Table II.
Arabidopsis RING domain-containing protein groups based on domain presence and organization
| Group No. | No. of Proteina | Additional Domainsb | Domain Description and/or Predicted Function | Examplec | Speciesd |
|---|---|---|---|---|---|
| 1 | 140 | None | Zinc-binding domain; protein-protein interactions; ubiquitin ligase domain (Lorick et al., 1999) | At2g47700 | At, Bn, Ce, Dm, Hs, Mm, Os, Sc, Sp, Xl, and Zm |
| 2.1 | 3 | PHD | Plant homeodomain C4HC3 type; found in proteins involved in chromatin-mediated transcriptional regulation; probable ubiquitin ligase domain (Aasland et al., 1995; Capili et al., 2001; Lu et al., 2002) | At3g05670 | At, Ce, Dm, Hs, Mm, Os, Sc, Sp, and Xl |
| 2.2 | 1 | ZNF_ZZ | Zinc-finger domain C-x2-C-x5-C-x2-C type; found in Dystophin and CREB-binding protein (Ponting et al., 1996) | At3g24800 | At |
| 3 | 4 | AAA ATPase | ATPase associated with diverse cellular activities; contains an ATP-binding site (Neuwald et al., 1999) | At2g44950 | At |
| 4.1 | 6 | ANK | Ankyrin repeats; protein-protein interaction domain (Bork, 1993) | At5g07270 | At, Ce, Dm, Hs, Mm, Os, and Xl |
| 4.2 | 1 | Protein kinase | Ser/Thr and tyrosine protein kinase; protein phosphorylation | At5g13530 | At |
| 5 | 2 | BRCT | Breast cancer carboxy terminus domain; phospho-protein-binding domain; found in proteins involved in cell cycle checkpoint or DNA damage repair (Callebaut and Mornon, 1997; Yu et al., 2003) | At4g21070 | At, Ce, Hs, Mm, Os, and Xl |
| 6 | 20 | Coiled coil | Protein-protein interaction/oligomerization motif made up of two to five α-helices (Burkhard et al., 2001) | At5g47050 | At, Bn, Ce, Dm, Hs, Mm, Os, Sc, Sp. and Xl |
| 7 | 2 | CUE | Ubiquitin-binding motif; found in proteins involved in ubiquitination (Kang et al., 2003; Shih et al., 2003) | At5g51450 | At, Ce, Hs, Mm, and Xl |
| TM | Transmembrane domain | ||||
| 8.1 | 10 | DEXDc | DEAD-like helicases; ATP-dependent helicase activity; found in proteins involved in DNA damage repair (Rocak and Linder, 2004) | At3g16600 | At, Hs, Mm, Os, Sc, and Sp |
| 8.2 | 2 | HELICc | Helicase superfamily C-terminal domain; found in a number of helicases (Rocak and Linder, 2004) | At5g10370 | At |
| 8.3 | 1 | KH | K homology RNA-binding domain; first identified in hnRNP K; proteins usually contain at least two copies (Ostareck-Lederer et al., 1998) | At3g54460 | At and Os |
| HA2 | Helicase-associated domain; found in a variety of RNA helicases and may be involved in nucleic acid binding | ||||
| F box | F-box domain found in proteins that are the substrate-binding component of the SCF E3 ligase; interacts with SKP1 (Kipreos and Pagano, 2000) | ||||
| IBR | See group 11.1 | ||||
| ZNF_C2H2 | See group 29.1 | ||||
| 9 | 1 | HHE | Function unknown; found as tandem repeats in plant, bacteria, and yeast proteins; implicated in cell wall physiology (Brunskill et al., 1997) | At3g18290 | At and Os |
| 10 | 1 | HIG_1_N | Hypoxia induced protein conserved region; found at the N terminus of TM proteins predicted to be involved in the response to hypoxia (Gracey et al., 2001) | At3g48030 | At |
| TM | Transmembrane domain | ||||
| 11.1 | 29 | IBR | In between ring fingers; Cys-rich region (C6HC) usually found between two RING domains; function unknown. (van der Reijden et al., 1999) | At3g14250 | At, Dm, Hs, Mm, Os, and Sp |
| 11.2 | 1 | RWD | RING finger- and WD repeat-containing proteins and DEXDc-like helicases; shows similarity to the UBCc domain; protein interaction domain. (Doerks et al., 2002) | At1g32340 | At, Ce, Hs, Mm, Os, and Sp |
| 12 | 5 | JmjC | Jumonji C domain; predicted to be cupin metalloenzyme that may regulate chromatin remodeling (Clissold and Ponting, 2001) | At1g62310 | At, Mt, and Ps |
| 13 | 2 | KISc | Kinesin motor catalytic domain; involved in cell division and organelle transport (Block, 1998) | At2g21380 | At and Os |
| Coiled coil | See group 6 | ||||
| 14 | 1 | LON | ATP-dependent protease La (LON) domain; ATP-dependent Ser peptidases (Van Dyck et al., 1994) | At1g18660 | At, Dm, Hs, Mm, and Sp |
| 15 | 2 | LisH | Lissencephaly type-1 (Lis1)-like homology motif; may be involved in regulating microtubule dynamics (Reiner, 2000) | At2g22690 | At and Dd |
