RL4_DEIRA
ID RL4_DEIRA Reviewed; 205 AA.
AC Q9RXK1;
DT 15-MAR-2004, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 127.
DE RecName: Full=50S ribosomal protein L4;
GN Name=rplD; OrderedLocusNames=DR_0312;
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: One of the primary rRNA binding proteins, this protein
CC initially binds near the 5'-end of the 23S rRNA. It is important during
CC the early stages of 50S assembly (By similarity). {ECO:0000250}.
CC -!- FUNCTION: Makes multiple contacts with different domains of the 23S
CC rRNA in the assembled 50S subunit.
CC -!- FUNCTION: This protein is located close to the polypeptide exit tunnel,
CC and interacts with the modified macrolide azithromycin, which blocks
CC the tunnel.
CC -!- SUBUNIT: Part of the 50S ribosomal subunit. Contacts proteins L15 and
CC L34. {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 uL4 family.
CC {ECO:0000305}.
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DR EMBL; AE000513; AAF09893.1; -; Genomic_DNA.
DR PIR; H75533; H75533.
DR RefSeq; NP_294035.1; NC_001263.1.
DR RefSeq; WP_010886957.1; NZ_CP015081.1.
DR PDB; 1J5A; X-ray; 3.50 A; K=1-205.
DR PDB; 1JZX; X-ray; 3.10 A; K=1-205.
DR PDB; 1JZY; X-ray; 3.50 A; K=1-205.
DR PDB; 1JZZ; X-ray; 3.80 A; K=1-205.
DR PDB; 1K01; X-ray; 3.50 A; K=1-205.
DR PDB; 1NKW; X-ray; 3.10 A; C=1-205.
DR PDB; 1NWX; X-ray; 3.50 A; C=2-205.
DR PDB; 1NWY; X-ray; 3.30 A; C=2-205.
DR PDB; 1SM1; X-ray; 3.42 A; C=1-205.
DR PDB; 1XBP; X-ray; 3.50 A; C=2-205.
DR PDB; 2ZJP; X-ray; 3.70 A; C=1-205.
DR PDB; 2ZJQ; X-ray; 3.30 A; C=1-205.
DR PDB; 2ZJR; X-ray; 2.91 A; C=1-205.
DR PDB; 3CF5; X-ray; 3.30 A; C=1-205.
DR PDB; 3DLL; X-ray; 3.50 A; C=1-205.
DR PDB; 3PIO; X-ray; 3.25 A; C=1-205.
DR PDB; 3PIP; X-ray; 3.45 A; C=1-205.
DR PDB; 4IO9; X-ray; 3.20 A; C=1-205.
DR PDB; 4IOA; X-ray; 3.20 A; C=1-205.
DR PDB; 4IOC; X-ray; 3.60 A; C=1-205.
DR PDB; 4U67; X-ray; 3.65 A; C=1-205.
DR PDB; 4V49; X-ray; 8.70 A; C=2-198.
DR PDB; 4V4A; X-ray; 9.50 A; C=2-198.
DR PDB; 4WFN; X-ray; 3.54 A; C=1-205.
DR PDB; 5DM6; X-ray; 2.90 A; C=2-198.
DR PDB; 5DM7; X-ray; 3.00 A; C=2-198.
DR PDB; 5JVG; X-ray; 3.43 A; C=1-205.
DR PDB; 5JVH; X-ray; 3.58 A; C=1-205.
DR PDB; 7A0R; X-ray; 3.30 A; C=2-198.
DR PDB; 7A0S; X-ray; 3.22 A; C=1-205.
DR PDB; 7A18; X-ray; 3.40 A; C=2-196.
DR PDBsum; 1J5A; -.
DR PDBsum; 1JZX; -.
DR PDBsum; 1JZY; -.
DR PDBsum; 1JZZ; -.
DR PDBsum; 1K01; -.
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; 4WFN; -.
DR PDBsum; 5DM6; -.
DR PDBsum; 5DM7; -.
DR PDBsum; 5JVG; -.
