ID RL13_DEIRA Reviewed; 174 AA.
AC Q9RXY1;
DT 15-MAR-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 16-OCT-2019, entry version 124.
DE RecName: Full=50S ribosomal protein L13;
GN Name=rplM; OrderedLocusNames=DR_0174;
OS Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 /
OS LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422).
OC Bacteria; Deinococcus-Thermus; Deinococci; Deinococcales;
OC Deinococcaceae; 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 /
RC NCIMB 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
RT radiodurans R1.";
RL Science 286:1571-1577(1999).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF THE 50S SUBUNIT, PROTEIN
RP SEQUENCE OF 1-5, AND CONTACTS WITH 23S RRNA.
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 /
RC NCIMB 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
RT mesophilic eubacterium.";
RL Cell 107:679-688(2001).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX
RP WITH FIVE ANTIBIOTICS.
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 /
RC NCIMB 9279 / R1 / VKM B-1422;
RX PubMed=11677599; DOI=10.1038/35101544;
RA Schluenzen F., Zarivach R., Harms J., Bashan A., Tocilj A.,
RA Albrecht R., 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
RP WITH TRNA MIMICS.
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 /
RC NCIMB 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.,
RA Kessler M., Yonath A.;
RT "Structural basis of the ribosomal machinery for peptide bond
RT formation, 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
RP WITH MODIFIED MACROLIDE ANTIBIOTICS.
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 /
RC NCIMB 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
RT azalides.";
RL Structure 11:329-338(2003).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (3.4 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX
RP WITH TROLEANDOMYCIN.
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 /
RC NCIMB 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
RP WITH THE STREPTOGRAMINS QUINUPRISTIN AND DALFOPRISTIN.
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 /
RC NCIMB 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
RT induced by the synergistic action of the streptogramins dalfopristin
RT and quinupristin.";
RL BMC Biol. 2:4-4(2004).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (3.5 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX
RP WITH TIAMULIN.
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 /
RC NCIMB 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
RT of the 50S ribosomal subunit from Deinococcus radiodurans in complex
RT with tiamulin.";
RL Mol. Microbiol. 54:1287-1294(2004).
CC -!- FUNCTION: This protein is one of the early assembly proteins of
CC the 50S ribosomal subunit (By similarity). Binds to the 23S rRNA.
CC {ECO:0000250}.
CC -!- SUBUNIT: Part of the 50S ribosomal subunit. Contacts proteins L3
CC and L20. {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 uL13
CC family. {ECO:0000305}.
DR EMBL; AE000513; AAF09760.1; -; Genomic_DNA.
DR PIR; E75552; E75552.
DR RefSeq; NP_293898.2; NC_001263.1.
DR PDB; 1GS2; Model; -; H=30-171.
DR PDB; 1NKW; X-ray; 3.10 A; H=1-174.
DR PDB; 1NWX; X-ray; 3.50 A; H=1-174.
DR PDB; 1NWY; X-ray; 3.30 A; H=1-174.
DR PDB; 1SM1; X-ray; 3.42 A; H=1-174.
DR PDB; 1XBP; X-ray; 3.50 A; H=1-174.
DR PDB; 2ZJP; X-ray; 3.70 A; G=1-174.
DR PDB; 2ZJQ; X-ray; 3.30 A; G=1-174.
DR PDB; 2ZJR; X-ray; 2.91 A; G=1-174.
DR PDB; 3CF5; X-ray; 3.30 A; G=1-174.
DR PDB; 3DLL; X-ray; 3.50 A; G=1-174.
DR PDB; 3PIO; X-ray; 3.25 A; G=1-174.
DR PDB; 3PIP; X-ray; 3.45 A; G=1-174.
DR PDB; 4IO9; X-ray; 3.20 A; G=1-174.
DR PDB; 4IOA; X-ray; 3.20 A; G=1-174.
DR PDB; 4IOC; X-ray; 3.60 A; G=1-174.
DR PDB; 4U67; X-ray; 3.65 A; G=1-174.
DR PDB; 4V49; X-ray; 8.70 A; H=29-171.
DR PDB; 4V4A; X-ray; 9.50 A; H=29-171.
DR PDB; 4V4G; X-ray; 11.50 A; K=29-171.
DR PDB; 4WFN; X-ray; 3.54 A; G=1-174.
DR PDB; 5DM6; X-ray; 2.90 A; G=30-171.
DR PDB; 5DM7; X-ray; 3.00 A; G=30-171.
