Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

Q5SHN9 (RL4_THET8) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 88. 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
Alternative name(s):
L1e
Gene names
Name:rplD
Ordered Locus Names:TTHA1691
OrganismThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) [Reference proteome] [HAMAP]
Taxonomic identifier300852 [NCBI]
Taxonomic lineageBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus

Protein attributes

Sequence length210 AA.
Sequence statusComplete.
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. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome By similarity. HAMAP-Rule MF_01328_B

Forms part of the polypeptide exit tunnel By similarity. HAMAP-Rule MF_01328_B

This protein can be incorporated into E.coli ribosomes in vivo, which resulted in decreased peptidyltransferase (Ptase) activity of the hybrid ribosomes. The hybrid 50S subunits associate less well with 30S subunits to form the ribosome. HAMAP-Rule MF_01328_B

Subunit structure

Part of the 50S ribosomal subunit.

Post-translational modification

The N-terminus is blocked. HAMAP-Rule MF_01328_B

Sequence similarities

Belongs to the ribosomal protein L4P family.

Mass spectrometry

Molecular mass is 22724 Da from positions 1 - 210. Determined by MALDI. Ref.5

Ontologies

Keywords
   LigandRNA-binding
rRNA-binding
   Molecular functionRibonucleoprotein
Ribosomal protein
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processtranslation

Inferred from electronic annotation. Source: UniProtKB-HAMAP

   Cellular_componentribosome

Inferred from electronic annotation. Source: UniProtKB-KW

   Molecular_functionrRNA binding

Inferred from electronic annotation. Source: UniProtKB-HAMAP

structural constituent of ribosome

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 21021050S ribosomal protein L4 HAMAP-Rule MF_01328_B
PRO_0000129300

Experimental info

Mutagenesis551G → A: Increases Ptase activity of hybrid ribosomes to a value greater than that of pure E.coli ribosomes. Increases binding of a tRNA analog to the P site. Ref.4
Mutagenesis551G → S: No effect on Ptase activity of hybrid ribosomes. No change in binding of a tRNA analog to the A or P site. Ref.4
Mutagenesis561E → A: Further decreases Ptase activity in E.coli hybrid ribosomes. Significantly decreases binding of a tRNA analog to the A or P site. Ref.4
Mutagenesis561E → Q: Restores Ptase activity of hybrid ribosomes to that of pure E.coli ribosomes. Significantly increases binding of a tRNA analog to the P site. Ref.4
Sequence conflict19 – 202EL → DV in AAA97862. Ref.1

Secondary structure

......................................... 210
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q5SHN9 [UniParc].

Last modified December 21, 2004. Version 1.
Checksum: BFB99AC179C110B4

FASTA21023,235
        10         20         30         40         50         60 
MKEVAVYQIP VLSPSGRREL AADLPAEINP HLLWEVVRWQ LAKRRRGTAS TKTRGEVAYS 

        70         80         90        100        110        120 
GRKIWPQKHT GRARHGDIGA PIFVGGGVVF GPKPRDYSYT LPKKVRKKGL AMAVADRARE 

       130        140        150        160        170        180 
GKLLLVEAFA GVNGKTKEFL AWAKEAGLDG SESVLLVTGN ELVRRAARNL PWVVTLAPEG 

