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Protein

50S ribosomal protein L4

Gene

rplD

Organism
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly (By similarity).By similarity
Makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit.
This protein is located close to the polypeptide exit tunnel, and interacts with the modified macrolide azithromycin, which blocks the tunnel.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein, Ribosomal protein

Keywords - Ligandi

RNA-binding, rRNA-binding

Enzyme and pathway databases

BioCyciDRAD243230:GH46-322-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
50S ribosomal protein L4
Gene namesi
Name:rplD
Ordered Locus Names:DR_0312
OrganismiDeinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Taxonomic identifieri243230 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciDeinococcalesDeinococcaceaeDeinococcus
Proteomesi
  • UP000002524 Componenti: Chromosome I

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved
Chaini2 – 20520450S ribosomal protein L4PRO_0000129214Add
BLAST

Proteomic databases

PRIDEiQ9RXK1.

Interactioni

Subunit structurei

Part of the 50S ribosomal subunit. Contacts proteins L15 and L34.6 Publications

Protein-protein interaction databases

STRINGi243230.DR_0312.

Structurei

Secondary structure

1
205
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi6 – 83Combined sources
Turni19 – 213Combined sources
Helixi24 – 3613Combined sources
Turni48 – 503Combined sources
Beta strandi61 – 666Combined sources
Beta strandi72 – 743Combined sources
Beta strandi77 – 804Combined sources
Helixi97 – 11216Combined sources
Turni113 – 1153Combined sources
Beta strandi117 – 1226Combined sources
Turni123 – 1253Combined sources
Turni126 – 1283Combined sources
Helixi130 – 13910Combined sources
Beta strandi144 – 1463Combined sources
Beta strandi148 – 1536Combined sources
Helixi155 – 1617Combined sources
Turni164 – 1663Combined sources
Beta strandi167 – 1715Combined sources
Helixi177 – 1826Combined sources
Beta strandi183 – 1908Combined sources
Turni191 – 1977Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1J5AX-ray3.50K1-205[»]
1JZXX-ray3.10K1-205[»]
1JZYX-ray3.50K1-205[»]
1JZZX-ray3.80K1-205[»]
1K01X-ray3.50K1-205[»]
1NKWX-ray3.10C1-205[»]
1NWXX-ray3.50C2-205[»]
1NWYX-ray3.30C2-205[»]
1SM1X-ray3.42C1-205[»]
1XBPX-ray3.50C2-205[»]
2ZJPX-ray3.70C1-205[»]
2ZJQX-ray3.30C1-205[»]
2ZJRX-ray2.91C1-205[»]
3CF5X-ray3.30C1-205[»]
3DLLX-ray3.50C1-205[»]
3PIOX-ray3.25C1-205[»]
3PIPX-ray3.45C1-205[»]
4IO9X-ray3.20C1-205[»]
4IOAX-ray3.20C1-205[»]
4IOCX-ray3.60C1-205[»]
4U67X-ray3.65C1-205[»]
4V49X-ray8.70C2-198[»]
4V4AX-ray9.50C2-198[»]
4WFNX-ray3.54C1-205[»]
5DM6X-ray2.90C2-198[»]
5DM7X-ray3.00C2-198[»]
ProteinModelPortaliQ9RXK1.
SMRiQ9RXK1. Positions 2-198.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9RXK1.

Family & Domainsi

Sequence similaritiesi

Belongs to the ribosomal protein L4P family.Curated

Phylogenomic databases

eggNOGiENOG4106U5A. Bacteria.
COG0088. LUCA.
HOGENOMiHOG000248767.
InParanoidiQ9RXK1.
KOiK02926.
OMAiTWKSLRN.
OrthoDBiEOG6M0T9G.

Family and domain databases

Gene3Di3.40.1370.10. 1 hit.
HAMAPiMF_01328_B. Ribosomal_L4_B.
InterProiIPR002136. Ribosomal_L4/L1e.
IPR023574. Ribosomal_L4_dom.
IPR013005. Ribosomal_uL4/L1e.
[Graphical view]
PANTHERiPTHR10746. PTHR10746. 1 hit.
PfamiPF00573. Ribosomal_L4. 1 hit.
[Graphical view]
SUPFAMiSSF52166. SSF52166. 1 hit.
TIGRFAMsiTIGR03953. rplD_bact. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q9RXK1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAQINVIGQN GGRTIELPLP EVNSGVLHEV VTWQLASRRR GTASTRTRAQ
60 70 80 90 100
VSKTGRKMYG QKGTGNARHG DRSVPTFVGG GVAFGPKPRS YDYTLPRQVR
110 120 130 140 150
QLGLAMAIAS RQEGGKLVAV DGFDIADAKT KNFISWAKQN GLDGTEKVLL
160 170 180 190 200
VTDDENTRRA ARNVSWVSVL PVAGVNVYDI LRHDRLVIDA AALEIVEEEA

GEEQQ
Length:205
Mass (Da):22,278
Last modified:January 23, 2007 - v3
Checksum:i760A6C160912477B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000513 Genomic DNA. Translation: AAF09893.1.
PIRiH75533.
RefSeqiNP_294035.1. NC_001263.1.
WP_010886957.1. NC_001263.1.

