ID A0R3D2_MYCS2 Unreviewed; 215 AA.
AC A0R3D2;
DT 09-JAN-2007, integrated into UniProtKB/TrEMBL.
DT 09-JAN-2007, sequence version 1.
DT 27-MAR-2024, entry version 131.
DE RecName: Full=Large ribosomal subunit protein bL25 {ECO:0000256|HAMAP-Rule:MF_01334};
DE AltName: Full=General stress protein CTC {ECO:0000256|HAMAP-Rule:MF_01334};
GN Name=rplY {ECO:0000256|HAMAP-Rule:MF_01334};
GN Synonyms=ctc {ECO:0000256|HAMAP-Rule:MF_01334};
GN OrderedLocusNames=MSMEG_5431 {ECO:0000313|EMBL:ABK75240.1};
OS Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (Mycobacterium
OS smegmatis).
OC Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Mycobacteriaceae;
OC Mycolicibacterium.
OX NCBI_TaxID=246196 {ECO:0000313|EMBL:ABK75240.1, ECO:0000313|Proteomes:UP000000757};
RN [1] {ECO:0000313|EMBL:ABK75240.1, ECO:0000313|Proteomes:UP000000757}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700084 / mc(2)155 {ECO:0000313|Proteomes:UP000000757};
RA Fleischmann R.D., Dodson R.J., Haft D.H., Merkel J.S., Nelson W.C.,
RA Fraser C.M.;
RL Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0007829|PDB:5O60, ECO:0007829|PDB:5O61}
RP STRUCTURE BY ELECTRON MICROSCOPY (3.20 ANGSTROMS).
RX PubMed=28683309; DOI=10.1016/j.celrep.2017.06.029;
RA Hentschel J., Burnside C., Mignot I., Leibundgut M., Boehringer D., Ban N.;
RT "The Complete Structure of the Mycobacterium smegmatis 70S Ribosome.";
RL Cell Rep. 20:149-160(2017).
RN [3] {ECO:0007829|PDB:6DZI, ECO:0007829|PDB:6DZP}
RP STRUCTURE BY ELECTRON MICROSCOPY (3.42 ANGSTROMS).
RX PubMed=30038002; DOI=10.1073/pnas.1804555115;
RA Li Y., Sharma M.R., Koripella R.K., Yang Y., Kaushal P.S., Lin Q.,
RA Wade J.T., Gray T.A., Derbyshire K.M., Agrawal R.K., Ojha A.K.;
RT "Zinc depletion induces ribosome hibernation in mycobacteria.";
RL Proc. Natl. Acad. Sci. U.S.A. 115:8191-8196(2018).
RN [4] {ECO:0007829|PDB:5XYM}
RP STRUCTURE BY ELECTRON MICROSCOPY (3.08 ANGSTROMS).
RX PubMed=28875450; DOI=10.1007/s13238-017-0456-9;
RA Li Z., Ge X., Zhang Y., Zheng L., Sanyal S., Gao N.;
RT "Cryo-EM structure of Mycobacterium smegmatis ribosome reveals two
RT unidentified ribosomal proteins close to the functional centers.";
RL Protein Cell 9:384-388(2018).
RN [5] {ECO:0007829|PDB:5ZEB, ECO:0007829|PDB:5ZEP}
RP STRUCTURE BY ELECTRON MICROSCOPY (3.20 ANGSTROMS).
RX PubMed=30206241; DOI=10.1038/s41598-018-31850-3;
RA Mishra S., Ahmed T., Tyagi A., Shi J., Bhushan S.;
RT "Structures of Mycobacterium smegmatis 70S ribosomes in complex with HPF,
RT tmRNA, and P-tRNA.";
RL Sci. Rep. 8:13587-13587(2018).
RN [6] {ECO:0007829|PDB:7S0S}
RP STRUCTURE BY ELECTRON MICROSCOPY (3.05 ANGSTROMS) OF 4-195.