DR PDB; 5JVG; X-ray; 3.43 A; G=1-174.
DR PDB; 5JVH; X-ray; 3.58 A; G=1-174.
DR PDBsum; 1GS2; -.
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 SMR; Q9RXY1; -.
DR STRING; 243230.DR_0174; -.
DR EnsemblBacteria; AAF09760; AAF09760; DR_0174.
DR GeneID; 1799575; -.
DR KEGG; dra:DR_0174; -.
DR PATRIC; fig|243230.17.peg.338; -.
DR eggNOG; ENOG4108UM5; Bacteria.
DR eggNOG; COG0102; LUCA.
DR HOGENOM; HOG000225286; -.
DR InParanoid; Q9RXY1; -.
DR KO; K02871; -.
DR OMA; DFVVIIN; -.
DR OrthoDB; 1822215at2; -.
DR EvolutionaryTrace; Q9RXY1; -.
DR Proteomes; UP000002524; Chromosome I.
DR GO; GO:0022625; C:cytosolic large ribosomal subunit; IBA:GO_Central.
DR GO; GO:0005840; C:ribosome; IBA:GO_Central.
DR GO; GO:0003729; F:mRNA binding; IBA:GO_Central.
DR GO; GO:0019843; F:rRNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003735; F:structural constituent of ribosome; IBA:GO_Central.
DR GO; GO:0017148; P:negative regulation of translation; IBA:GO_Central.
DR GO; GO:0006412; P:translation; IEA:UniProtKB-UniRule.
DR CDD; cd00392; Ribosomal_L13; 1.
DR Gene3D; 3.90.1180.10; -; 1.
DR HAMAP; MF_01366; Ribosomal_L13; 1.
DR InterPro; IPR005822; Ribosomal_L13.
DR InterPro; IPR005823; Ribosomal_L13_bac-type.
DR InterPro; IPR023563; Ribosomal_L13_CS.
DR InterPro; IPR036899; Ribosomal_L13_sf.
DR PANTHER; PTHR11545; PTHR11545; 1.
DR Pfam; PF00572; Ribosomal_L13; 1.
DR PIRSF; PIRSF002181; Ribosomal_L13; 1.
DR SUPFAM; SSF52161; SSF52161; 1.
DR TIGRFAMs; TIGR01066; rplM_bact; 1.
DR PROSITE; PS00783; RIBOSOMAL_L13; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Complete proteome; Direct protein sequencing;
KW Reference proteome; Ribonucleoprotein; Ribosomal protein; RNA-binding;
KW rRNA-binding.
FT CHAIN 1 174 50S ribosomal protein L13.
FT /FTId=PRO_0000133733.
FT STRAND 41 45 {ECO:0000244|PDB:5DM6}.
FT STRAND 47 50 {ECO:0000244|PDB:2ZJQ}.
FT HELIX 51 63 {ECO:0000244|PDB:5DM6}.
FT STRAND 72 74 {ECO:0000244|PDB:2ZJR}.
FT STRAND 79 83 {ECO:0000244|PDB:5DM6}.
FT HELIX 85 87 {ECO:0000244|PDB:5DM6}.
FT HELIX 94 97 {ECO:0000244|PDB:5DM6}.
FT STRAND 99 102 {ECO:0000244|PDB:5DM6}.
FT STRAND 105 108 {ECO:0000244|PDB:5JVG}.
FT STRAND 111 114 {ECO:0000244|PDB:5DM6}.
FT HELIX 115 121 {ECO:0000244|PDB:5DM6}.
FT HELIX 124 133 {ECO:0000244|PDB:5DM6}.
FT HELIX 139 145 {ECO:0000244|PDB:5DM6}.
FT STRAND 148 150 {ECO:0000244|PDB:5DM6}.
FT STRAND 154 156 {ECO:0000244|PDB:4IOA}.
FT HELIX 159 161 {ECO:0000244|PDB:5DM6}.
FT STRAND 166 168 {ECO:0000244|PDB:5JVG}.
SQ SEQUENCE 174 AA; 19190 MW; 9F7B977882CB715E CRC64;
MAFPDTDVSP PRGGPSSPAK SPLLRSFKVK TYIPKNDEQN WVVVDASGVP LGRLATLIAS
RIRGKHRPDF TPNMIQGDFV VVINAAQVAL TGKKLDDKVY TRYTGYQGGL KTETAREALS
KHPERVIEHA VFGMLPKGRQ GRAMHTRLKV YAGETHPHSA QKPQVLKTQP LEVK
//
