RL13_DEIRA
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 25-MAY-2022, entry version 132.
DE RecName: Full=50S ribosomal protein L13;
GN Name=rplM; OrderedLocusNames=DR_0174;
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, PROTEIN SEQUENCE
RP OF 1-5, AND CONTACTS WITH 23S RRNA.
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 protein is one of the early assembly proteins of the 50S
CC ribosomal subunit (By similarity). Binds to the 23S rRNA.
CC {ECO:0000250}.
CC -!- SUBUNIT: Part of the 50S ribosomal subunit. Contacts proteins L3 and
CC L20. {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 uL13 family.
CC {ECO:0000305}.
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DR EMBL; AE000513; AAF09760.1; -; Genomic_DNA.
DR PIR; E75552; E75552.
DR RefSeq; NP_293898.2; NC_001263.1.
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 PDB; 7A0R; X-ray; 3.30 A; G=30-172.
DR PDB; 7A0S; X-ray; 3.22 A; G=30-172.
DR PDB; 7A18; X-ray; 3.40 A; G=30-171.
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; Q9RXY1; -.
DR SMR; Q9RXY1; -.
DR IntAct; Q9RXY1; 1.
DR STRING; 243230.DR_0174; -.
DR EnsemblBacteria; AAF09760; AAF09760; DR_0174.
DR KEGG; dra:DR_0174; -.
DR PATRIC; fig|243230.17.peg.338; -.
DR eggNOG; COG0102; Bacteria.
DR HOGENOM; CLU_082184_2_2_0; -.
DR InParanoid; Q9RXY1; -.
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; Direct protein sequencing; Reference proteome;
KW Ribonucleoprotein; Ribosomal protein; RNA-binding; rRNA-binding.
FT CHAIN 1..174
FT /note="50S ribosomal protein L13"
FT /id="PRO_0000133733"
FT REGION 1..22
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 153..174
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT STRAND 41..45
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 47..50
FT /evidence="ECO:0007829|PDB:2ZJQ"
FT HELIX 51..63
FT /evidence="ECO:0007829|PDB:5DM6"
FT TURN 64..66
FT /evidence="ECO:0007829|PDB:7A18"
FT STRAND 72..74
FT /evidence="ECO:0007829|PDB:2ZJR"
FT STRAND 79..83
FT /evidence="ECO:0007829|PDB:5DM6"
FT HELIX 85..87
FT /evidence="ECO:0007829|PDB:5DM6"
FT TURN 91..93
FT /evidence="ECO:0007829|PDB:7A0R"
FT HELIX 94..97
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 99..102
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 107..109
FT /evidence="ECO:0007829|PDB:7A0R"
FT STRAND 111..114
FT /evidence="ECO:0007829|PDB:5DM6"
FT HELIX 115..121
FT /evidence="ECO:0007829|PDB:5DM6"
FT HELIX 124..133
FT /evidence="ECO:0007829|PDB:5DM6"
FT HELIX 139..145
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 148..150
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 154..156
FT /evidence="ECO:0007829|PDB:4IOA"
FT HELIX 159..161
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 164..166
FT /evidence="ECO:0007829|PDB:7A18"
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
