Score = 82.6 bits (204), Expect = 5e-21
Identities = 32/61 (52%), Positives = 35/61 (57%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFT 60
MRGA+GKP GT ARV IGQ I SV + EALRRA KFP KI + K W
Sbjct: 112 MRGAFGKPVGTAARVKIGQKIFSVWTKPSNFDVAKEALRRAAMKFPVPCKIVIEKGWELL 171
Query: 61 K 61
K
Sbjct: 172 K 172
e. This model finds the archaeal and eukaryotic forms of ribosomal protein L10. The protein is encoded by multiple loci in some eukaryotes and has been assigned a number of extra-ribosomal functions, some of which will require re-evaluation in the context of identification as a ribosomal protein. L10.e is distantly related to eubacterial ribosomal protein L16 [Protein synthesis, Ribosomal proteins: synthesis and modification]. Length = 172
>gnl|CDD|238714 cd01433, Ribosomal_L16_L10e, Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts
Score = 69.8 bits (172), Expect = 1e-16
Identities = 24/52 (46%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIY 52
M GKP+G VARV GQ + VR + + A EALRRA K P + KI
Sbjct: 62 MGKGKGKPEGWVARVKPGQILFEVRGVPEEEVA-KEALRRAAKKLPIKTKIV 112
Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with the 30S subunit, binding of aminoacyl-tRNA and interaction with antibiotics. L16 is required for the function of elongation factor P (EF-P), a protein involved in peptide bond synthesis through the stimulation of peptidyl transferase activity by the ribosome. Mutations in L16 and the adjoining bases of 23S rRNA confer antibiotic resistance in bacteria, suggesting a role for L16 in the formation of the antibiotic binding site. The GTPase RbgA (YlqF) is essential for the assembly of the large subunit, and it is believed to regulate the incorporation of L16. L10e is the archaeal and eukaryotic cytosolic homolog of bacterial L16. L16 and L10e exhibit structural differences at the N-terminus. Length = 112
>gnl|CDD|235252 PRK04199, rpl10e, 50S ribosomal protein L10e; Reviewed
Score = 64.9 bits (159), Expect = 2e-14
Identities = 29/61 (47%), Positives = 34/61 (55%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFT 60
MR A+GKP GT ARV GQ I +VR + + A EALRRA K P +I V K
Sbjct: 112 MRLAFGKPVGTAARVEKGQKIFTVRVNPEHLEAAKEALRRAAMKLPTPCRIVVEKGKELL 171
Query: 61 K 61
K
Sbjct: 172 K 172
Length = 172
>gnl|CDD|215820 pfam00252, Ribosomal_L16, Ribosomal protein L16p/L10e
Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with the 30S subunit, binding of aminoacyl-tRNA and interaction with antibiotics. L16 is required for the function of elongation factor P (EF-P), a protein involved in peptide bond synthesis through the stimulation of peptidyl transferase activity by the ribosome. Mutations in L16 and the adjoining bases of 23S rRNA confer antibiotic resistance in bacteria, suggesting a role for L16 in the formation of the antibiotic binding site. The GTPase RbgA (YlqF) is essential for the assembly of the large subunit, and it is believed to regulate the incorporation of L16. L10e is the archaeal and eukaryotic cytosolic homolog of bacterial L16. L16 and L10e exhibit structural differences at the N-terminus.
This model describes bacterial and organellar ribosomal protein L16. The homologous protein of the eukaryotic cytosol is designated L10
>PF00252 Ribosomal_L16: Ribosomal protein L16p/L10e; InterPro: IPR016180 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 [, ]. This entry represents a structural domain with an alpha/beta-hammerhead fold, where the beta-hammerhead motif is similar to that in barrel-sandwich hybrids. Domains of this structure can be found in ribosomal proteins L10e and L16. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 2ZJR_J 1Y69_K 3DLL_J 2ZJQ_J 2ZJP_J 3PIO_J 3CF5_J 3PIP_J 2ZKR_h 3J11_O ....
>PF07831 PYNP_C: Pyrimidine nucleoside phosphorylase C-terminal domain; InterPro: IPR013102 This domain is found at the C-terminal end of the large alpha/beta domain making up various pyrimidine nucleoside phosphorylases [, ]
It has slightly different conformations in different members of this family. For example, in pyrimidine nucleoside phosphorylase (PYNP, P77826 from SWISSPROT) there is an added three-stranded anti-parallel beta sheet as compared to other members of the family, such as Escherichia coli thymidine phosphorylase (TP, P07650 from SWISSPROT) []. The domain contains an alpha/ beta hammerhead fold and residues in this domain seem to be important in formation of the homodimer []. ; GO: 0016763 transferase activity, transferring pentosyl groups, 0006213 pyrimidine nucleoside metabolic process; PDB: 1AZY_A 1OTP_A 2TPT_A 3H5Q_A 1BRW_A 2WK5_C 2J0F_C 2WK6_B 1UOU_A 2DSJ_B ....
>pdb|2ZKR|HH Chain h, Structure Of A Mammalian Ribosomal 60s Subunit Within An 80s Complex Obtained By Docking Homology Models Of The Rna And Proteins Into An 8.7 A Cryo-Em Map Length = 214
>pdb|3IZR|I Chain I, Localization Of The Large Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 224
>pdb|3IZS|I Chain I, Localization Of The Large Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 221
>pdb|3JYW|I Chain I, Structure Of The 60s Proteins For Eukaryotic Ribosome Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome At 8.9a Resolution Length = 165
>pdb|1S1I|I Chain I, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From Yeast Obtained By Docking Atomic Models For Rna And Protein Components Into A 11.7 A Cryo-Em Map. This File, 1s1i, Contains 60s Subunit. The 40s Ribosomal Subunit Is In File 1s1h Length = 168
>pdb|3J21|N Chain N, Promiscuous Behavior Of Proteins In Archaeal Ribosomes Revealed By Cryo-em: Implications For Evolution Of Eukaryotic Ribosomes (50s Ribosomal Proteins) Length = 181
Score = 41.1 bits (96), Expect = 1e-05
Identities = 13/51 (25%), Positives = 21/51 (41%), Gaps = 2/51 (3%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKI 51
M G + V+ V G+ + V + + EA R A K P + K+
Sbjct: 84 MGKGKGAVEYWVSVVKPGRVMFEVAGVTEEQ--AKEAFRLAGHKLPIQTKM 132
Score = 36.6 bits (84), Expect = 4e-04
Identities = 11/50 (22%), Positives = 18/50 (36%), Gaps = 1/50 (2%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQK 50
M G G V V G+ ++ + +F+ L + K P K
Sbjct: 70 MGGGKGAIDHYVTPVKAGRLVVEMGGRCEFEEV-QGFLDQVAHKLPFAAK 118
>2pa2_A 60S ribosomal protein L10; QM protein, , structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.50A {Homo sapiens} SCOP: d.41.4.1
