E/F clan
Description
The crystal structure of the heterodimer of CpcE-I/F-I from Nostoc sp. PCC7120 was determined at a 1.89-Å resolution (Zhao et al., 2017; PDB: 5N3U). However, the crescent-shaped architecture described by these authors has recently been disputed after the resolution at 2.5-Å of the structure of the lyase-isomerase MpeQ from Synechococcus sp. A15-62 (Kumaraperruma et al. 2022). The latter authors posit that the E/F family of bilin lyases, including the single-chain and heterodimeric enzymes, share a common structural framework represented by the question-mark architecture of MpeQ (PDB: 7MC4 and 7MCH).
References
- Kumarapperuma et al., 2022. Crystal structure and molecular mechanism of an E/F type bilin lyase-isomerase Structure, 30, 564-574.
- Schluchter et al., 2010. Phycobiliprotein Biosynthesis in Cyanobacteria: Structure and Function of Enzymes Involved in Post-translational Modification Adv Exp Med Biol, 675, 211-228.
- Zhao et al., 2017. Structures and enzymatic mechanisms of phycobiliprotein lyases CpcE/F and PecE/F Proc Natl Acad Sci USA, 114, 3170–13175,.
Showing only unsure genes
| Gene | Locus tag | Genbank | Species | Strain | PBP in rods | Pigment type | Remark | Length | Last change |
|---|---|---|---|---|---|---|---|---|---|
| CpcE/RpcE family | WH7805_06756 | ZP_01123351.1 | Synechococcus sp. | WH7805 | PC+PEI | 2 | The R-PC-III present in this strain has a PCB:PEB ratio of 2:1 (Sidler, 1994). It is unclear whether WH7805 has CpcE/F or RpcE/F but the presence of CpcT (and not RpcT) however argues for the following pigmentation: alpha-84=PEB; beta-84=PCB; beta-155=PCB. | 265 | 09-19-2012 |
| CpcE/RpcE family | SynRCC307_2066 | YP_001228322.1 | Synechococcus sp. | RCC307 | PC+PEI+PEII | 3eA | Unclear whether this strain has CpcE/F or RpcE/F | 274 | 12-06-2011 |
| CpcE/RpcE family | S7335_2363 | ZP_05035931.1 | Synechococcus sp. | PCC7335 | PC+PEI | CA3 | CpcEII or RpcE | 274 | 12-06-2011 |
| CpcE-I subfamily | N9414_13270 | ZP_01632751.1 | Nodularia spumigena | CCY9414 | PC | 1 | Sequence incomplete: lacks C-term (end of contig) | 158 | 01-10-2012 |
| CpcE-I subfamily | CYB_2736 | YP_478924.1 | Synechococcus sp. | JA-2-3B'a(2-13) | PC | 1 | This is a second copy of cpcE (cpcE-2) NOT associated with a cpcF | 276 | 12-06-2011 |
| CpcE-I subfamily | CYA_2040 | YP_475443.1 | Synechococcus sp. | JA-3-3Ab | PC | 1 | This is a second copy of cpcE (cpcE-2) NOT associated with a cpcF | 275 | 12-06-2011 |
| CpcE-I subfamily | CMJ043C | Cyanidioschyzon merolae | 10D | PC | 1 | Distantly related to cyanobacterial CpcE : many insertions in matching sequences and much longer N-term, found by tblastn | 516 | 02-21-2012 | |
| CpcE-I subfamily | CWATWH0003_3128t1 | EHJ12159.1 | Crocosphaera watsonii | WH0003 | PC+PEI | Incomplete (end of contig) | 212 | 02-22-2012 | |
| CpcE-I subfamily | Pse7367_3924 | YP_007083576.1 | Pseudanabaena sp. | PCC7367 | PC+PEI | 2 copies? | 303 | 06-20-2013 | |
| CpcE-I subfamily | ZP_18907676 | ZP_18907676.1 | Leptolyngbya sp. | PCC7375 | PC+PEI | 2 | Low protomatch score | 279 | 06-20-2013 |
| CpcE-I subfamily | Pse7367_2387 | YP_007103076.1 | Pseudanabaena sp. | PCC7367 | PC+PEI | 2 copies? | 273 | 06-20-2013 | |
