RL5_DEIRA
ID RL5_DEIRA Reviewed; 180 AA.
AC Q9RXJ0;
DT 15-MAR-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 25-MAY-2022, entry version 125.
DE RecName: Full=50S ribosomal protein L5;
GN Name=rplE; OrderedLocusNames=DR_0323;
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 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 [3]
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 [4]
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 [5]
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 [6]
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 [7]
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 [8]
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 1 of the proteins that binds and probably mediates
CC the attachment of the 5S RNA into the large ribosomal subunit, where it
CC forms part of the central protuberance. In the 70S ribosome it contacts
CC protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits;
CC this bridge is implicated in subunit movement (By similarity). Contacts
CC the P site tRNA; the 5S rRNA and some of its associated proteins might
CC help stabilize positioning of ribosome-bound tRNAs. {ECO:0000250}.
CC -!- SUBUNIT: Forms a bridge to the 30S subunit in the 70S ribosome (By
CC similarity). Part of the 50S ribosomal subunit; part of the 5S
CC rRNA/L5/L18/L25 (CTC) subcomplex. Is known to contact the 5S rRNA, 23S
CC rRNA and the P site tRNA. {ECO:0000250, ECO:0000269|PubMed:11677599,
CC ECO:0000269|PubMed:12535524, ECO:0000269|PubMed:12623020,
CC ECO:0000269|PubMed:12665853, ECO:0000269|PubMed:15059283,
CC ECO:0000269|PubMed:15554968}.
CC -!- SIMILARITY: Belongs to the universal ribosomal protein uL5 family.
CC {ECO:0000305}.
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DR EMBL; AE000513; AAF09904.1; -; Genomic_DNA.
DR PIR; C75535; C75535.
DR RefSeq; NP_294046.1; NC_001263.1.
DR RefSeq; WP_010886968.1; NZ_CP015081.1.
DR PDB; 1NKW; X-ray; 3.10 A; D=1-180.
DR PDB; 1NWX; X-ray; 3.50 A; D=1-180.
DR PDB; 1NWY; X-ray; 3.30 A; D=1-180.
DR PDB; 1SM1; X-ray; 3.42 A; D=1-180.
DR PDB; 1XBP; X-ray; 3.50 A; D=1-180.
DR PDB; 2ZJP; X-ray; 3.70 A; D=1-180.
DR PDB; 2ZJQ; X-ray; 3.30 A; D=1-180.
DR PDB; 2ZJR; X-ray; 2.91 A; D=1-180.
DR PDB; 3CF5; X-ray; 3.30 A; D=1-180.
DR PDB; 3DLL; X-ray; 3.50 A; D=1-180.
DR PDB; 3PIO; X-ray; 3.25 A; D=1-180.
DR PDB; 3PIP; X-ray; 3.45 A; D=1-180.
DR PDB; 4IO9; X-ray; 3.20 A; D=1-180.
DR PDB; 4IOA; X-ray; 3.20 A; D=1-180.
DR PDB; 4IOC; X-ray; 3.60 A; D=1-180.
DR PDB; 4U67; X-ray; 3.65 A; D=1-180.
DR PDB; 4V49; X-ray; 8.70 A; D=2-179.
DR PDB; 4V4A; X-ray; 9.50 A; D=2-179.
DR PDB; 4V4G; X-ray; 11.50 A; G=2-179.
DR PDB; 4WFN; X-ray; 3.54 A; D=1-180.
DR PDB; 5DM6; X-ray; 2.90 A; D=3-179.
DR PDB; 5DM7; X-ray; 3.00 A; D=3-179.
DR PDB; 5JVG; X-ray; 3.43 A; D=1-180.
DR PDB; 5JVH; X-ray; 3.58 A; D=1-180.
DR PDB; 7A0R; X-ray; 3.30 A; D=3-179.
DR PDB; 7A0S; X-ray; 3.22 A; D=3-179.
DR PDB; 7A18; X-ray; 3.40 A; D=2-177.
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; 4WFN; -.
DR PDBsum; 5DM6; -.
DR PDBsum; 5DM7; -.