| CTLH | C-terminal to LisH motif; function unknown | ||||
| 16 | 6 | PA | Protease-associated domain; found in plant vacuolar sorting proteins and E3 ligases (Borchers et al., 2002) | At4g09560 | At, Dm, Hs, Mm, Os, Sp, and Xl |
| TM | Transmembrane domain | ||||
| 17.1 | 1 | Pep3_Vps18 | Region found in Pep3/Vps18 proteins; found in protein involved in Golgi function and vacuolar sorting; usually precedes a RING domain (Warner et al., 1998) | At1g12470 | At, Ce, Dm, Os, Sc, and Sp |
| 17.2 | 1 | Clathrin/CLH | Region in Clathrin and VPS; found as one or two repeats in vacuolar membrane proteins (Warner et al., 1998) | At1g08190 | At, Dm, Le, and Os |
| WD40 | See group 28 | ||||
| Coiled Coil | See group 6 | ||||
| 18 | 2 | PEX | Similar to the N-terminal region of Pex2/12 peroxisomal biogenesis proteins (Sparkes and Baker, 2002) | At1g79810 | At, Ce, Dd, Dm, Hs, Mm, Os, Sc, and Sp |
| 19 | 1 | PPR | Pentatricopeptide repeat; found as four or more tandem repeats in plant proteins (Small and Peeters, 2000) | At4g17910 | At |
| TM | Transmembrane domain | ||||
| 20 | 2 | RRM | RNA recognition motif; putative RNA-binding motif; found in proteins implicated in regulation of alternative splicing and transcriptional regulation (Birney et al., 1993) | At3g45630 | At, Dm, Hs, Mm, Os, and Xl |
| 21 | 13 | SINA | Seven in absentia protein family; similar to the Drosophila Sina E3 ligase (Hu et al., 1997) | At2g41980 | At, Bn, Ce, Dm, Hs, Mm, Os, and Xl |
| 22 | 1 | SPRY | Domain in SPla and the ryanodine receptor; function unknown (Ponting et al., 1997) | Atg2g22010 | At, Ce, Dm, and Hs |
| 23 | 2 | SPX | Domain named after SYG1/Pho81/XPR1 proteins; usually found at the amino terminus of a variety of proteins; function unknown. | At1g02860 | At, Os, and Sp |
| 24 | 107 | One/more TM | Transmembrane domains | At5g57750 | |
| 25 | 29 | Signal peptide | At1g76410 | ||
| 26 | 6 | SRA | SET- and RING finger-associated domain; found in SET domain-containing proteins; histone- and chromatin-binding domain (Citterio et al., 2004) | At5g39550 | At, Hs, Mm, and Os |
| PHD | See group 2.1 | ||||
| 27.1 | 9 | VWA N-terminal | von Willebrand factor type A domain; protein-protein interactions; found in cell adhesion and extracellular matrix/intracellular proteins (Whittaker and Hynes, 2002) | At2g22680 | At and Os |
| 27.2 | 5 | VWA C-terminal | At1g79380 | At and Os | |
| 28 | 2 | WD40 | Found as tandem repeats each containing a central Trp/Asp motif; Phospho-Ser/Thr-binding domain (Yaffe and Elia, 2001) | At1g21655 | At, Ce, Dm, Hs, Le, Mm, Os, Sc, and Xl |
| 29.1 | 4 | ZNF_C2H2 | Zinc-finger domain C-x2-C-x12-H-x3-H type; implicated in nucleic acid binding (Yaffe and Elia, 2001) | At1g77770 | At, Ce, Dm, Hs, Mm, Os, Sc, Sp, and Xl |
| 29.2 | 3 | ZNF_C3H1 | Zinc-finger domain C-x8-C-x5-C-x3-H type; nucleic acid binding (Worthington et al., 1996) | At5g06420 | At, Ce, Dm, Hs, Mm, Os, Ps, Sc, and Sp |
| 29.3 | 2 | ZNF_UBP | Ubiquitin C-terminal hydrolase-like zinc finger; found in ubiquitin-specific proteases and HDAC6; ubiquitin-binding domain (Seigneurin-Berny et al., 2001; Hook et al., 2002) | At2g42160 | At, Ce, Dm, Hs, Mm, Os, Sc, Sp, and Xl |
| Coiled coil | See group 6 | ||||
| 30 | 3 | DUF1117 | Domain of unknown function | At5g59550 | At and Os |
a
Numbers do not include the RING-v domain-containing and RING-D domain-containing proteins. These types of RING proteins either did not contain any other known/detectable domains or were found to contain predicted transmembrane domains.
b
Domains found in RING proteins as determined by SMART, Pfam, or Prosite databases.
c
See Supplemental Table II for schematic of representative Arabidopsis proteins from each group.
d
Species that have RING proteins with similar domain architecture. BLAST searches and SMART and Pfam databases were used to determine the species distribution of each RING group. At, Arabidopsis; Bn, Brassica napus; Ce, C. elegans; Dd, Dictyostelium discoideum; Dm, D. melanogaster; Hs, human; Le, Lycopersicon esculentum; Mm, M. musculus; Mt, M. truncatula; Os, O. sativa; Ps, P. sativum; Sc, yeast; Sp, Schizosaccharomyces pombe; Xl, Xenopus laevis; Zm, Zea mays.