APPENDIX A Cytochrome P450 Nomenclature and Alignment of Selected Sequences DAVID R. NELSON 1. Doing the Numbers This chapter is a summary of sequence data available for cytochrome P450 genes and proteins. It serves as a vehicle to update the nomenclature since the last major listing was published in January of 1993. 1 It is now April, 1994, about 16 months since that list appeared, and many new P450 sequences have been determined. Table I consists of 368 entries, covering 281 genes and 15 pseudogenes. Also included are 29 different expressed sequence tags (ESTs) or peR fragments from Caenorhabditis elegans, Arabidopsis thaliana, and Catharanthus roseus that have not yet been assigned to P450 families. Some of the Arabidopsis sequences are probably from the same gene, so the 29 EST sequences really represent less than 29 genes. Nevertheless, at least 325 different cytochrome P450 sequences are listed in Table I. This is amazing progress since the first P450 sequence was published in 1982. The sequences belong to 50 families and 82 subfamilies, and they come from 67 species. Fourteen new families have appeared since the 1993 nomenclature update. 1 There are 19 vertebrates (12 mammals, 5 fish, and 2 birds). Invertebrates include six insect species, the nematode worm C. elegans, with five ESTs but no complete sequences, a spiny lobster, and a pond snail. Plants have 13 species represented and there are 11 lower eukaryote P450s. The bacteria now have 8 genera and 15 species including gram-positive as well as gram-negative bacteria. A cyanobacterium is present and there is a partial sequence from the heat-tolerant bacterium Streptomyces thermotolerans, but no sequence is available from an archaebacterium. DAVID R. NELSON • Departtnent of Biochemistry, The University of Tennessee, Memphis, Memphis, Tennessee 38163. Cytochrome P450: Structure, Mechanism, and Biochemistry (Second Edition), edited by Paul R. Ortiz de Montellano. Plenum Press, New York, 1995. 575 576 APPENDIX A In a single species, rats have 45 genes and 2 pseudogenes. Rats will have CYPIB 1, CYP8, and CYP21 genes, but these are not sequenced yet. This gives a total of 50 genes in the rat. Humans have 34 genes and 7 pseudogenes so far. Nineteen of the human sequences are included in Fig. 1. Humans appear to have fewer sequences in the 2B, 2C, and 2D subfamilies when compared to rats. It is interesting to estimate the number ofP450s in C. elegans, assuming random sampling. About 3-4% of the genome of C. elegans has been sequenced, and there are four different P450 ESTs represented. This extrapolates to about 100 P450 sequences in C. elegans. Of course, the numbers are very small and the estimate could be off by quite a bit. A more representative value will be available when about 10% of the genome is done, probably within a year. 2. The Scope of Table I Table I does not reproduce all of the data in the 1993 nomenclature update. That would be a great waste, since there are over 700 references and 1200 accession numbers given there. The table is meant to be used in conjunction with that earlier tabulation to obtain comprehensive coverage through the end of 1993 and the early part of 1994. Table I does include all of the gene names from the 1993 list, plus any new entries made since then. New entries include reference to journal articles and Genbank accession numbers if they are available. References from the 1993 update that were incomplete or lacked accession numbers, have been included again to complete them. The 1993 update should be consulted for trivial names (Tables 2 and 4) and chromosomal mapping data (Table 1). This old information has not changed since 1993. 3. Cytochrome P450 Sequence Alignment The sequences in this alignment represent 65 of the 82 subfamilies and 41 of the 50 cytochrome P450 families. Those families and subfamilies not included were confidential or unavailable at the time the alignment was made. The sequences are arranged in the same order as the branching pattern ofthe phylogenetic tree in Fig. 2. This automatically clusters the most similar sequences together for ease of comparison. On the left, the sequences are numbered for identification. On the right, the number of amino acids up to that point is given. To the far right on the first page, the Genbank accession numbers are given for each sequence. Two sequences have an insert that has been removed to save space. In sequence 22 CYP5 human, 27 amino acids have been removed between amino acids 298 and 299-IVRDVFSSTGCKPNPSRQHQPSPMARP. Sequence 24 CYP6B 1 had 7 amino acids removed between 280 and 281-EDVKALE. These inserts occur before the I-helix in a highly variable part of the P450 sequences. 