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Q5SHN9

- RL4_THET8

UniProt

Q5SHN9 - RL4_THET8

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Protein
50S ribosomal protein L4
Gene
rplD, TTHA1691
Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Status
Reviewed - 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. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome By similarity.UniRule annotation
Forms part of the polypeptide exit tunnel By similarity.UniRule annotation
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.UniRule annotation

GO - Molecular functioni

  1. rRNA binding Source: UniProtKB-HAMAP
  2. structural constituent of ribosome Source: InterPro

GO - Biological processi

  1. translation Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein, Ribosomal protein

Keywords - Ligandi

RNA-binding, rRNA-binding

Enzyme and pathway databases

BioCyciTTHE300852:GH8R-1730-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
50S ribosomal protein L4
Alternative name(s):
L1e
Gene namesi
Name:rplD
Ordered Locus Names:TTHA1691
OrganismiThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Taxonomic identifieri300852 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
ProteomesiUP000000532: Chromosome

Subcellular locationi

GO - Cellular componenti

  1. ribosome Source: UniProtKB-KW
Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi55 – 551G → 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. 1 Publication
Mutagenesisi55 – 551G → S: No effect on Ptase activity of hybrid ribosomes. No change in binding of a tRNA analog to the A or P site. 1 Publication
Mutagenesisi56 – 561E → A: Further decreases Ptase activity in E.coli hybrid ribosomes. Significantly decreases binding of a tRNA analog to the A or P site. 1 Publication
Mutagenesisi56 – 561E → 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. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 21021050S ribosomal protein L4UniRule annotation
PRO_0000129300Add
BLAST

Post-translational modificationi

The N-terminus is blocked.UniRule annotation

Interactioni

Subunit structurei

Part of the 50S ribosomal subunit.

Protein-protein interaction databases

STRINGi300852.TTHA1691.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi8 – 103
Beta strandi11 – 133
Beta strandi14 – 163
Helixi21 – 233
Beta strandi24 – 263
Helixi30 – 4314
Turni54 – 563
Beta strandi57 – 593
Beta strandi67 – 726
Beta strandi78 – 803
Beta strandi83 – 864
Beta strandi88 – 903
Helixi103 – 11917
Beta strandi123 – 1275
Helixi136 – 14510
Beta strandi150 – 1523
Beta strandi154 – 1574
Helixi161 – 1677
Beta strandi173 – 1764
Helixi178 – 1803
Helixi183 – 1886
Beta strandi189 – 1957
Helixi196 – 20611

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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[»]
ProteinModelPortaliQ5SHN9.
SMRiQ5SHN9. Positions 3-210.

Miscellaneous databases

EvolutionaryTraceiQ5SHN9.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0088.
HOGENOMiHOG000248767.
KOiK02926.
OMAiRSIMANQ.
OrthoDBiEOG6M0T9G.

Family and domain databases

Gene3Di3.40.1370.10. 1 hit.
HAMAPiMF_01328_B. Ribosomal_L4_B.
InterProiIPR002136. Ribosomal_L4/L1e.
IPR013005. Ribosomal_L4/L1e_bac-type.
IPR023574. Ribosomal_L4_dom.
[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.

Q5SHN9-1 [UniParc]FASTAAdd to Basket

« Hide

MKEVAVYQIP VLSPSGRREL AADLPAEINP HLLWEVVRWQ LAKRRRGTAS    50
TKTRGEVAYS GRKIWPQKHT GRARHGDIGA PIFVGGGVVF GPKPRDYSYT 100
LPKKVRKKGL AMAVADRARE GKLLLVEAFA GVNGKTKEFL AWAKEAGLDG 150
SESVLLVTGN ELVRRAARNL PWVVTLAPEG LNVYDIVRTE RLVMDLDAWE 200
VFQNRIGGEA 210
Length:210
Mass (Da):23,235
Last modified:December 21, 2004 - v1
Checksum:iBFB99AC179C110B4
GO

Mass spectrometryi

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

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti19 – 202EL → DV in AAA97862. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U36480 Genomic DNA. Translation: AAA97862.1.
AP008226 Genomic DNA. Translation: BAD71514.1.
RefSeqiYP_144957.2. NC_006461.1.