DR PDBsum; 5JVH; -.
DR PDBsum; 7A0R; -.
DR PDBsum; 7A0S; -.
DR PDBsum; 7A18; -.
DR AlphaFoldDB; Q9RXK1; -.
DR SMR; Q9RXK1; -.
DR IntAct; Q9RXK1; 1.
DR STRING; 243230.DR_0312; -.
DR EnsemblBacteria; AAF09893; AAF09893; DR_0312.
DR KEGG; dra:DR_0312; -.
DR PATRIC; fig|243230.17.peg.478; -.
DR eggNOG; COG0088; Bacteria.
DR HOGENOM; CLU_041575_5_1_0; -.
DR InParanoid; Q9RXK1; -.
DR OMA; PQVHILE; -.
DR OrthoDB; 1572673at2; -.
DR EvolutionaryTrace; Q9RXK1; -.
DR Proteomes; UP000002524; Chromosome I.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProt.
DR GO; GO:0005840; C:ribosome; IEA:UniProtKB-KW.
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:0006412; P:translation; IEA:UniProtKB-UniRule.
DR Gene3D; 3.40.1370.10; -; 1.
DR HAMAP; MF_01328_B; Ribosomal_L4_B; 1.
DR InterPro; IPR002136; Ribosomal_L4/L1e.
DR InterPro; IPR023574; Ribosomal_L4_dom_sf.
DR InterPro; IPR013005; Ribosomal_uL4/L1e.
DR PANTHER; PTHR10746; PTHR10746; 1.
DR Pfam; PF00573; Ribosomal_L4; 1.
DR SUPFAM; SSF52166; SSF52166; 1.
DR TIGRFAMs; TIGR03953; rplD_bact; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Reference proteome;
KW Ribonucleoprotein; Ribosomal protein; RNA-binding; rRNA-binding.
FT INIT_MET 1
FT /note="Removed"
FT CHAIN 2..205
FT /note="50S ribosomal protein L4"
FT /id="PRO_0000129214"
FT STRAND 6..8
FT /evidence="ECO:0007829|PDB:5DM7"
FT TURN 19..21
FT /evidence="ECO:0007829|PDB:5DM6"
FT HELIX 24..36
FT /evidence="ECO:0007829|PDB:5DM6"
FT TURN 48..50
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 61..66
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 72..74
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 77..80
FT /evidence="ECO:0007829|PDB:5DM7"
FT HELIX 97..112
FT /evidence="ECO:0007829|PDB:5DM6"
FT TURN 113..115
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 117..122
FT /evidence="ECO:0007829|PDB:5DM6"
FT TURN 123..125
FT /evidence="ECO:0007829|PDB:4IO9"
FT TURN 126..128
FT /evidence="ECO:0007829|PDB:5DM6"
FT HELIX 130..139
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 144..146
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 148..153
FT /evidence="ECO:0007829|PDB:5DM6"
FT HELIX 155..161
FT /evidence="ECO:0007829|PDB:5DM6"
FT TURN 164..166
FT /evidence="ECO:0007829|PDB:4IOA"
FT STRAND 167..171
FT /evidence="ECO:0007829|PDB:5DM6"
FT HELIX 177..182
FT /evidence="ECO:0007829|PDB:5DM6"
FT STRAND 183..190
FT /evidence="ECO:0007829|PDB:5DM6"
FT TURN 191..197
FT /evidence="ECO:0007829|PDB:5DM6"
SQ SEQUENCE 205 AA; 22278 MW; 760A6C160912477B CRC64;
MAQINVIGQN GGRTIELPLP EVNSGVLHEV VTWQLASRRR GTASTRTRAQ VSKTGRKMYG
QKGTGNARHG DRSVPTFVGG GVAFGPKPRS YDYTLPRQVR QLGLAMAIAS RQEGGKLVAV
DGFDIADAKT KNFISWAKQN GLDGTEKVLL VTDDENTRRA ARNVSWVSVL PVAGVNVYDI
LRHDRLVIDA AALEIVEEEA GEEQQ
