S/U clan
Description
The X-ray structure of one member of this phycobilin lyase group was determined at 2.8 Å resolution : CpcS-III from Thermosynechococcus elongatus BP1 (Kuzin et al., 2007; Kupka et al., 2009; Schluchter el al., 2010; PDB: 3BDR). CpcS-III is structurally related to the calyx-shaped lipocalin family (InterPro IPR002345). It possesses a 8-stranded anti-parallel, β-barrel structure with an α-helix. Searches using Phyre2 show that all members of the S/U clan have the same fold.
References
- Kupka et al., 2009. Catalytic mechanism of S-type phycobiliprotein lyase: chaperone-like action and functional amino acid residues J Biol Chem, 284, 36405-36414.
- Kuzin et al., 2007. Crystal Structure Of Fatty Acid-Binding Protein-Like Ycf58 From Thermosynecoccus Elongatus. Northeast Structural Genomics Consortium Target Ter13 Protein Data Base, PDB_ID: 3BDR.
- 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.
Showing only unsure genes
| Gene | Locus tag | Genbank | Species | Strain | PBP in rods | Pigment type | Remark | Length | Last change |
|---|---|---|---|---|---|---|---|---|---|
| CpcS family | AM1_4215 | YP_001518512.1 | Acaryochloris marina | MBIC11017 (AM1) | PC | 1 | 1st copy, strange position in phylogeny. By blast: closer from CpcSI. | 197 | 08-20-2012 |
| CpcS family | AM1_C0217 | YP_001521653.1 | Acaryochloris marina | MBIC11017 (AM1) | PC | 1 | 2nd copy,strange position in phylogeny. By blast: closer from CpcSI. Located on preb3 plasmid. | 208 | 08-20-2012 |
| CpcS family | CMR092C | Cyanidioschyzon merolae | 10D | PC | 1 | long N-term compared to cyanobacterial CpcS sequences, found by tblastn | 405 | 02-21-2012 | |
| CpcS-I subfamily | gvip161 | NP_924137.1 | Gloeobacter violaceus | PCC7421 | PC+PEI | 2 | strange position in phylogenetic trees | 201 | 01-18-2018 |
| CpcS-I subfamily | Npun_F3809 | YP_001867136.1 | Nostoc punctiforme | ATCC29133 (PCC73102) | PC+PEI | 2 | CpcSIII in Schluchter et al., 2010? | 206 | 09-26-2011 |
| CpcS-I subfamily | ACCM5_010100032969 | ZP_09252138.1 | Acaryochloris sp. | CCMEE5410 | APC only | 196 | 08-24-2012 | ||
| CpcS-III subfamily | Mic7113_0798 | YP_007120112.1 | Microcoleus sp. | PCC7113 | PC+PEI | 2 | Found both CpcS-I and CpcS-III in this strain? | 188 | 06-20-2013 |
| CpcU-I subfamily | LYNGBM3L_17960 | ZP_08426426.1 | Lyngbya majuscula | 3L | PC+PEI | 2 | Protomata tells it is CpcU. Blast tells it is CpcSIII (but with a 17aa gap) |
190 | 10-19-2011 |
| CpcU-I subfamily | ACCM5_010100021921 | ZP_09249963.1 | Acaryochloris sp. | CCMEE5410 | APC only | 184 | 01-24-2012 | ||
| CpcU-I subfamily | PCC7418_3771 | YP_007170089.1 | Halothece sp. | PCC7418 | PC | 179 | 06-20-2013 | ||
| CpcU-I subfamily | Dacsa_0519 | YP_007170660.1 | Dactylococcopsis salina | PCC8305 | 190 | 06-20-2013 | |||
| CpcU-I subfamily | AM1_5938 | YP_001520196.1 | Acaryochloris marina | MBIC11017 (AM1) | PC | 1 | N-term extended (22 aa added). Low blast and protomatch score with other CpcU-I sequences. | 184 | 09-16-2012 |
| CpcU-II subfamily | CPCC7001_xx | Cyanobium sp. | PCC7001 | PC | 1 | Found using tblastn. Orf not detected in refseq. | 166 | 02-21-2012 | |
| CpeS-I subfamily | gi|145967347|gb|ABP99029.1| | ABP99029.1 | Fremyella diplosiphon (Tolypothrix sp. / Calothrix sp.) | Fd33 (UTEX481/PCC7601) | PC+PEI | CA3 | N-term shortened (6 aa removed: METKVL). C-term much longer than in other CpeS-I sequences and also includes a specific sequence at between aa 103-112. | 215 | 09-17-2012 |
Model strains, Marine strains
Last update: 20 Apr 2023 14:57:39
