RL4_THEMA
ID RL4_THEMA Reviewed; 235 AA.
AC P38516;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2000, sequence version 2.
DT 03-AUG-2022, entry version 141.
DE RecName: Full=50S ribosomal protein L4;
DE AltName: Full=TmaL4;
GN Name=rplD; OrderedLocusNames=TM_1499;
OS Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826
OS / MSB8).
OC Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga.
OX NCBI_TaxID=243274;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=8002596; DOI=10.1128/jb.176.24.7703-7710.1994;
RA Sanangelantoni A.M., Bocchetta M., Cammarano P., Tiboni O.;
RT "Phylogenetic depth of S10 and spc operons: cloning and sequencing of a
RT ribosomal protein gene cluster from the extremely thermophilic bacterium
RT Thermotoga maritima.";
RL J. Bacteriol. 176:7703-7710(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=10360571; DOI=10.1038/20601;
RA Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H.,
RA Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A., McDonald L.A.,
RA Utterback T.R., Malek J.A., Linher K.D., Garrett M.M., Stewart A.M.,
RA Cotton M.D., Pratt M.S., Phillips C.A., Richardson D.L., Heidelberg J.F.,
RA Sutton G.G., Fleischmann R.D., Eisen J.A., White O., Salzberg S.L.,
RA Smith H.O., Venter J.C., Fraser C.M.;
RT "Evidence for lateral gene transfer between Archaea and Bacteria from
RT genome sequence of Thermotoga maritima.";
RL Nature 399:323-329(1999).
RN [3]
RP MUTAGENESIS OF LOOPS SPECIFIC TO T.MARITIMA AND NUCLEIC ACID-BINDING
RP RESIDUES, AND REPLACEMENT STUDIES IN E.COLI.
RX PubMed=12457561; DOI=10.1016/s0300-9084(02)01410-4;
RA Worbs M., Wahl M.C., Lindahl L., Zengel J.M.;
RT "Comparative anatomy of a regulatory ribosomal protein.";
RL Biochimie 84:731-743(2002).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 2-226.
RX PubMed=10698923; DOI=10.1093/emboj/19.5.807;
RA Worbs M., Huber R., Wahl M.C.;
RT "Crystal structure of ribosomal protein L4 shows RNA-binding sites for
RT ribosome incorporation and feedback control of the S10 operon.";
RL EMBO J. 19:807-818(2000).
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. It makes multiple contacts with
CC different domains of the 23S rRNA in the assembled 50S subunit and
CC ribosome (By similarity). {ECO:0000250}.
CC -!- FUNCTION: This protein only weakly controls expression of the E.coli
CC S10 operon. It is incorporated into E.coli ribosomes, however it is not
CC as firmly associated as the endogenous protein.
CC -!- FUNCTION: Forms part of the polypeptide exit tunnel. {ECO:0000250}.
CC -!- SUBUNIT: Part of the 50S ribosomal subunit.
CC -!- DOMAIN: The structure indicates that the N-terminal domain may bind to
CC the 23S rRNA, while the C-terminal domain may bind to the mRNA, which
CC could then be implicated in transcriptional and translational control
CC of the S10 operon. However, it is not known if the S10 operon is
CC controlled in this fashion in this organism.
CC -!- MISCELLANEOUS: A protein containing 11 mutations, chosen as amino acids
CC which probably interact with nucleic acids (K140A, E141Q, Q144K, Q147A,
CC S149E, K151delta, K152delta, I155M, P158G, W159E and K160L), gained the
CC ability to regulate the E.coli S10 operon, suggesting it is now able to
CC mediate contacts of L4 with the S10 mRNA leader in E.coli. This mutant
CC protein did not associate any better with E.coli ribosomes however,
CC indicating a separation of residues interacting with rRNA and mRNA.
CC -!- SIMILARITY: Belongs to the universal ribosomal protein uL4 family.
CC {ECO:0000305}.
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DR EMBL; Z21677; CAA79778.1; -; Genomic_DNA.
DR EMBL; AE000512; AAD36565.1; -; Genomic_DNA.
DR PIR; C72250; C72250.
DR RefSeq; NP_229299.1; NC_000853.1.