Genome annotation databases

EnsemblBacteriaiBAD71514; BAD71514; BAD71514.
GeneIDi3167923.
KEGGittj:TTHA1691.
PATRICi23958337. VBITheThe93045_1661.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U36480 Genomic DNA. Translation: AAA97862.1 .
AP008226 Genomic DNA. Translation: BAD71514.1 .
RefSeqi YP_144957.2. NC_006461.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1GIY X-ray 5.50 F 1-210 [» ]
1TWV model - D 1-210 [» ]
1YL3 X-ray 5.50 F 1-210 [» ]
2HGJ X-ray 5.00 F 1-210 [» ]
2HGQ X-ray 5.50 F 1-210 [» ]
2HGU X-ray 4.51 F 1-210 [» ]
2J01 X-ray 2.80 F 1-210 [» ]
2J03 X-ray 2.80 F 1-210 [» ]
2V47 X-ray 3.80 F 1-210 [» ]
2V49 X-ray 3.80 F 1-210 [» ]
2WDI X-ray 3.30 F 1-210 [» ]
2WDJ X-ray 3.30 F 1-210 [» ]
2WDL X-ray 3.50 F 1-210 [» ]
2WDN X-ray 3.50 F 1-210 [» ]
2WH2 X-ray 3.45 F 1-210 [» ]
2WH4 X-ray 3.45 F 1-210 [» ]
2WRJ X-ray 3.60 F 1-210 [» ]
2WRL X-ray 3.60 F 1-210 [» ]
2WRO X-ray 3.60 F 1-210 [» ]
2WRR X-ray 3.60 F 1-210 [» ]
2X9S X-ray 3.10 F 1-210 [» ]
2X9U X-ray 3.10 F 1-210 [» ]
2XG0 X-ray 3.20 F 1-210 [» ]
2XG2 X-ray 3.20 F 1-210 [» ]
2XQE X-ray 3.10 F 1-210 [» ]
2XTG electron microscopy 7.80 F 1-210 [» ]
2XUX electron microscopy 7.60 F 1-210 [» ]
2Y0V X-ray 3.10 F 1-210 [» ]
2Y0X X-ray 3.10 F 1-210 [» ]
2Y0Z X-ray 3.10 F 1-210 [» ]
2Y11 X-ray 3.10 F 1-210 [» ]
2Y13 X-ray 3.10 F 1-210 [» ]
2Y15 X-ray 3.10 F 1-210 [» ]
2Y17 X-ray 3.10 F 1-210 [» ]
2Y19 X-ray 3.10 F 1-210 [» ]
3F1F X-ray 3.00 F 1-210 [» ]
3F1H X-ray 3.00 F 1-210 [» ]
3FIN electron microscopy 6.40 F 1-208 [» ]
3HUX X-ray 3.10 F 1-210 [» ]
3HUZ X-ray 3.10 F 1-210 [» ]
3I8F X-ray 3.10 F 1-210 [» ]
3I8I X-ray 3.10 F 1-210 [» ]
3I9C X-ray 3.50 F 1-210 [» ]
3I9E X-ray 3.50 F 1-210 [» ]
3KIR X-ray 3.30 F 1-210 [» ]
3KIT X-ray 3.30 F 1-210 [» ]
3KIW X-ray 3.60 F 1-210 [» ]
3KIY X-ray 3.60 F 1-210 [» ]
3KNI X-ray 3.00 F 1-210 [» ]
3KNK X-ray 3.00 F 1-210 [» ]
3KNM X-ray 3.45 F 1-210 [» ]
3KNO X-ray 3.45 F 1-210 [» ]
3OHJ X-ray 3.00 F 1-210 [» ]
3OHZ X-ray 3.00 F 1-210 [» ]
3OI5 X-ray 3.10 F 1-210 [» ]
3TVE X-ray 3.10 F 6-207 [» ]
3TVH X-ray 3.10 F 1-208 [» ]
3UXQ X-ray 3.20 F 6-210 [» ]
3UXR X-ray 3.20 F 6-210 [» ]
3UYE X-ray 3.00 F 1-210 [» ]
3UYG X-ray 3.00 F 1-210 [» ]
3UZ1 X-ray 3.30 F 1-210 [» ]
3UZ2 X-ray 3.30 F 1-210 [» ]
3UZ8 X-ray 3.00 F 1-210 [» ]
3UZ9 X-ray 3.00 F 1-210 [» ]
3UZF X-ray 3.30 F 1-210 [» ]
3UZH X-ray 3.30 F 1-210 [» ]
3UZK X-ray 3.30 F 1-210 [» ]
3UZN X-ray 3.30 F 1-210 [» ]
3V23 X-ray 3.00 F 1-210 [» ]
3V25 X-ray 3.00 F 1-210 [» ]
3V27 X-ray 3.10 F 1-210 [» ]
3V29 X-ray 3.10 F 1-210 [» ]
3V2D X-ray 2.70 F 1-210 [» ]
3V2F X-ray 2.70 F 1-210 [» ]
3V6W X-ray 3.90 F 1-210 [» ]
3V6X X-ray 3.90 F 1-210 [» ]
3ZN9 X-ray 3.10 F 1-210 [» ]
3ZNE X-ray 3.10 F 1-210 [» ]
3ZVP X-ray 3.80 F 1-210 [» ]
4ABS X-ray 3.10 F 1-210 [» ]
4B8G X-ray 3.70 F 1-210 [» ]
4B8I X-ray 3.70 F 1-210 [» ]
4BTD X-ray 2.95 F 1-210 [» ]
4BYC X-ray 3.35 F 1-210 [» ]
4BYE X-ray 3.35 F 1-210 [» ]
4DHA X-ray 3.20 F 1-210 [» ]
4DHC X-ray 3.20 F 1-210 [» ]
4EJB X-ray 3.52 F 1-210 [» ]
4EJC X-ray 3.52 F 1-210 [» ]
4G5L X-ray 3.30 F 1-210 [» ]
4G5N X-ray 3.30 F 1-210 [» ]
4G5U X-ray 3.10 F 1-210 [» ]
4G5W X-ray 3.10 F 1-210 [» ]
4JUX X-ray 2.86 F 1-210 [» ]
4K0M X-ray 3.30 F 1-207 [» ]
4K0Q X-ray 3.30 F 1-207 [» ]
4NVV X-ray 3.00 F 1-210 [» ]
4NVX X-ray 3.00 F 1-210 [» ]
4NVZ X-ray 3.10 F 1-210 [» ]
4NW1 X-ray 3.10 F 1-210 [» ]
ProteinModelPortali Q5SHN9.
SMRi Q5SHN9. Positions 3-210.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 300852.TTHA1691.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAD71514 ; BAD71514 ; BAD71514 .
GeneIDi 3167923.
KEGGi ttj:TTHA1691.
PATRICi 23958337. VBITheThe93045_1661.

