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Database: UniProt
Entry: Q9RXY1
LinkDB: Q9RXY1
Original site: Q9RXY1 
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
//
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