Subsystem: YrdC-YciO-Sua5 and associated protein families

This subsystem's description is:

This subsystem has been originally encoded by Dr. El Yacoubi, whose contribution to the SEED database we gratefully acknowledge.

Plant-Prokaryote project SUMMARY for YciO and YciV families (in Arabidopsis: At3g01920 and At2g13840 respectively)

Most organisms harbor only one member of the YrdC/Sua5 (COG009) protein family. Exceptions include plants and several bacteria that have two homologs. Expression of the second COG009 encoding gene of E. coli, yciO, failed to complement the t6A-minus phenotype of yeast strains lacking a functional SUA5 gene (El Yacoubi, et al., 2009). The two subfamilies can also be distinguished by sequence analysis, as residues K50 and R52 are strictly conserved in the YrdC/Sua5 subfamily but absent in YciO sequences. These residues are essential for YrdC/Sua5 function as shown by site directed mutagenesis and complementation experiments.

Therefore the YciO branch of COG009 is separated in this database from the YrdC and Sua5 subfamilies, as the results presented here suggest that function of the YciO subgroup of COG0009 is distinct from that of YrdC/Sua5 (El Yacoubi, et al., 2009). It's function is still unknown.

Protein family YciV appears to be involved in strong functional coupling with the YciO subfamily (as the corresponding genes appear to co-occur and co-localize in the majority of genomes where they are present). We predict that the YciO and YciV protein families are jointly involved in yet unknown modification of RNA or proteins


1. El Yacoubi B, Lyons B, Cruz Y, Reddy R, Nordin B, Agnelli F, Williamson JR, Schimmel P, Swairjo MA, de Crécy-Lagard V. 2009. The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA. Nucleic Acids Res, 37(9):2894-909.

Agari Y, Sato S, Wakamatsu T, Bessho Y, Ebihara A, Yokoyama S, Kuramitsu S, Shinkai A. X-ray crystal structure of a hypothetical Sua5 protein from Sulfolobus tokodaii strain. Proteins (2008) 70:1108–1111

Durant PC, Bajji AC, Sundaram M, Kumar RK, Davis DR. Structural effects of hypermodified nucleosides in the Escherichia coli and human tRNALys anticodon loop: the effect of nucleosides s(2)U, mcm(5)U, mcm(5)s(2)U, mnm(5)s(2)U, t(6)A, and ms(2)t(6)A. Biochemistry (2005) 44:8078–8089.

Elkins BN, Keller EB. The enzymatic synthesis of N-(purin-6-ylcarbamoyl)threonine, an anticodon-adjacent base in transfer ribonucleic acid. Biochemistry (1974) 13:4622–4628

Na JG, Pinto I, Hampsey M. Isolation and characterization of SUA5, a novel gene required for normal growth in Saccharomyces cerevisiae. Genetics (1992) 131:791–801.

Teplova M, Tereshko V, Sanishvili R, Joachimiak A, Bushueva T, Anderson WF, Egli M. The structure of the yrdC gene product from Escherichia coli reveals a new fold and suggests a role in RNA binding. Protein Sci. (2000) 9:2557–2566.

Yarian C, Townsend H, Czestkowski W, Sochacka E, Malkiewicz AJ, Guenther R, Miskiewicz A, Agris PF. Accurate translation of the genetic code depends on tRNA modified nucleosides. J. Biol. Chem. (2002) 277:16391–16395

For more information, please check out the description and the additional notes tabs, below

Literature ReferencesA neutral glycoprotease of Pasteurella haemolytica A1 specifically cleaves O-sialoglycoproteins. Abdullah KM Infection and immunity 1992 Jan1729196
A genome-based approach for the identification of essential bacterial genes. Arigoni F Nature biotechnology 1998 Sep9743119
A global approach to identify novel broad-spectrum antibacterial targets among proteins of unknown function. Zalacain M Journal of molecular microbiology and biotechnology 200315044829
Structural characterization of Salmonella typhimurium YeaZ, an M22 O-sialoglycoprotein endopeptidase homolog. Nichols CE Proteins 2006 Jul 116617437
Cloning, nucleotide sequence, and expression of the Pasteurella haemolytica A1 glycoprotease gene. Abdullah KM Journal of bacteriology 1991 Sep1885539
DiagramFunctional RolesSubsystem SpreadsheetDescriptionAdditional Notes 

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Group Alias
Abbrev.Functional RoleReactionsScenario ReactionsGOLiterature

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