Score = 97 (39.2 bits), Expect = 3.9e-05, P = 3.9e-05
Identities = 26/68 (38%), Positives = 38/68 (55%)
Query: 50 RKGGKGKQIFGSVTAQDVVDIIKAQLQRDVDKKIVDLPE--IRETGEYIAQLKLHPEVTA 107
+ G +GK +FGS+ +D+ D I A + V K V LPE +R G Y ++LH EV A
Sbjct: 83 KAGDEGK-LFGSIGTRDIADAITAAGVK-VSKSEVRLPEGALRNVGAYEVSVQLHSEVFA 140
Query: 108 RIRLNVFA 115
++ V A
Sbjct: 141 TAKVQVVA 148
GO:0003735 "structural constituent of ribosome" evidence=ISS
Score = 97 (39.2 bits), Expect = 3.9e-05, P = 3.9e-05
Identities = 26/68 (38%), Positives = 38/68 (55%)
Query: 50 RKGGKGKQIFGSVTAQDVVDIIKAQLQRDVDKKIVDLPE--IRETGEYIAQLKLHPEVTA 107
+ G +GK +FGS+ +D+ D I A + V K V LPE +R G Y ++LH EV A
Sbjct: 83 KAGDEGK-LFGSIGTRDIADAITAAGVK-VSKSEVRLPEGALRNVGAYEVSVQLHSEVFA 140
Query: 108 RIRLNVFA 115
++ V A
Sbjct: 141 TAKVQVVA 148
GO:0003735 "structural constituent of ribosome" evidence=ISS
Score = 53.5 bits (129), Expect = 4e-10
Identities = 36/114 (31%), Positives = 62/114 (54%), Gaps = 4/114 (3%)
Query: 2 GKAQIVTPLLLKEMKMEEERIEAEKKRVKEEAQQLALIFETVGAFKVKRKGGKGKQIFGS 61
G A T ++ + +++E + K A +L + E G + +K G ++FGS
Sbjct: 34 GLAVPATKKNIEFFEARRKKLEEKLAANKAAAARLKEVLEL-GTLTISKKVGDEGKLFGS 92
Query: 62 VTAQDVVDIIKAQLQRDVDKKIVDLPE--IRETGEYIAQLKLHPEVTARIRLNV 113
+T + + D +KA D+DKK ++LP+ IR TGE+ +KLH EV A +++ V
Sbjct: 93 ITTKQIADALKAAGL-DLDKKKIELPDGVIRTTGEHEVTIKLHEEVFAVLKVIV 145
Ribosomal protein L9 appears to be universal in, but restricted to, eubacteria and chloroplast [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 148
>PF03948 Ribosomal_L9_C: Ribosomal protein L9, C-terminal domain; InterPro: IPR020069 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms
The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L9 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins grouped on the basis of sequence similarities [, ]. The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker []. Each domain contains an rRNA binding site, and the protein functions as a structural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an alpha-helix and a three-stranded mixed parallel, anti-parallel beta-sheet packed against the central alpha-helix. The long central alpha-helix is exposed to solvent in the middle and participates in the hydrophobic cores of the two domains at both ends. ; PDB: 3D5B_I 3PYV_H 3F1H_I 3PYR_H 3MRZ_H 1VSP_G 3MS1_H 1VSA_G 3PYT_H 2WH4_I ....
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
>PF01281 Ribosomal_L9_N: Ribosomal protein L9, N-terminal domain; InterPro: IPR020070 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms
The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L9 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins grouped on the basis of sequence similarities [, ]. The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker []. Each domain contains an rRNA binding site, and the protein functions as a structural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an alpha-helix and a three-stranded mixed parallel, anti-parallel beta-sheet packed against the central alpha-helix. The long central alpha-helix is exposed to solvent in the middle and participates in the hydrophobic cores of the two domains at both ends. ; PDB: 3D5B_I 3PYV_H 3F1H_I 3PYR_H 3MRZ_H 1VSP_G 3MS1_H 1VSA_G 3PYT_H 2WH4_I ....
>PF10045 DUF2280: Uncharacterized conserved protein (DUF2280); InterPro: IPR018738 This entry is represented by Burkholderia phage Bups phi1, Orf2
>pdb|487D|K Chain K, Seven Ribosomal Proteins Fitted To A Cryo-Electron Microscopic Map Of The Large 50s Subunit At 7.5 Angstroms Resolution Length = 149
>pdb|3TVE|K Chain K, Crystal Structure Analysis Of Ribosomal Decoding. This Entry Contains The 50s Ribosomal Subunit Of The First 70s Molecule In The Asymmetric Unit For The Cognate Trna-Leu Complex Length = 146
>pdb|2HGJ|K Chain K, Crystal Structure Of The 70s Thermus Thermophilus Ribosome Showing How The 16s 3'-End Mimicks Mrna E And P Codons. This Entry 2hgj Contains 50s Ribosomal Subunit. The 30s Ribosomal Subunit Can Be Found In Pdb Entry 2hgi. Length = 148
>pdb|2V47|I Chain I, Structure Of The Ribosome Recycling Factor Bound To The Thermus Thermophilus 70s Ribosome With Mrna, Asl-Phe And Trna-Fmet (Part 2 Of 4). This File Contains The 50s Subunit For Molecule 1. Length = 148
>pdb|1VSA|G Chain G, Crystal Structure Of A 70s Ribosome-Trna Complex Reveals Functional Interactions And Rearrangements. This File, 1vsa, Contains The 50s Ribosome Subunit. 30s Ribosome Subunit Is In The File 2ow8 Length = 148
>pdb|3FIN|I Chain I, T. Thermophilus 70s Ribosome In Complex With Mrna, Trnas And Ef- Tu.Gdp.Kirromycin Ternary Complex, Fitted To A 6.4 A Cryo-Em Map. This File Contains The 50s Subunit Length = 146
>pdb|3UXQ|I Chain I, The Structure Of Thermorubin In Complex With The 70s Ribosome From Thermus Thermophilus. This File Contains The 50s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes. Length = 148
>pdb|3PYO|H Chain H, Crystal Structure Of A Complex Containing Domain 3 From The Psiv Igr Ires Rna Bound To The 70s Ribosome. This File Contains The 50s Subunit Of The First 70s Ribosome. Length = 145
>pdb|1P85|F Chain F, Real Space Refined Coordinates Of The 50s Subunit Fitted Into The Low Resolution Cryo-Em Map Of The Ef-G.Gtp State Of E. Coli 70s Ribosome Length = 149