4. Phylogenetic Tree of Cytochrome P450 Sequences This tree was computed using a PAM250 scoring matrix. This tree and more detailed trees of individual families and groups of families are the basis for the nomenclature described in detail in the 1993 nomenclature update. l The percent similarity between P450 NOMENCLATURE AND SEQUENCE DATA 577 1 2C9 mp4 human -----------------------MOS---------------lVV-lVLCLS 12 M21940 2 2El j human ---------------------- -MFALGV- ---------- -TVA-lLWAA 15 J02843 3 2Hl CHP3 chicken -----------------------MOFLGLP----·------TIL-llVCIS 16 M13454 42Fl IIFl human ---------------------. ·MOSI- -------- -----STA-llLLLL 13 J02906 5 2B6 lM2 human ---------------------·-MELS-----·--------VLL-FLALLT 13 Xl6864 62Gl olfl rat -----------------------MALGGAF-----------SIF-MTLCLS 16 J04715 72A6 IIA3 human -----------------------MLASGML-----------lVA-LLVCLT 16 X13929 8 2Kl trout -------------·-MSLIEOILQTSSTVT-----------LLG-TVLFLL 24 Ll1528 9 2Jl ib rabbi t ----------------MVAALSSLAAALGAGLH--------PKT-LLLGAV 26 090405 10 206 dbl human -------- -. ------------ -MGL -- -EALV-- ----- -PLA-VIVAI F 16 Y00300 11 lAl Pl human -----------------·--MLFPISMSATEFL--------LAS-VIFCLV 22 X04300 12 17 17a human ----------------------------------------MWEL-VALlLL 10 M14564 13 21 C21 human -------------------------------------------M-LLLGLL 7 Ml7252 14 71Al avocado -----------------------MAIL-----·-·----VSLLF-LAIALT 15 M32885 15 71Bl Thlaspi arvense -------------------- ---MOLL -------- --- -L -YIV-AALVI F 14 L24438 16 75Al petunia -------------------- ---MMLL TELG- --- --- -AATSI-FLIAHI 19 X71130 17 76Al eggplant o X71658 18 73 Jerusalem artichoke -----------------------MOLLLI----------EKTLV-ALFAAI 27 Zl7369 19 78 Zea mays ---------------------------------------ALLAW-ATSPGG 11 L23029 20 77Al eggplant ---------------------------------------IFTAF·SLlFSl 11 X71655 21 3A3 Hlp human -----------------------MALIPOlAME-------TWLL-LAVSLV 20 M13785 22 5Al TXS human ----------------MMEALGFLKLEVNGPMV·------TVAL-SVALLA 27 M74055 23 6Al Musca domestica -----------------------MOFGSFLLYA-------LGVL----ASL 17 M25367 24 6Bl Butterfly --------------------------MLYLLAL-------VTVL----AGL 14 M80828 25 4A 11 human ----------------------- -MSVSVLSPSRLLGOVSGILQ-AASLLI 26 L04751 26 4Bl IVBl human ------------------------MSGTATMVPSFLSLSFSSLG-LWASGL 26 J02871 27 4F3 human ------------------------MPQLSlSSLGLWPMAASPWL-LLLLVG 26 012620 28 4Cl cockroach ----------------------------·---·--MEFITILLS-TALFHS 15 M63798 29 4El Orosophi la o K00045 30 401 Orosophi la ----------------------------------MFLVIGAILA-SALFVG 16 X67645 31 102 BM3 B. megaterium o J04832 32 110 Anabaena cyanobact. o M38044 33 72Al Catharanthus ros. --------- -MEMOMOT I RKAIAAT I FAL VMAWAWRV- LOWAWF - TPKR I E 39 Ll0081 34 53 bphA Asperg. niger ------------ -----------MlAl- -- - --LLS-PYGAYLG-LAL- LV 19 X52521 35 10 pond snail MAIMKKFIHHSLKQLIKPNLTSTKRVVSTSPRKEQGVAAISLEP-SEMAQC 50 S46130 36 llAl scc human ------------------------MLAKGLPPRSVlVKGCQTFL-SAPREG 26 M28253 37 llBl llBl human ---------------------------- --- --MALRAKAEVCM-AVPWLS 17 x55764 38 24 250H 03 24hyd rat -------------MSCPIOKRRTLIAFLRRLROLGQPPRSVTSK-AS-ASR 36 L04618 39 27 270H human ------------ -MAALGCARLRWAL --- RGAGRGLCPHGARAK -AAI PAA 34 M62401 40 51 140M S. cerevisiae ----MSATKSIVGEALEYVNIGLSHFL-ALPLAQ-----RISLI-III-PF 39 M15663 41 7 Chol7a human ---------------. ------- -MMTTSL 1- - -WGIAIAACCC-LWLI L- 22 X56088 42 56 0lT2 S. cerevisiae -----------------------MELL----·---K-LLCLILF-LTLSYV 18 X55713 43 52Al alkl C. tropicalis ----MSSSPSIAQEFlATITPYVEYCQ·ENYTKWYYFIPlVILS-LNLISM 45 M15945 44 5201 AlK4-A C. maltosa -------------MAIF--------------·TPELWLICFAVT-VYIFOY 22 012716 45 52Bl alk6 C. tropicalis ----------·MSLTETTATFIY----·---NYWYIIFHLYFYTTSKIIKY 32 Z13013 4652Cl alk7 C. tropicalis ----------- ----. ---------- ----MYQLFCFLAGIIVV-YKAAQY 20 Z13014 47 19 arom human ------------------------MVLE-------------MLN-PIHYNI 13 M28420 48 105A SUl Str. griseolus -------------------------------------TOTATTP-QTTOAP 13 M32238 49 1050 P450soy St.griseus ----------------------------MTESTTOPARQNLOPT-SPAPAT 22 X63601 50 105B SU2 Str. griseolus -------------------------------- ---- -TTAERTA-PPOALT 13 M32239 51 105C Streptomyces sp. ----------------------------·--------MTQA--------AP 6 M31939 52 lOSE Rhodococ.fascians ----------------------------. -. ------------ -- -MAGTA 5 Z29635 53 107Al eryF Sacc.eryth. -------------------------------------M-TT--V-POLESO 10 M54983 54 55 Fusarium oxysporum ---------------------------. --. ----- -MASGAP- ----- -- 6 M63340 55 112 BJ-l Bradyrhiz.jap. ------------------------------. ---------- -MS-EQQPLP 8 L02323 56 114 BJ-3 Bradyrhiz.jap. o L12971 57 113 eryK Sacc.eryth. -------------------------·-VCAOVETTCCA-RRTLT-TIOEVP 22 L05776 58 106Al BMl B.megaterium -------------------------------------MNKE-------VIP