Genome annotation databases

EnsemblBacteriaiAAF09893; AAF09893; DR_0312.
GeneIDi1799571.
KEGGidra:DR_0312.
PATRICi21628122. VBIDeiRad64572_0478.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000513 Genomic DNA. Translation: AAF09893.1.
PIRiH75533.
RefSeqiNP_294035.1. NC_001263.1.
WP_010886957.1. NC_001263.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1J5AX-ray3.50K1-205[»]
1JZXX-ray3.10K1-205[»]
1JZYX-ray3.50K1-205[»]
1JZZX-ray3.80K1-205[»]
1K01X-ray3.50K1-205[»]
1NKWX-ray3.10C1-205[»]
1NWXX-ray3.50C2-205[»]
1NWYX-ray3.30C2-205[»]
1SM1X-ray3.42C1-205[»]
1XBPX-ray3.50C2-205[»]
2ZJPX-ray3.70C1-205[»]
2ZJQX-ray3.30C1-205[»]
2ZJRX-ray2.91C1-205[»]
3CF5X-ray3.30C1-205[»]
3DLLX-ray3.50C1-205[»]
3PIOX-ray3.25C1-205[»]
3PIPX-ray3.45C1-205[»]
4IO9X-ray3.20C1-205[»]
4IOAX-ray3.20C1-205[»]
4IOCX-ray3.60C1-205[»]
4U67X-ray3.65C1-205[»]
4V49X-ray8.70C2-198[»]
4V4AX-ray9.50C2-198[»]
4WFNX-ray3.54C1-205[»]
5DM6X-ray2.90C2-198[»]
5DM7X-ray3.00C2-198[»]
ProteinModelPortaliQ9RXK1.
SMRiQ9RXK1. Positions 2-198.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243230.DR_0312.

Proteomic databases

PRIDEiQ9RXK1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAF09893; AAF09893; DR_0312.
GeneIDi1799571.
KEGGidra:DR_0312.
PATRICi21628122. VBIDeiRad64572_0478.

Phylogenomic databases

eggNOGiENOG4106U5A. Bacteria.
COG0088. LUCA.
HOGENOMiHOG000248767.
InParanoidiQ9RXK1.
KOiK02926.
OMAiTWKSLRN.
OrthoDBiEOG6M0T9G.

Enzyme and pathway databases

BioCyciDRAD243230:GH46-322-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ9RXK1.

Family and domain databases

Gene3Di3.40.1370.10. 1 hit.
HAMAPiMF_01328_B. Ribosomal_L4_B.
InterProiIPR002136. Ribosomal_L4/L1e.
IPR023574. Ribosomal_L4_dom.
IPR013005. Ribosomal_uL4/L1e.
[Graphical view]
PANTHERiPTHR10746. PTHR10746. 1 hit.
PfamiPF00573. Ribosomal_L4. 1 hit.
[Graphical view]
SUPFAMiSSF52166. SSF52166. 1 hit.
TIGRFAMsiTIGR03953. rplD_bact. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
  2. "High resolution structure of the large ribosomal subunit from a mesophilic eubacterium."
    Harms J., Schluenzen F., Zarivach R., Bashan A., Gat S., Agmon I., Bartels H., Franceschi F., Yonath A.
    Cell 107:679-688(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF THE 50S SUBUNIT, PROTEIN SEQUENCE OF 1-6.
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
  3. "Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria."
    Schluenzen F., Zarivach R., Harms J., Bashan A., Tocilj A., Albrecht R., Yonath A., Franceschi F.
    Nature 413:814-821(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH FIVE ANTIBIOTICS.
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
  4. "Structural basis of the ribosomal machinery for peptide bond formation, translocation, and nascent chain progression."
    Bashan A., Agmon I., Zarivach R., Schluenzen F., Harms J., Berisio R., Bartels H., Franceschi F., Auerbach T., Hansen H.A., Kossoy E., Kessler M., Yonath A.
    Mol. Cell 11:91-102(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.5 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH TRNA MIMICS.
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
  5. "Structural basis for the antibiotic activity of ketolides and azalides."
    Schluenzen F., Harms J.M., Franceschi F., Hansen H.A., Bartels H., Zarivach R., Yonath A.
    Structure 11:329-338(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH MODIFIED MACROLIDE ANTIBIOTICS.
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
  6. "Structural insight into the role of the ribosomal tunnel in cellular regulation."
    Berisio R., Schluenzen F., Harms J., Bashan A., Auerbach T., Baram D., Yonath A.
    Nat. Struct. Biol. 10:366-370(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.4 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH TROLEANDOMYCIN.
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
  7. "Alterations at the peptidyl transferase centre of the ribosome induced by the synergistic action of the streptogramins dalfopristin and quinupristin."
    Harms J.M., Schluenzen F., Fucini P., Bartels H., Yonath A.
    BMC Biol. 2:4-4(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.4 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH THE STREPTOGRAMINS QUINUPRISTIN AND DALFOPRISTIN.
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
  8. "Inhibition of peptide bond formation by pleuromutilins: the structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with tiamulin."
    Schluenzen F., Pyetan E., Fucini P., Yonath A., Harms J.M.
    Mol. Microbiol. 54:1287-1294(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.5 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH TIAMULIN.
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.

Entry informationi

Entry nameiRL4_DEIRA
AccessioniPrimary (citable) accession number: Q9RXK1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 15, 2004
Last sequence update: January 23, 2007
Last modified: February 17, 2016
This is version 101 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Ribosomal proteins
    Ribosomal proteins families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.