RL25_DEIRA
ID RL25_DEIRA Reviewed; 237 AA.
AC Q9RX88;
DT 15-MAR-2004, integrated into UniProtKB/Swiss-Prot.
DT 15-MAR-2004, sequence version 2.
DT 25-MAY-2022, entry version 147.
DE RecName: Full=50S ribosomal protein L25;
DE AltName: Full=General stress protein CTC;
GN Name=rplY; Synonyms=ctc; OrderedLocusNames=DR_0427;
OS Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG
OS 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422).
OC Bacteria; Deinococcus-Thermus; Deinococci; Deinococcales; Deinococcaceae;
OC Deinococcus.
OX NCBI_TaxID=243230;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB
RC 9279 / R1 / VKM B-1422;
RX PubMed=10567266; DOI=10.1126/science.286.5444.1571;
RA White O., Eisen J.A., Heidelberg J.F., Hickey E.K., Peterson J.D.,
RA Dodson R.J., Haft D.H., Gwinn M.L., Nelson W.C., Richardson D.L.,
RA Moffat K.S., Qin H., Jiang L., Pamphile W., Crosby M., Shen M.,
RA Vamathevan J.J., Lam P., McDonald L.A., Utterback T.R., Zalewski C.,
RA Makarova K.S., Aravind L., Daly M.J., Minton K.W., Fleischmann R.D.,
RA Ketchum K.A., Nelson K.E., Salzberg S.L., Smith H.O., Venter J.C.,
RA Fraser C.M.;
RT "Genome sequence of the radioresistant bacterium Deinococcus radiodurans
RT R1.";
RL Science 286:1571-1577(1999).
RN [2]
RP PROTEIN SEQUENCE OF 1-22.
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB
RC 9279 / R1 / VKM B-1422;
RX PubMed=15249204; DOI=10.1016/j.bbrc.2004.06.062;
RA Joshi B.S., Schmid R., Altendorf K., Apte S.K.;
RT "Protein recycling is a major component of post-irradiation recovery in
RT Deinococcus radiodurans strain R1.";
RL Biochem. Biophys. Res. Commun. 320:1112-1117(2004).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF THE 50S SUBUNIT, AND PROTEIN
RP SEQUENCE OF 1-5.
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB
RC 9279 / R1 / VKM B-1422;
RX PubMed=11733066; DOI=10.1016/s0092-8674(01)00546-3;
RA Harms J., Schluenzen F., Zarivach R., Bashan A., Gat S., Agmon I.,
RA Bartels H., Franceschi F., Yonath A.;
RT "High resolution structure of the large ribosomal subunit from a mesophilic
RT eubacterium.";
RL Cell 107:679-688(2001).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH
RP FIVE ANTIBIOTICS.
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB
RC 9279 / R1 / VKM B-1422;
RX PubMed=11677599; DOI=10.1038/35101544;
RA Schluenzen F., Zarivach R., Harms J., Bashan A., Tocilj A., Albrecht R.,
RA Yonath A., Franceschi F.;
RT "Structural basis for the interaction of antibiotics with the peptidyl
RT transferase centre in eubacteria.";
RL Nature 413:814-821(2001).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (3.5 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH
RP TRNA MIMICS.
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB
RC 9279 / R1 / VKM B-1422;
RX PubMed=12535524; DOI=10.1016/s1097-2765(03)00009-1;
RA Bashan A., Agmon I., Zarivach R., Schluenzen F., Harms J., Berisio R.,
RA Bartels H., Franceschi F., Auerbach T., Hansen H.A., Kossoy E., Kessler M.,
RA Yonath A.;
RT "Structural basis of the ribosomal machinery for peptide bond formation,
RT translocation, and nascent chain progression.";
RL Mol. Cell 11:91-102(2003).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH
RP MODIFIED MACROLIDE ANTIBIOTICS.