| CpcF/RpcF family | WH7805_06761 | ZP_01123352.1 | Synechococcus sp. | WH7805 | PC+PEI | 2 | Unclear whether this strain has CpcE/F or RpcE/F. Two possibilities: a-84 and b-84 = PCB; b-155 = PEB a-84 = PEB,b-84 and b-155 = PCB |
212 | 12-06-2011 |
| CpcF/RpcF family | SynRCC307_2067 | YP_001228323.1 | Synechococcus sp. | RCC307 | PC+PEI+PEII | 3eA | Unclear whether this strain has CpcE/F or RpcE/F | 218 | 12-06-2011 |
| CpcF/RpcF family | S7335_4405 | ZP_05037964.1 | Synechococcus sp. | PCC7335 | PC+PEI | CA3 | CpcFII or RpcF | 225 | 12-06-2011 |
| CpcF-I subfamily | CMJ044C | Cyanidioschyzon merolae | 10D | PC | 1 | found by tblastn | 312 | 02-21-2012 | |
| PecF family | Aazo_0293 | YP_003720001.1 | Anabaena (Nostoc) azollae | 0708 | PC+PEC | Sequence with an N-term shorter than others (seemingly lacks about 22 otherwise conserved aa) but no obvious problem in genome sequence. The missing N-term contains 3 or 4 His in other strains. | 151 | 08-28-2012 | |
| CpeF family | Tery_0978 | YP_720832.1 | Trichodesmium erythraeum | IMS101 | PC+PEI | N-term shortened (24 aa removed) | 310 | 08-30-2012 | |
| CpeF family | Tery_0987 | YP_720840.1 | Trichodesmium erythraeum | IMS101 | PC+PEI | Best BlastP hit on CpeF (but lower than Tery_0978) | 285 | 08-30-2012 | |
| CpeF family | S7335_4282 | ZP_05037842.1 | Synechococcus sp. | PCC7335 | PC+PEI | CA3 | Low blast and protomatch score. | 332 | 01-02-2012 |
| CpeF family | CWATWH0003_5310t4 | EHJ09925.1 | Crocosphaera watsonii | WH0003 | PC+PEI | incomplete n-term (start of contig) | 262 | 02-22-2012 | |
| CpeY family | CwatDRAFT_0665 | ZP_00518425.1 | Crocosphaera watsonii | WH8501 | PC+PEI | There is another partial CpeY sequence in this genome almost 100% identical to this one (possibly an assembly error). | 419 | 08-27-2012 | |
| CpeY family | CwatDRAFT_5980 | ZP_00514215.1 | Crocosphaera watsonii | WH8501 | PC+PEI | Sequence incomplete. N-term extended (35 aa added) but still incomplete. | 282 | 08-27-2012 | |
| CpeZ family | Tery_0980 | YP_720834.1 | Trichodesmium erythraeum | IMS101 | PC+PEI | Blastp hit on cpeZ (but lower than >Tery_0995) | 219 | 09-26-2011 | |
| CpeZ family | CAJ73184.1| | CAJ73184.1 | Guillardia theta | CCMP2712 | Cr-PE 545 | n.a. | Low protoscan score | 229 | 10-28-2011 |
| CpeZ family | CwatDRAFT_0406 | ZP_00518848.1 | Crocosphaera watsonii | WH8501 | PC+PEI | Low score, similar to Tery_0980 (IMS101) | 219 | 12-02-2011 | |
| CpeZ family | CWATWH0003_5315a1 | EHJ09924.1 | Crocosphaera watsonii | WH0003 | PC+PEI | Incomplete, 2nd copy? | 186 | 02-22-2012 | |
| L8106_11777 homologs family | AplaP_010100002137 | ZP_06380464.1 | Arthrospira (Spirulina) platensis | Paraca | PC | 1 | Incomplete n-term (end of contig). Almost identical to homologs in other Arthrospira species. | 179 | 08-27-2012 |
| L8106_22089 homologs family | IPF_5551 | CAO86824.1 | Microcystis aeruginosa | PCC7806 | PC | 1 | Incomplete sequence. Another chunk is in IPF_6118 (CAO87604.1) | 325 | 01-10-2012 |
| L8106_22089 homologs family | CwatDRAFT_0171 | ZP_00519405.1 | Crocosphaera watsonii | WH8501 | PC+PEI | split between 3 different contigs: ZP_00517336.1 (CwatDRAFT_2581), ZP_00513741.1 (CwatDRAFT_6637) and ZP_00519405.1 (CwatDRAFT_0171) | 107 | 08-29-2012 | |
