RL16_DEIRA
ID RL16_DEIRA Reviewed; 141 AA.
AC Q9RXJ5;
DT 15-MAR-2004, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 25-MAY-2022, entry version 131.
DE RecName: Full=50S ribosomal protein L16;
GN Name=rplP; OrderedLocusNames=DR_0318;
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 1-6.
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: Binds the 5S and 23S rRNAs and is also seen to make contacts
CC with the A and P site tRNAs. Interacts with A site tRNA mimics, and is
CC probably one of the key factors, along with a helix of the 23S rRNA, in
CC positioning tRNA stems in the peptidyl-transferase center.
CC -!- SUBUNIT: Part of the 50S ribosomal subunit. Contacts the CTC protein
CC (RL25). {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 universal ribosomal protein uL16 family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF09899.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; AE000513; AAF09899.1; ALT_INIT; Genomic_DNA.
DR PIR; F75534; F75534.
DR RefSeq; NP_294041.1; NC_001263.1.
DR RefSeq; WP_025567820.1; NZ_CP015081.1.
DR PDB; 1NJM; X-ray; 3.60 A; K=1-141.
DR PDB; 1NJP; X-ray; 3.50 A; K=1-141.
DR PDB; 1NKW; X-ray; 3.10 A; K=1-141.
DR PDB; 1NWX; X-ray; 3.50 A; K=1-141.
DR PDB; 1NWY; X-ray; 3.30 A; K=1-141.
DR PDB; 1SM1; X-ray; 3.42 A; K=1-141.
DR PDB; 1XBP; X-ray; 3.50 A; K=1-141.
DR PDB; 1Y69; X-ray; 3.33 A; K=1-141.
DR PDB; 2ZJP; X-ray; 3.70 A; J=1-141.
DR PDB; 2ZJQ; X-ray; 3.30 A; J=1-141.
DR PDB; 2ZJR; X-ray; 2.91 A; J=1-141.
DR PDB; 3CF5; X-ray; 3.30 A; J=1-141.
DR PDB; 3DLL; X-ray; 3.50 A; J=1-141.
DR PDB; 3PIO; X-ray; 3.25 A; J=1-141.
DR PDB; 3PIP; X-ray; 3.45 A; J=1-141.
DR PDB; 4IO9; X-ray; 3.20 A; J=1-141.
DR PDB; 4IOA; X-ray; 3.20 A; J=1-141.
DR PDB; 4IOC; X-ray; 3.60 A; J=1-141.
DR PDB; 4U67; X-ray; 3.65 A; J=1-141.
DR PDB; 4V49; X-ray; 8.70 A; K=7-130.
DR PDB; 4V4A; X-ray; 9.50 A; K=7-130.
DR PDB; 4V4G; X-ray; 11.50 A; N=7-130.
DR PDB; 4WFN; X-ray; 3.54 A; J=1-141.
DR PDB; 5DM6; X-ray; 2.90 A; J=5-140.
DR PDB; 5DM7; X-ray; 3.00 A; J=5-140.
DR PDB; 5JVG; X-ray; 3.43 A; J=1-141.
DR PDB; 5JVH; X-ray; 3.58 A; J=1-141.
DR PDB; 7A0R; X-ray; 3.30 A; J=5-140.
DR PDB; 7A0S; X-ray; 3.22 A; J=5-140.
DR PDB; 7A18; X-ray; 3.40 A; J=5-138.
DR PDBsum; 1NJM; -.
DR PDBsum; 1NJP; -.
DR PDBsum; 1NKW; -.
DR PDBsum; 1NWX; -.
DR PDBsum; 1NWY; -.
DR PDBsum; 1SM1; -.
DR PDBsum; 1XBP; -.
DR PDBsum; 1Y69; -.
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; Q9RXJ5; -.
DR SMR; Q9RXJ5; -.
DR IntAct; Q9RXJ5; 1.
DR STRING; 243230.DR_0318; -.
DR EnsemblBacteria; AAF09899; AAF09899; DR_0318.
DR GeneID; 59165585; -.
DR KEGG; dra:DR_0318; -.
DR PATRIC; fig|243230.17.peg.484; -.
DR eggNOG; COG0197; Bacteria.
DR HOGENOM; CLU_078858_2_1_0; -.
DR InParanoid; Q9RXJ5; -.
DR OMA; KGAVEYW; -.
DR OrthoDB; 1786618at2; -.
DR EvolutionaryTrace; Q9RXJ5; -.
DR Proteomes; UP000002524; Chromosome I.
DR GO; GO:0022625; C:cytosolic large ribosomal subunit; IBA:GO_Central.
DR GO; GO:0019843; F:rRNA binding; IBA:GO_Central.
DR GO; GO:0003735; F:structural constituent of ribosome; IBA:GO_Central.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-KW.
DR GO; GO:0006412; P:translation; IEA:UniProtKB-UniRule.
DR CDD; cd01433; Ribosomal_L16_L10e; 1.
DR Gene3D; 3.90.1170.10; -; 1.
DR HAMAP; MF_01342; Ribosomal_L16; 1.
DR InterPro; IPR016180; Ribosomal_L10e/L16.
DR InterPro; IPR036920; Ribosomal_L10e/L16_sf.
DR InterPro; IPR000114; Ribosomal_L16.
DR InterPro; IPR020798; Ribosomal_L16_CS.
DR PANTHER; PTHR12220; PTHR12220; 1.
DR Pfam; PF00252; Ribosomal_L16; 1.
DR PRINTS; PR00060; RIBOSOMALL16.
DR SUPFAM; SSF54686; SSF54686; 1.
DR TIGRFAMs; TIGR01164; rplP_bact; 1.
DR PROSITE; PS00586; RIBOSOMAL_L16_1; 1.
DR PROSITE; PS00701; RIBOSOMAL_L16_2; 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 INIT_MET 1
FT /note="Removed"
FT CHAIN 2..141
FT /note="50S ribosomal protein L16"
FT /id="PRO_0000062093"
FT STRAND 29..36
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 40..43
FT /evidence="ECO:0007829|PDB:4IO9"
FT HELIX 44..58
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 63..66
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 72..74
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 78..80
FT /evidence="ECO:0007829|PDB:2ZJR"
FT STRAND 84..86
FT /evidence="ECO:0007829|PDB:2ZJR"
FT HELIX 89..91
FT /evidence="ECO:0007829|PDB:3DLL"
FT STRAND 92..95
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 102..109
FT /evidence="ECO:0007829|PDB:5DM6"
FT HELIX 111..123
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 125..127
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 129..132
FT /evidence="ECO:0007829|PDB:5DM6"
SQ SEQUENCE 141 AA; 16095 MW; F6666E00FF79FA5B CRC64;
MLLPKRTKFR KQFRGRMTGD AKGGDYVAFG DYGLIAMEPA WIKSNQIEAC RIVMSRHFRR
GGKIYIRIFP DKPVTKKPAE TRMGKGKGAV EYWVSVVKPG RVMFEVAGVT EEQAKEAFRL
AGHKLPIQTK MVKREVYDEA Q