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB
RC 9279 / R1 / VKM B-1422;
RX PubMed=12623020; DOI=10.1016/s0969-2126(03)00022-4;
RA Schluenzen F., Harms J.M., Franceschi F., Hansen H.A., Bartels H.,
RA Zarivach R., Yonath A.;
RT "Structural basis for the antibiotic activity of ketolides and azalides.";
RL Structure 11:329-338(2003).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (3.4 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH
RP TROLEANDOMYCIN.
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB
RC 9279 / R1 / VKM B-1422;
RX PubMed=12665853; DOI=10.1038/nsb915;
RA Berisio R., Schluenzen F., Harms J., Bashan A., Auerbach T., Baram D.,
RA Yonath A.;
RT "Structural insight into the role of the ribosomal tunnel in cellular
RT regulation.";
RL Nat. Struct. Biol. 10:366-370(2003).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (3.4 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH
RP THE STREPTOGRAMINS QUINUPRISTIN AND DALFOPRISTIN.
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB
RC 9279 / R1 / VKM B-1422;
RX PubMed=15059283; DOI=10.1186/1741-7007-2-4;
RA Harms J.M., Schluenzen F., Fucini P., Bartels H., Yonath A.;
RT "Alterations at the peptidyl transferase centre of the ribosome induced by
RT the synergistic action of the streptogramins dalfopristin and
RT quinupristin.";
RL BMC Biol. 2:4-4(2004).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (3.5 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH
RP TIAMULIN.
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB
RC 9279 / R1 / VKM B-1422;
RX PubMed=15554968; DOI=10.1111/j.1365-2958.2004.04346.x;
RA Schluenzen F., Pyetan E., Fucini P., Yonath A., Harms J.M.;
RT "Inhibition of peptide bond formation by pleuromutilins: the structure of
RT the 50S ribosomal subunit from Deinococcus radiodurans in complex with
RT tiamulin.";
RL Mol. Microbiol. 54:1287-1294(2004).
CC -!- FUNCTION: This is one of 3 proteins that mediate the attachment of the
CC 5S rRNA onto the large ribosomal subunit. This protein has three
CC domains. The N-terminal one is bound on the solvent face, the middle
CC domain fills the space between the 5S rRNA and the L11 arm contacting
CC the 23S rRNA while the C-terminal domain is on the edge of the
CC intersubunit interface and contacts the A site. The protein
CC conformation changes upon binding of a tRNA mimic to the A site,
CC although the mimic does not interact directly with CTC itself,
CC consistent with CTCs presumed role in moderating A site binding.
CC -!- SUBUNIT: Part of the 50S ribosomal subunit. Contacts proteins L11 and
CC L16, the A site tRNA, and the 5S and 23S rRNAs.
CC {ECO:0000269|PubMed:11677599, ECO:0000269|PubMed:12535524,
CC ECO:0000269|PubMed:12623020, ECO:0000269|PubMed:12665853,
CC ECO:0000269|PubMed:15059283, ECO:0000269|PubMed:15554968}.
CC -!- SIMILARITY: Belongs to the bacterial ribosomal protein bL25 family. CTC
CC subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF10004.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; AE000513; AAF10004.1; ALT_INIT; Genomic_DNA.
DR PIR; A75521; A75521.
DR RefSeq; NP_294150.1; NC_001263.1.
DR RefSeq; WP_027479566.1; NC_001263.1.
DR PDB; 1NJM; X-ray; 3.60 A; T=1-237.
DR PDB; 1NJP; X-ray; 3.50 A; T=1-237.
DR PDB; 1NKW; X-ray; 3.10 A; T=1-237.
DR PDB; 1NWX; X-ray; 3.50 A; T=1-237.
DR PDB; 1NWY; X-ray; 3.30 A; T=1-237.
DR PDB; 1SM1; X-ray; 3.42 A; T=1-237.
DR PDB; 1XBP; X-ray; 3.50 A; T=1-237.
DR PDB; 2ZJP; X-ray; 3.70 A; S=1-237.
DR PDB; 2ZJQ; X-ray; 3.30 A; S=1-237.
DR PDB; 2ZJR; X-ray; 2.91 A; S=1-237.
