region of all full-length Arabidopsis P450s.
A logo of the PXRX motif of all full-length Arabidopsis P450s.

Please see the introduction for information on intron phase markings and map specifications.
Arabidopsis A-type P450 intron map and legend. (17.5k, PDF)
Arabidopsis Non-A type P450 intron map and legend. (14.6k, PDF)

There are currently 1932 P450 ESTs over 39 gene families and 67 gene subfamilies in TAIR's Arabidopsis EST dataset. These ESTs were identified via BLAST using NCBI's blastall for the Windows 32 platform. The P450 EST dataset is available on our local BLAST site as a searchable database.


• Click here for a table of the Arabidopsis P450s that do not currently have ESTs listed in GenBank.
  
• Click here for a PDF-graph showing the number of ESTs for each Arabidopsis P450 Family represented in the TAIR EST dataset (39).
  
• Click here for a PDF-graph showing the number of ESTs for each Arabidopsis P450 SubFamily represented in the TAIR EST dataset (67).

The EST dataset was last updated September 10th, 2004.

All P450s have links to the NCBI record for their ESTs on their individual pages.

The genetic chromosome maps were made with marker information from Stanford University's Arabidopsis thaliana database, which now resides at the TAIR site. The chromosome sizes and the scale in cM were taken from this webpage. Cytochromes P450 were located on a BAC, YAC, or P1 clone, and the nearest Lister and Dean RI marker to this clone was located using the Illustra Database's genetic maps.

The base-pair maps were made by obtaining the complete chromosomal sequence from NCBI's website, creating a BLAST database from them, and searching with the current P450 database against these chromosomes. Positions are based on start codons.

The CYP2C5 image shown here and on the frontpage for the site is PDB entry 1DT6. The following article is the literature reference for this structure:

Williams PA, Cosme J, Sridhar V, Johnson EF, McRee DE (2000) The crystallographic structure of a mammalian microsomal cytochrome P450 monooxygenase: Structural adaptations for membrane binding and functional diversity. Mol Cell 5: 121-132