| L8106_22089 homologs family | IPF_6118 | CAO87604.1 | Microcystis aeruginosa | PCC7806 | PC | 1 | Shorter than other L8106_22089 homologs | 251 | 04-24-2013 |
| MC7420_3535 homologs family | OSCI_440025 | ZP_07108865.1 | Oscillatoria sp. | PCC6506 (PCC9029/ATCC29081 /UTEX 1547) | PC | 1 | 992 | 12-07-2011 | |
| MC7420_3535 homologs family | alr2986 | NP_487026.1 | Anabaena (Nostoc) sp. | PCC7120 | PC+PEC | 885 | 12-07-2011 | ||
| MC7420_3535 homologs family | IPF_2635 | CAO90934.1 | Microcystis aeruginosa | PCC7806 | PC | 1 | Much shorter than other MC7420_3535 homologs | 263 | 12-07-2011 |
| MC7420_3535 homologs family | L8106_24365 | ZP_01619849.1 | Lyngbya aestuarii | CCY9616 (PCC8106/CCY8106) | PC | 1 | 1044 | 12-07-2011 | |
| MC7420_3535 homologs family | PCC7424_1763 | YP_002377065.1 | Cyanothece sp. | PCC7424 | PC+PEI | 2 | 1475 | 12-07-2011 | |
| MC7420_3535 homologs family | MC7420_2915 | ZP_05024179.1 | Microcoleus chthonoplastes | PCC7420 | PC+PEC | 1355 | 12-07-2011 | ||
| MC7420_3535 homologs family | LYNGBM3L_40770 | ZP_08429450.1 | Lyngbya majuscula | 3L | PC+PEI | 2 | 1273 | 12-07-2011 | |
| MC7420_3535 homologs family | AmaxDRAFT_0188 | ZP_03271372.1 | Arthrospira (Spirulina) maxima | CS-328 | PC | 1 | 786 | 12-07-2011 | |
| MC7420_3535 homologs family | PCC8801_0753 | YP_002370992.1 | Cyanothece sp. | PCC8801 | PC+PEI | 2 | 838 | 12-07-2011 | |
| MC7420_4701 homologs family | MC7420_1061 | ZP_05028540.1 | Microcoleus chthonoplastes | PCC7420 | PC+PEC | This sequence has a much shorter N-term than others. But not a frameshift. | 173 | 09-11-2012 | |
| CotB homologs 1 family | Cyan7425_3615 | YP_002484296.1 | Cyanothece sp. | PCC7425 | PC | 1 | 221 | 09-26-2011 | |
| CotB homologs 1 family | Synpcc7942_2325 | YP_401342.1 | Synechococcus elongatus | PCC7942 | PC | 1 | N-term shortened (30 aa removed : MASAIAKLSAAPASVTPCGSVKDERLSCAS) | 225 | 08-28-2012 |
| CotB homologs 1 family | syc1777_d | YP_172487.1 | Synechococcus elongatus | PCC6301 (ATCC 27144) | PC | 1 | 225 | 09-26-2011 | |
| CotB homologs 2 family | gvip128 | NP_923927.1 | Gloeobacter violaceus | PCC7421 | PC+PEI | 2 | 233 | 11-24-2011 | |
| CotB homologs 2 family | gvip219 | NP_924521.1 | Gloeobacter violaceus | PCC7421 | PC+PEI | 2 | 234 | 11-24-2011 | |
| CotB homologs 2 family | AM1_0043 | YP_001514445.1 | Acaryochloris marina | MBIC11017 (AM1) | PC | 1 | 221 | 09-26-2011 | |
| CotB homologs 2 family | CMS328C | Cyanidioschyzon merolae | 10D | PC | 1 | on contig c19f0009, found by tblastn | 332 | 02-21-2012 | |
| CotB homologs 2 family | CMM226C | Cyanidioschyzon merolae | 10D | PC | 1 | on contig c13f0002, found by tblastn | 420 | 02-21-2012 | |
| CotB homologs 2 family | AplaP_010100006817 | ZP_06381377.1 | Arthrospira (Spirulina) platensis | Paraca | PC | 1 | Incomplete - lacks C-term (end of contig) | 154 | 09-13-2012 |
| CotB homologs 2 family | ACCM5_010100026572 | ZP_09250884.1 | Acaryochloris sp. | CCMEE5410 | APC only | 221 | 01-24-2012 |
Model strains, Marine strains
Last update: 21 Apr 2023 8:10:17
