Score = 75.1 bits (183), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 45/113 (39%), Positives = 64/113 (56%), Gaps = 4/113 (3%)
Query: 12 ENLTKFELPKAPTE-AYDPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMHLHW 70
+ L K +P+E + D E LT+EE+ +R K V +GRRGIF GV+ +H HW
Sbjct: 543 QALAKLHSSWSPSEQSADREHLTEEEKIMFRRIGRKMDGLVLLGRRGIFDGVIEEIHQHW 602
Query: 71 KKHETVKVVSKPCEPWKIHEYAEVLAQLSKGIVIDI---NPSNTIIFYRGKNY 120
K E VKV++K + +I A +L + GI+I + S+ II YRGKNY
Sbjct: 603 KHKEVVKVITKQNQTRQIMYAASLLEVETGGILIAVEKLTTSHAIILYRGKNY 655
Required for the splicing of group IIA introns in chloroplasts, and especially for atpF, by regulating the intron folding. Forms splicing particles with RNA. Also involved in chloroplast protein translation.
Score = 70.9 bits (172), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 39/96 (40%), Positives = 57/96 (59%), Gaps = 3/96 (3%)
Query: 28 DPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKKHETVKVVSKPCEPWK 87
D E+LT+EER ++ K +V +GRRG+F GV+ +H HWK E VKV++K + +
Sbjct: 562 DRELLTEEERRIFRKIGLKMDEHVLLGRRGVFEGVIEEIHQHWKHKEVVKVITKQNQASQ 621
Query: 88 IHEYAEVLAQLSKGIVIDI---NPSNTIIFYRGKNY 120
I + +L + G +I I S+ II YRGKNY
Sbjct: 622 ITYTSMMLEVETGGTLIAIERFTTSHAIILYRGKNY 657
Required for the splicing of group IIA introns in chloroplasts, by regulating the intron folding. Forms splicing particles with RNA. Also involved in chloroplast protein translation.
Required for the splicing of group IIA introns in chloroplasts, by regulating the intron folding. Forms splicing particles with RNA. May also be involved in chloroplast protein translation.
Arabidopsis thaliana (taxid: 3702)
Close Homologs in the Non-Redundant Database Detected by BLAST
Score = 325 (119.5 bits), Expect = 2.7e-29, P = 2.7e-29
Identities = 64/120 (53%), Positives = 84/120 (70%)
Query: 2 KEKRKEAWLIENLTKFELPKAPTEAYDPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGG 61
K ++KE L+E + K E ++ +DPEILT EE Y + K KNYV VGRRGI+ G
Sbjct: 147 KARKKEERLMETMKKLEPSESAETTHDPEILTPEEHFYYLKMGLKCKNYVPVGRRGIYQG 206
Query: 62 VVLNMHLHWKKHETVKVVSKPCEPWKIHEYAEVLAQLSKGIVIDINPSNTIIFYRGKNYV 121
V+LNMHLHWKKH+T++VV K P ++ E A LA+L+ GIV+D++ NTII YRGKNYV
Sbjct: 207 VILNMHLHWKKHQTLQVVIKTFTPDEVKEIAVELARLTGGIVLDVHEGNTIIMYRGKNYV 266
Score = 214 (80.4 bits), Expect = 2.6e-16, P = 2.6e-16
Identities = 47/122 (38%), Positives = 70/122 (57%)
Query: 2 KEKRKEAWLIENLTKFELPKAPTEAYDPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGG 61
K +R E L+ + +P P YD E++++EER ++ K K Y+ +G RG+F G
Sbjct: 626 KFQRAEK-LLSKIEASMIPNGPD--YDQEVISEEERAMFRKVGLKMKAYLPIGIRGVFDG 682
Query: 62 VVLNMHLHWKKHETVKVVSKPCEPWKIHEYAEVLAQLSKGIVIDIN--PSN-TIIFYRGK 118
V+ NMHLHWK E VK++SK + E A +L S G+++ I P +I+YRGK
Sbjct: 683 VIENMHLHWKHRELVKLISKQKNQAFVEETARLLEYESGGVLVAIEKVPKGFALIYYRGK 742
Query: 119 NY 120
NY
Sbjct: 743 NY 744
Score = 189 (71.6 bits), Expect = 1.3e-13, P = 1.3e-13
Identities = 45/111 (40%), Positives = 62/111 (55%)
Query: 14 LTKFELPKAPTEAY-DPEILTDEERHYLKRTDEKKKNYVQVGRRGIFGGVVLNMHLHWKK 72
L K E+ P E DPE +TDEER ++ K K ++ +GRRG+F G V NMHLHWK
Sbjct: 619 LAKVEVCLKPAEQREDPESITDEERFMFRKLGLKMKAFLLLGRRGVFDGTVENMHLHWKY 678
Query: 73 HETVKVVSKPCEPWKIHEYAEVLAQLSKGIVIDINPSN---TIIFYRGKNY 120
E VK++ K + + A L S GI++ I+ II YRG++Y
Sbjct: 679 RELVKIIVKAKTFDGVKKVALALEAESGGILVSIDKVTKGYAIIVYRGQDY 729
>gnl|CDD|198171 smart01103, CRS1_YhbY, Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly
GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome. Length = 84
Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome. Length = 84
A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.
>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain
The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
