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Q9RXK1 (RL4_DEIRA) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 72. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
50S ribosomal protein L4
Gene names
Name:rplD
Ordered Locus Names:DR_0312
OrganismDeinococcus radiodurans
Taxonomic identifier1299 [NCBI]
Taxonomic lineageBacteriaDeinococcus-ThermusDeinococciDeinococcalesDeinococcaceaeDeinococcus

Protein attributes

Sequence length205 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. HAMAP MF_01328_B

Makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit. HAMAP MF_01328_B

This protein is located close to the polypeptide exit tunnel, and interacts with the modified macrolide azithromycin, which blocks the tunnel. HAMAP MF_01328_B

Subunit structure

Part of the 50S ribosomal subunit. Contacts proteins L15 and L34. Ref.2 Ref.3 Ref.4 Ref.5 Ref.6 Ref.7 Ref.8

Sequence similarities

Belongs to the ribosomal protein L4P family.

Ontologies

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed HAMAP MF_01328_B
Chain2 – 20520450S ribosomal protein L4 HAMAP MF_01328_B
PRO_0000129214

Secondary structure

........................ 205
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9RXK1 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: 760A6C160912477B

FASTA20522,278
        10         20         30         40         50         60 
MAQINVIGQN GGRTIELPLP EVNSGVLHEV VTWQLASRRR GTASTRTRAQ VSKTGRKMYG 

        70         80         90        100        110        120 
QKGTGNARHG DRSVPTFVGG GVAFGPKPRS YDYTLPRQVR QLGLAMAIAS RQEGGKLVAV 

       130        140        150        160        170        180 
DGFDIADAKT KNFISWAKQN GLDGTEKVLL VTDDENTRRA ARNVSWVSVL PVAGVNVYDI 

       190        200 
LRHDRLVIDA AALEIVEEEA GEEQQ 

« Hide

References

« Hide 'large scale' references
[1]"Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1."
White O., Eisen J.A., Heidelberg J.F., Hickey E.K., Peterson J.D., Dodson R.J., Haft D.H., Gwinn M.L., Nelson W.C., Richardson D.L., Moffat K.S., Qin H., Jiang L., Pamphile W., Crosby M., Shen M., Vamathevan J.J., Lam P. expand/collapse author list , McDonald L.A., Utterback T.R., Zalewski C., Makarova K.S., Aravind L., Daly M.J., Minton K.W., Fleischmann R.D., Ketchum K.A., Nelson K.E., Salzberg S.L., Smith H.O., Venter J.C., Fraser C.M.
Science 286:1571-1577(1999) [PubMed: 10567266] [Abstract]
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: 11733066] [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: 11677599] [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: 12535524] [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: 12623020] [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: 12665853] [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: 15059283] [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: 15554968] [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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AE000513 Genomic DNA. Translation: AAF09893.1.
PIRH75533.
RefSeqNP_294035.1. NC_001263.1.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
1PNUX-ray8.70C2-198[»]
1PNYX-ray9.50C2-198[»]
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[»]
ProteinModelPortalQ9RXK1.
SMRQ9RXK1. Positions 2-198.
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID1799571.
GenomeReviewsGene locus DR_0312 in contig AE000513_GR.
KEGGdra:DR_0312.
NMPDRfig|243230.1.peg.494.
PATRIC21628122. VBIDeiRad64572_0478.
TIGRDR_0312.

Phylogenomic databases

HOGENOMHBG545479.
OMAQAHSRQG.
ProtClustDBPRK05319.

Enzyme and pathway databases

BioCycDRAD243230:DR_0312-MONOMER.

Family and domain databases

HAMAPMF_01328_B. Ribosomal_L4_B.
[Tree]
InterProIPR002136. Ribosomal_L4/L1e.
IPR013005. Ribosomal_L4/L1e_bac-type.
IPR023574. Ribosomal_L4_dom.
[Graphical view]
Gene3DG3DSA:3.40.1370.10. G3DSA:3.40.1370.10. 1 hit.
KOK02926.
PANTHERPTHR10746. Ribos_L4_L1E_bac. 1 hit.
PfamPF00573. Ribosomal_L4. 1 hit.
[Graphical view]
SUPFAMSSF52166. Ribosomal_L4/L1E. 1 hit.
TIGRFAMsTIGR03953. RplD_bact. 1 hit.
ProtoNetSearch...

Entry information

Entry nameRL4_DEIRA
AccessionPrimary (citable) accession number: Q9RXK1
Entry history
Integrated into UniProtKB/Swiss-Prot: March 15, 2004
Last sequence update: January 23, 2007
Last modified: January 25, 2012
This is version 72 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

Ribosomal proteins

Ribosomal proteins families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families