Phylogenomic databases

eggNOGi COG0088.
HOGENOMi HOG000248767.
KOi K02926.
OMAi RSIMANQ.
OrthoDBi EOG6M0T9G.

Enzyme and pathway databases

BioCyci TTHE300852:GH8R-1730-MONOMER.

Miscellaneous databases

EvolutionaryTracei Q5SHN9.

Family and domain databases

Gene3Di 3.40.1370.10. 1 hit.
HAMAPi MF_01328_B. Ribosomal_L4_B.
InterProi IPR002136. Ribosomal_L4/L1e.
IPR013005. Ribosomal_L4/L1e_bac-type.
IPR023574. Ribosomal_L4_dom.
[Graphical view ]
PANTHERi PTHR10746. PTHR10746. 1 hit.
Pfami PF00573. Ribosomal_L4. 1 hit.
[Graphical view ]
SUPFAMi SSF52166. SSF52166. 1 hit.
TIGRFAMsi TIGR03953. rplD_bact. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. Cited for: X-RAY CRYSTALLOGRAPHY (5.5 ANGSTROMS) OF THE RIBOSOME.

Entry informationi

Entry nameiRL4_THET8
AccessioniPrimary (citable) accession number: Q5SHN9
Entry historyi
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 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

External Data

Dasty 3

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