CyanoLyase

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.

Fold

Phyre2 found the following protein fold for this family:


c3bdrA_

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 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-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-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 strain Model strains, Marine strains

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