DR PDB; 3CF5; X-ray; 3.30 A; S=1-237.
DR PDB; 3DLL; X-ray; 3.50 A; S=1-237.
DR PDB; 3PIO; X-ray; 3.25 A; S=1-237.
DR PDB; 3PIP; X-ray; 3.45 A; S=1-237.
DR PDB; 4IO9; X-ray; 3.20 A; S=1-237.
DR PDB; 4IOA; X-ray; 3.20 A; S=1-237.
DR PDB; 4IOC; X-ray; 3.60 A; S=1-237.
DR PDB; 4U67; X-ray; 3.65 A; S=1-237.
DR PDB; 4V49; X-ray; 8.70 A; T=1-173.
DR PDB; 4V4A; X-ray; 9.50 A; T=1-173.
DR PDB; 4V4G; X-ray; 11.50 A; W=1-173.
DR PDB; 4V4P; X-ray; 5.50 A; V=1-237.
DR PDB; 4V4R; X-ray; 5.90 A; Z=1-237.
DR PDB; 4V4S; X-ray; 6.76 A; Z=1-237.
DR PDB; 4V4T; X-ray; 6.46 A; Z=1-237.
DR PDB; 4WFN; X-ray; 3.54 A; S=1-237.
DR PDB; 5DM6; X-ray; 2.90 A; S=1-175.
DR PDB; 5DM7; X-ray; 3.00 A; S=1-175.
DR PDB; 5JVG; X-ray; 3.43 A; S=1-237.
DR PDB; 5JVH; X-ray; 3.58 A; S=1-237.
DR PDB; 7A0R; X-ray; 3.30 A; S=1-175.
DR PDB; 7A0S; X-ray; 3.22 A; S=1-175.
DR PDB; 7A18; X-ray; 3.40 A; S=1-175.
DR PDBsum; 1NJM; -.
DR PDBsum; 1NJP; -.
DR PDBsum; 1NKW; -.
DR PDBsum; 1NWX; -.
DR PDBsum; 1NWY; -.
DR PDBsum; 1SM1; -.
DR PDBsum; 1XBP; -.
DR PDBsum; 2ZJP; -.
DR PDBsum; 2ZJQ; -.
DR PDBsum; 2ZJR; -.
DR PDBsum; 3CF5; -.
DR PDBsum; 3DLL; -.
DR PDBsum; 3PIO; -.
DR PDBsum; 3PIP; -.
DR PDBsum; 4IO9; -.
DR PDBsum; 4IOA; -.
DR PDBsum; 4IOC; -.
DR PDBsum; 4U67; -.
DR PDBsum; 4V49; -.
DR PDBsum; 4V4A; -.
DR PDBsum; 4V4G; -.
DR PDBsum; 4V4P; -.
DR PDBsum; 4V4R; -.
DR PDBsum; 4V4S; -.
DR PDBsum; 4V4T; -.
DR PDBsum; 4WFN; -.
DR PDBsum; 5DM6; -.
DR PDBsum; 5DM7; -.
DR PDBsum; 5JVG; -.
DR PDBsum; 5JVH; -.
DR PDBsum; 7A0R; -.
DR PDBsum; 7A0S; -.
DR PDBsum; 7A18; -.
DR AlphaFoldDB; Q9RX88; -.
DR SMR; Q9RX88; -.
DR IntAct; Q9RX88; 1.
DR STRING; 243230.DR_0427; -.
DR EnsemblBacteria; AAF10004; AAF10004; DR_0427.
DR KEGG; dra:DR_0427; -.
DR PATRIC; fig|243230.17.peg.601; -.
DR eggNOG; COG1825; Bacteria.
DR HOGENOM; CLU_075939_2_0_0; -.
DR InParanoid; Q9RX88; -.
DR OMA; HVDFYEV; -.
DR OrthoDB; 1673077at2; -.
DR EvolutionaryTrace; Q9RX88; -.
DR Proteomes; UP000002524; Chromosome I.