RX PubMed=35357969; DOI=10.1073/pnas.2120352119;
RA Laughlin Z.T., Nandi S., Dey D., Zelinskaya N., Witek M.A., Srinivas P.,
RA Nguyen H.A., Kuiper E.G., Comstock L.R., Dunham C.M., Conn G.L.;
RT "50S subunit recognition and modification by the <i>Mycobacterium
RT tuberculosis</i> ribosomal RNA methyltransferase TlyA.";
RL Proc. Natl. Acad. Sci. U.S.A. 119:e2120352119-e2120352119(2022).
RN [7] {ECO:0007829|PDB:7XAM, ECO:0007829|PDB:7Y41}
RP STRUCTURE BY ELECTRON MICROSCOPY (2.80 ANGSTROMS).
RA Sengupta J., Baid P.;
RT "Cryo-EM structures reveal a unique conformational dynamics of the
RT Mycobacterium 23S rRNA helices.";
RL Submitted (JUN-2022) to the PDB data bank.
RN [8] {ECO:0007829|PDB:8FR8}
RP STRUCTURE BY ELECTRON MICROSCOPY (2.76 ANGSTROMS) OF 4-195.
RX PubMed=37216503; DOI=10.1073/pnas.2302006120;
RA Li Y., Majumdar S., Treen R., Sharma M.R., Corro J., Gamper H.B.,
RA Manjari S.R., Prusa J., Banavali N.K., Stallings C.L., Hou Y.M.,
RA Agrawal R.K., Ojha A.K.;
RT "Starvation sensing by mycobacterial RelA/SpoT homologue through
RT constitutive surveillance of translation.";
RL Proc. Natl. Acad. Sci. U.S.A. 120:e2302006120-e2302006120(2023).
CC -!- FUNCTION: This is one of the proteins that binds to the 5S RNA in the
CC ribosome where it forms part of the central protuberance.
CC {ECO:0000256|HAMAP-Rule:MF_01334}.
CC -!- SUBUNIT: Part of the 50S ribosomal subunit; part of the 5S
CC rRNA/L5/L18/L25 subcomplex. Contacts the 5S rRNA. Binds to the 5S rRNA
CC independently of L5 and L18. {ECO:0000256|HAMAP-Rule:MF_01334}.
CC -!- SIMILARITY: Belongs to the bacterial ribosomal protein bL25 family. CTC
CC subfamily. {ECO:0000256|HAMAP-Rule:MF_01334}.
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DR EMBL; CP000480; ABK75240.1; -; Genomic_DNA.
DR RefSeq; WP_003896828.1; NZ_SIJM01000006.1.
DR RefSeq; YP_889670.1; NC_008596.1.
DR PDB; 5O60; EM; 3.20 A; W=1-215.
DR PDB; 5O61; EM; 3.31 A; W=1-215.
DR PDB; 5XYM; EM; 3.08 A; V=1-215.
DR PDB; 5ZEB; EM; 3.40 A; W=1-215.
DR PDB; 5ZEP; EM; 3.40 A; W=1-215.
DR PDB; 5ZET; EM; 3.20 A; W=1-215.
DR PDB; 6DZI; EM; 3.46 A; W=4-195.
DR PDB; 6DZP; EM; 3.42 A; W=1-215.
DR PDB; 7S0S; EM; 3.05 A; X=4-195.
DR PDB; 7XAM; EM; 2.80 A; W=1-215.
DR PDB; 7Y41; EM; 4.10 A; W=1-215.
DR PDB; 8FR8; EM; 2.76 A; 2=4-195.
DR PDBsum; 5O60; -.
DR PDBsum; 5O61; -.
DR PDBsum; 5XYM; -.
DR PDBsum; 5ZEB; -.
DR PDBsum; 5ZEP; -.
DR PDBsum; 5ZET; -.
DR PDBsum; 6DZI; -.
DR PDBsum; 6DZP; -.
DR AlphaFoldDB; A0R3D2; -.
DR EMDB; EMD-3750; -.
DR EMDB; EMD-3751; -.
DR EMDB; EMD-6789; -.
DR EMDB; EMD-6920; -.
DR EMDB; EMD-6921; -.
DR EMDB; EMD-6922; -.
DR EMDB; EMD-8932; -.
DR EMDB; EMD-8937; -.
DR SMR; A0R3D2; -.
DR IntAct; A0R3D2; 3.