DR PDBsum; 5JVG; -.
DR PDBsum; 5JVH; -.
DR PDBsum; 7A0R; -.
DR PDBsum; 7A0S; -.
DR PDBsum; 7A18; -.
DR AlphaFoldDB; Q9RXJ0; -.
DR SMR; Q9RXJ0; -.
DR IntAct; Q9RXJ0; 1.
DR STRING; 243230.DR_0323; -.
DR EnsemblBacteria; AAF09904; AAF09904; DR_0323.
DR KEGG; dra:DR_0323; -.
DR PATRIC; fig|243230.17.peg.489; -.
DR eggNOG; COG0094; Bacteria.
DR HOGENOM; CLU_061015_2_1_0; -.
DR InParanoid; Q9RXJ0; -.
DR OMA; ERMYAFL; -.
DR OrthoDB; 1456375at2; -.
DR EvolutionaryTrace; Q9RXJ0; -.
DR Proteomes; UP000002524; Chromosome I.
DR GO; GO:0022625; C:cytosolic large ribosomal subunit; IBA:GO_Central.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0019843; F:rRNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003735; F:structural constituent of ribosome; IBA:GO_Central.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0006412; P:translation; IEA:UniProtKB-UniRule.
DR Gene3D; 3.30.1440.10; -; 1.
DR HAMAP; MF_01333_B; Ribosomal_L5_B; 1.
DR InterPro; IPR002132; Ribosomal_L5.
DR InterPro; IPR020930; Ribosomal_L5_bac-type.
DR InterPro; IPR031309; Ribosomal_L5_C.
DR InterPro; IPR022803; Ribosomal_L5_dom_sf.
DR InterPro; IPR031310; Ribosomal_L5_N.
DR PANTHER; PTHR11994; PTHR11994; 1.
DR Pfam; PF00281; Ribosomal_L5; 1.
DR Pfam; PF00673; Ribosomal_L5_C; 1.
DR PIRSF; PIRSF002161; Ribosomal_L5; 1.
DR SUPFAM; SSF55282; SSF55282; 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..180
FT /note="50S ribosomal protein L5"
FT /id="PRO_0000124923"
FT HELIX 4..20
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 25..28
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 33..35
FT /evidence="ECO:0007829|PDB:2ZJR"
FT STRAND 36..38
FT /evidence="ECO:0007829|PDB:5DM7"
FT STRAND 42..44
FT /evidence="ECO:0007829|PDB:2ZJR"
FT HELIX 47..61
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 66..69
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 76..78
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 81..83
FT /evidence="ECO:0007829|PDB:5JVG"
FT STRAND 84..89
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 90..92
FT /evidence="ECO:0007829|PDB:3DLL"
FT HELIX 93..106
FT /evidence="ECO:0007829|PDB:5DM6"
FT TURN 107..110
FT /evidence="ECO:0007829|PDB:5DM7"
FT STRAND 111..113
FT /evidence="ECO:0007829|PDB:5DM7"
FT STRAND 114..116
FT /evidence="ECO:0007829|PDB:7A18"
FT TURN 124..126
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 127..132
FT /evidence="ECO:0007829|PDB:4IO9"
FT STRAND 134..137
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 138..140
FT /evidence="ECO:0007829|PDB:4IO9"
FT HELIX 143..145
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 146..148
FT /evidence="ECO:0007829|PDB:2ZJR"
FT STRAND 156..158
FT /evidence="ECO:0007829|PDB:5DM6"
FT HELIX 163..172
FT /evidence="ECO:0007829|PDB:5DM6"
SQ SEQUENCE 180 AA; 20350 MW; 755B760BA0E90F5B CRC64;
MQQLKTKYND QVRPALMQQF GYSSVMAVPR IEKIVVNEGL GSSKEDSKAI DKAAKELALI
TLQKPIITKA KKSISNFKLR QGMPVGIKVT LRGERMYVFL EKLINIGLPR IRDFRGINPN
AFDGRGNYNL GIKEQLIFPE ITYDMVDKTR GMDITIVTTA KTDEEARALL QSMGLPFRKQ