DR GO; GO:0022625; C:cytosolic large ribosomal subunit; IBA:GO_Central.
DR GO; GO:0008097; F:5S rRNA binding; IBA:GO_Central.
DR GO; GO:0003735; F:structural constituent of ribosome; IEA:InterPro.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-KW.
DR GO; GO:0006412; P:translation; IBA:GO_Central.
DR CDD; cd00495; Ribosomal_L25_TL5_CTC; 1.
DR Gene3D; 2.170.120.20; -; 1.
DR Gene3D; 2.40.240.10; -; 1.
DR HAMAP; MF_01334; Ribosomal_L25_CTC; 1.
DR InterPro; IPR020056; Rbsml_L25/Gln-tRNA_synth_N.
DR InterPro; IPR029751; Ribosomal_L25.
DR InterPro; IPR011035; Ribosomal_L25/Gln-tRNA_synth.
DR InterPro; IPR020057; Ribosomal_L25_b-dom.
DR InterPro; IPR037121; Ribosomal_L25_C.
DR InterPro; IPR001021; Ribosomal_L25_long.
DR Pfam; PF01386; Ribosomal_L25p; 1.
DR Pfam; PF14693; Ribosomal_TL5_C; 1.
DR SUPFAM; SSF50715; SSF50715; 1.
DR TIGRFAMs; TIGR00731; bL25_bact_ctc; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Reference proteome;
KW Ribonucleoprotein; Ribosomal protein; RNA-binding; rRNA-binding;
KW tRNA-binding.
FT CHAIN 1..237
FT /note="50S ribosomal protein L25"
FT /id="PRO_0000181543"
FT REGION 1..104
FT /note="N-terminal domain"
FT REGION 105..189
FT /note="Middle domain"
FT REGION 190..237
FT /note="C-terminal domain"
FT REGION 205..237
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 211..225
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT STRAND 2..4
FT /evidence="ECO:0007829|PDB:7A0S"
FT TURN 11..13
FT /evidence="ECO:0007829|PDB:5DM6"
FT TURN 15..17
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 18..24
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 26..35
FT /evidence="ECO:0007829|PDB:5DM6"
FT HELIX 36..46
FT /evidence="ECO:0007829|PDB:5DM6"
FT HELIX 47..49
FT /evidence="ECO:0007829|PDB:5DM7"
FT STRAND 52..55
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 57..59
FT /evidence="ECO:0007829|PDB:4IO9"
FT STRAND 61..72
FT /evidence="ECO:0007829|PDB:5DM6"
FT TURN 73..76
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 77..85
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 88..90
FT /evidence="ECO:0007829|PDB:7A0S"
FT STRAND 94..97
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 99..102
FT /evidence="ECO:0007829|PDB:2ZJR"
FT TURN 107..110
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 112..114
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 116..123
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 127..129
FT /evidence="ECO:0007829|PDB:5JVG"
FT STRAND 135..137
FT /evidence="ECO:0007829|PDB:2ZJR"
FT HELIX 138..140
FT /evidence="ECO:0007829|PDB:7A18"
FT STRAND 147..149
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 155..157
FT /evidence="ECO:0007829|PDB:4IO9"
FT STRAND 159..162
FT /evidence="ECO:0007829|PDB:4IO9"
FT STRAND 166..172
FT /evidence="ECO:0007829|PDB:5DM6"
SQ SEQUENCE 237 AA; 25390 MW; 1B67F7DD4D385C21 CRC64;
MELTAKPRTP KQKLDESMIA AVAYNKENNV SFALDRKAFD RAFRQQSTTG LFDITVEGGE
TFPALVKAVQ MDKRKRAPIH VDFYMVTYGE PVEVSVPVHT TGRSQGEVQG GLVDIVVHNL
QIVAPGPRRI PQELVVDVTK MNIGDHITAG DIKLPEGCTL AADPELTVVS VLPPRLTAEE
LEAEVQAAQV AGLVAAGELS EEAAEAVLEG DASLEEVKAE ASEDNAGTDS EDNSDAQ