       190        200        210 
LNVYDIVRTE RLVMDLDAWE VFQNRIGGEA 

« Hide

References

« Hide 'large scale' references
[1]"Direct linkage of str-, S10- and spc-related gene clusters in Thermus thermophilus HB8, and sequences of ribosomal proteins L4 and S10."
Pfeiffer T., Jorcke D., Feltens R., Hartmann R.K.
Gene 167:141-145(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"Complete genome sequence of Thermus thermophilus HB8."
Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T., Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.
Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: HB8 / ATCC 27634 / DSM 579.
[3]"Identification of the 50S ribosomal proteins from the eubacterium Thermus thermophilus."
Katsani K.R., Tsiboli P., Anagnostopoulos K., Urlaub H., Choli-Papadopoulou T.
Biol. Chem. 381:1079-1087(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 6-17, BLOCKAGE OF N-TERMINUS.
[4]"On the structural and functional importance of the highly conserved Glu56 of Thermus thermophilus L4 ribosomal protein."
Leontiadou F., Xaplanteri M.A., Papadopoulos G., Gerassimou C., Kalpaxis D.L., Choli-Papadopoulou T.
J. Mol. Biol. 332:73-84(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF GLY-55 AND GLU-56.
[5]"Extending ribosomal protein identifications to unsequenced bacterial strains using matrix-assisted laser desorption/ionization mass spectrometry."
Suh M.-J., Hamburg D.M., Gregory S.T., Dahlberg A.E., Limbach P.A.
Proteomics 5:4818-4831(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: MASS SPECTROMETRY.
[6]"The path of messenger RNA through the ribosome."
Yusupova G.Z., Yusupov M.M., Cate J.H.D., Noller H.F.
Cell 106:233-241(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (5.0 ANGSTROMS) OF THE RIBOSOME.
[7]"Crystal structure of the ribosome at 5.5 A resolution."
Yusupov M.M., Yusupova G.Z., Baucom A., Lieberman K., Earnest T.N., Cate J.H.D., Noller H.F.
Science 292:883-896(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (5.5 ANGSTROMS) OF THE RIBOSOME.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U36480 Genomic DNA. Translation: AAA97862.1.
AP008226 Genomic DNA. Translation: BAD71514.1.
RefSeqYP_144957.2. NC_006461.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1GIYX-ray5.50F1-210[»]
1TWVmodel-D1-210[»]
1YL3X-ray5.50F1-210[»]
2HGJX-ray5.00F1-210[»]
2HGQX-ray5.50F1-210[»]
2HGUX-ray4.51F1-210[»]
2J01X-ray2.80F1-210[»]
2J03X-ray2.80F1-210[»]
2V47X-ray3.80F1-210[»]
2V49X-ray3.80F1-210[»]
2WDIX-ray3.30F1-210[»]
2WDJX-ray3.30F1-210[»]
2WDLX-ray3.50F1-210[»]
2WDNX-ray3.50F1-210[»]
2WH2X-ray3.45F1-210[»]
2WH4X-ray3.45F1-210[»]
2WRJX-ray3.60F1-210[»]
2WRLX-ray3.60F1-210[»]
2WROX-ray3.60F1-210[»]
2WRRX-ray3.60F1-210[»]
2X9SX-ray3.10F1-210[»]
2X9UX-ray3.10F1-210[»]
2XG0X-ray3.20F1-210[»]
2XG2X-ray3.20F1-210[»]
2XQEX-ray3.10F1-210[»]
2XTGelectron microscopy7.80F1-210[»]
2XUXelectron microscopy7.60F1-210[»]
2Y0VX-ray3.10F1-210[»]
2Y0XX-ray3.10F1-210[»]