DR STRING; 246196.MSMEG_5431; -.
DR PaxDb; 246196-MSMEI_5282; -.
DR GeneID; 66736734; -.
DR KEGG; msm:MSMEG_5431; -.
DR PATRIC; fig|246196.19.peg.5292; -.
DR eggNOG; COG1825; Bacteria.
DR OrthoDB; 5242980at2; -.
DR Proteomes; UP000000757; Chromosome.
DR GO; GO:1990904; C:ribonucleoprotein complex; IEA:UniProtKB-KW.
DR GO; GO:0005840; C:ribosome; IEA:UniProtKB-KW.
DR GO; GO:0008097; F:5S rRNA binding; IEA:InterPro.
DR GO; GO:0003735; F:structural constituent of ribosome; IEA:InterPro.
DR GO; GO:0006412; P:translation; IEA:UniProtKB-UniRule.
DR CDD; cd00495; Ribosomal_L25_TL5_CTC; 1.
DR Gene3D; 2.170.120.20; Ribosomal protein L25, beta domain; 1.
DR HAMAP; MF_01334; Ribosomal_L25_CTC; 1.
DR InterPro; IPR020056; Rbsml_bL25/Gln-tRNA_synth_N.
DR InterPro; IPR011035; Ribosomal_bL25/Gln-tRNA_synth.
DR InterPro; IPR020057; Ribosomal_bL25_b-dom.
DR InterPro; IPR037121; Ribosomal_bL25_C.
DR InterPro; IPR001021; Ribosomal_bL25_long.
DR InterPro; IPR029751; Ribosomal_L25_dom.
DR NCBIfam; TIGR00731; bL25_bact_ctc; 1.
DR PANTHER; PTHR33284; RIBOSOMAL PROTEIN L25/GLN-TRNA SYNTHETASE, ANTI-CODON-BINDING DOMAIN-CONTAINING PROTEIN; 1.
DR PANTHER; PTHR33284:SF1; RIBOSOMAL PROTEIN L25_GLN-TRNA SYNTHETASE, ANTI-CODON-BINDING DOMAIN-CONTAINING PROTEIN; 1.
DR Pfam; PF01386; Ribosomal_L25p; 1.
DR Pfam; PF14693; Ribosomal_TL5_C; 1.
DR SUPFAM; SSF50715; Ribosomal protein L25-like; 1.
PE 1: Evidence at protein level;
KW 3D-structure {ECO:0007829|PDB:5O60, ECO:0007829|PDB:5O61};
KW Reference proteome {ECO:0000313|Proteomes:UP000000757};
KW Ribonucleoprotein {ECO:0000256|ARBA:ARBA00023274, ECO:0000256|HAMAP-
KW Rule:MF_01334};
KW Ribosomal protein {ECO:0000256|ARBA:ARBA00022980, ECO:0000256|HAMAP-
KW Rule:MF_01334};
KW RNA-binding {ECO:0000256|ARBA:ARBA00022884, ECO:0000256|HAMAP-
KW Rule:MF_01334};
KW rRNA-binding {ECO:0000256|ARBA:ARBA00022730, ECO:0000256|HAMAP-
KW Rule:MF_01334}.
FT DOMAIN 11..97
FT /note="Large ribosomal subunit protein bL25 L25"
FT /evidence="ECO:0000259|Pfam:PF01386"
FT DOMAIN 105..183
FT /note="Large ribosomal subunit protein bL25 beta"
FT /evidence="ECO:0000259|Pfam:PF14693"
FT REGION 1..29
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 188..215
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..21
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 215 AA; 22550 MW; DB64968DA17CD3E9 CRC64;
MAKTANIPNK LTANVRTRTG KGASRQARRD GKVPAVLYGH GTDPQHLELN ARDFAAVLRS
HGTNAILTLD IEGTEQLALT KALDVHPIRR NIQHADLLVV QRGEKVTVEV TVLVEGDATP
GTLVTQDANT IEIEAEALSI PEQLTVSVEG VEAGTQITAG QISLPEGVNL ISDPELLVVN
VVEAPSAEAL EEEGAGETGA AEAPAEEAPA EEPAE
//