DR RefSeq; WP_004081834.1; NZ_CP011107.1.
DR PDB; 1DMG; X-ray; 1.70 A; A=2-226.
DR PDBsum; 1DMG; -.
DR AlphaFoldDB; P38516; -.
DR SMR; P38516; -.
DR STRING; 243274.THEMA_06805; -.
DR DrugBank; DB04272; Citric acid.
DR EnsemblBacteria; AAD36565; AAD36565; TM_1499.
DR KEGG; tma:TM1499; -.
DR eggNOG; COG0088; Bacteria.
DR InParanoid; P38516; -.
DR OMA; PQVHILE; -.
DR OrthoDB; 1572673at2; -.
DR EvolutionaryTrace; P38516; -.
DR Proteomes; UP000008183; Chromosome.
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 DisProt; DP01961; -.
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; Reference proteome; Ribonucleoprotein; Ribosomal protein;
KW RNA-binding; rRNA-binding.
FT CHAIN 1..235
FT /note="50S ribosomal protein L4"
FT /id="PRO_0000129301"
FT REGION 45..75
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 140
FT /note="K->A: Able to regulate the E.coli S10 operon, but
FT does not improve association with E.coli ribosome; when
FT associated with E141Q, Q144K, Q147A, S149E, K151delta,
FT K152delta, I155M, P158G, W159E and K160L."
FT /evidence="ECO:0000269|PubMed:12457561"
FT MUTAGEN 163..165
FT /note="Missing: Little change in either regulation of the
FT E.coli S10 operon or ribosome assembly."
FT /evidence="ECO:0000269|PubMed:12457561"
FT MUTAGEN 184..198
FT /note="Missing: Considerably improves stable incorporation
FT into E.coli ribosomes, however no change in regulation of
FT the E.coli S10 operon."
FT /evidence="ECO:0000269|PubMed:12457561"
FT CONFLICT 74
FT /note="R -> S (in Ref. 1; CAA79778)"
FT /evidence="ECO:0000305"
FT CONFLICT 128
FT /note="D -> H (in Ref. 1; CAA79778)"
FT /evidence="ECO:0000305"
FT CONFLICT 155
FT /note="I -> M (in Ref. 1; CAA79778)"
FT /evidence="ECO:0000305"
FT STRAND 3..7
FT /evidence="ECO:0007829|PDB:1DMG"
FT STRAND 13..18
FT /evidence="ECO:0007829|PDB:1DMG"
FT HELIX 21..24
FT /evidence="ECO:0007829|PDB:1DMG"
FT HELIX 30..41
FT /evidence="ECO:0007829|PDB:1DMG"
FT HELIX 97..119
FT /evidence="ECO:0007829|PDB:1DMG"
FT STRAND 123..127
FT /evidence="ECO:0007829|PDB:1DMG"
FT HELIX 136..145
FT /evidence="ECO:0007829|PDB:1DMG"
FT STRAND 153..157
FT /evidence="ECO:0007829|PDB:1DMG"
FT HELIX 162..171
FT /evidence="ECO:0007829|PDB:1DMG"
FT STRAND 177..181
FT /evidence="ECO:0007829|PDB:1DMG"
FT HELIX 202..207
FT /evidence="ECO:0007829|PDB:1DMG"
FT STRAND 208..214
FT /evidence="ECO:0007829|PDB:1DMG"
FT HELIX 215..225
FT /evidence="ECO:0007829|PDB:1DMG"
SQ SEQUENCE 235 AA; 26631 MW; 40BC63279019B74E CRC64;
MAQVDLLNVK GEKVGTLEIS DFVFNIDPNY DVMWRYVDMQ LSNRRAGTAS TKTRGEVSGG
GRKPWPQKHT GRARHGSIRS PIWRHGGVVH GPKPRDWSKK LNKKMKKLAL RSALSVKYRE
NKLLVLDDLK LERPKTKSLK EILQNLQLSD KKTLIVLPWK EEGYMNVKLS GRNLPDVKVI
IADNPNNSKN GEKAVRIDGL NVFDMLKYDY LVLTRDMVSK IEEVLGNEAG KALTA