2Y0ZX-ray3.10F1-210[»]
2Y11X-ray3.10F1-210[»]
2Y13X-ray3.10F1-210[»]
2Y15X-ray3.10F1-210[»]
2Y17X-ray3.10F1-210[»]
2Y19X-ray3.10F1-210[»]
3F1FX-ray3.00F1-210[»]
3F1HX-ray3.00F1-210[»]
3FINelectron microscopy6.40F1-208[»]
3HUXX-ray3.10F1-210[»]
3HUZX-ray3.10F1-210[»]
3I8FX-ray3.10F1-210[»]
3I8IX-ray3.10F1-210[»]
3I9CX-ray3.50F1-210[»]
3I9EX-ray3.50F1-210[»]
3KIRX-ray3.30F1-210[»]
3KITX-ray3.30F1-210[»]
3KIWX-ray3.60F1-210[»]
3KIYX-ray3.60F1-210[»]
3KNIX-ray3.00F1-210[»]
3KNKX-ray3.00F1-210[»]
3KNMX-ray3.45F1-210[»]
3KNOX-ray3.45F1-210[»]
3OHJX-ray3.00F1-210[»]
3OHZX-ray3.00F1-210[»]
3OI5X-ray3.10F1-210[»]
3TVEX-ray3.10F6-207[»]
3TVHX-ray3.10F1-208[»]
3UXQX-ray3.20F6-210[»]
3UXRX-ray3.20F6-210[»]
3UYEX-ray3.00F1-210[»]
3UYGX-ray3.00F1-210[»]
3UZ1X-ray3.30F1-210[»]
3UZ2X-ray3.30F1-210[»]
3UZ8X-ray3.00F1-210[»]
3UZ9X-ray3.00F1-210[»]
3UZFX-ray3.30F1-210[»]
3UZHX-ray3.30F1-210[»]
3UZKX-ray3.30F1-210[»]
3UZNX-ray3.30F1-210[»]
3V23X-ray3.00F1-210[»]
3V25X-ray3.00F1-210[»]
3V27X-ray3.10F1-210[»]
3V29X-ray3.10F1-210[»]
3V2DX-ray2.70F1-210[»]
3V2FX-ray2.70F1-210[»]
3V6WX-ray3.90F1-210[»]
3V6XX-ray3.90F1-210[»]
3ZN9X-ray3.10F1-210[»]
3ZNEX-ray3.10F1-210[»]
3ZVPX-ray3.80F1-210[»]
4ABSX-ray3.10F1-210[»]
4B8GX-ray3.70F1-210[»]
4B8IX-ray3.70F1-210[»]
4BTDX-ray2.95F1-210[»]
4BYCX-ray3.35F1-210[»]
4BYEX-ray3.35F1-210[»]
4DHAX-ray3.20F1-210[»]
4DHCX-ray3.20F1-210[»]
4EJBX-ray3.52F1-210[»]
4EJCX-ray3.52F1-210[»]
4G5LX-ray3.30F1-210[»]
4G5NX-ray3.30F1-210[»]
4G5UX-ray3.10F1-210[»]
4G5WX-ray3.10F1-210[»]
4JUXX-ray2.86F1-210[»]
4K0MX-ray3.30F1-207[»]
4K0QX-ray3.30F1-207[»]
4NVVX-ray3.00F1-210[»]
4NVXX-ray3.00F1-210[»]
4NVZX-ray3.10F1-210[»]
4NW1X-ray3.10F1-210[»]
ProteinModelPortalQ5SHN9.
SMRQ5SHN9. Positions 3-210.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING300852.TTHA1691.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaBAD71514; BAD71514; BAD71514.
GeneID3167923.
KEGGttj:TTHA1691.
PATRIC23958337. VBITheThe93045_1661.

Phylogenomic databases

eggNOGCOG0088.
HOGENOMHOG000248767.
KOK02926.
OMARSIMANQ.
OrthoDBEOG6M0T9G.

Enzyme and pathway databases

BioCycTTHE300852:GH8R-1730-MONOMER.

Family and domain databases

Gene3D3.40.1370.10. 1 hit.
HAMAPMF_01328_B. Ribosomal_L4_B.
InterProIPR002136. Ribosomal_L4/L1e.
IPR013005. Ribosomal_L4/L1e_bac-type.
IPR023574. Ribosomal_L4_dom.
[Graphical view]
PANTHERPTHR10746. PTHR10746. 1 hit.
PfamPF00573. Ribosomal_L4. 1 hit.
[Graphical view]
SUPFAMSSF52166. SSF52166. 1 hit.
TIGRFAMsTIGR03953. rplD_bact. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceQ5SHN9.

Entry information

Entry nameRL4_THET8
AccessionPrimary (citable) accession number: Q5SHN9
Entry history
Integrated into UniProtKB/Swiss-Prot: March 29, 2005
Last sequence update: December 21, 2004
Last modified: July 9, 2014
This is version 88 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Ribosomal proteins

Ribosomal proteins families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references