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Q5SHZ1

- RL25_THET8

UniProt

Q5SHZ1 - RL25_THET8

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Protein
50S ribosomal protein L25
Gene
rplY, rpl25, rptL5, TTHA1589
Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Status
Reviewed - Annotation score: 3 out of 5 - Experimental evidence at protein leveli

Functioni

This is one of 3 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit.UniRule annotation

GO - Molecular functioni

  1. 5S rRNA binding Source: InterPro
  2. structural constituent of ribosome Source: InterPro
Complete GO annotation...

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-1628-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
50S ribosomal protein L25
Short name:
TL5
Gene namesi
Name:rplY
Synonyms:rpl25, rptL5
Ordered Locus Names:TTHA1589
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...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 20620650S ribosomal protein L25UniRule annotation
PRO_0000181608Add
BLAST

Interactioni

Subunit structurei

Part of the 50S ribosomal subunit. Contacts the 5S rRNA; has been isolated in a complex with 5S rRNA and RL5, 5S rRNA and DNA binding protein II; 5S rRNA and RL18; 5S rRNA, RL5 and DNA binding protein II (1 Publication).

Protein-protein interaction databases

STRINGi300852.TTHA1589.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 97
Beta strandi11 – 133
Helixi15 – 206
Beta strandi23 – 308
Beta strandi33 – 408
Helixi41 – 5111
Turni52 – 543
Beta strandi57 – 604
Beta strandi62 – 643
Beta strandi66 – 7712
Turni78 – 814
Beta strandi82 – 909
Beta strandi92 – 943
Beta strandi96 – 1016
Beta strandi103 – 1064
Turni107 – 1093
Turni111 – 1144
Beta strandi116 – 1183
Beta strandi122 – 1287
Beta strandi130 – 1323
Beta strandi138 – 1403
Beta strandi142 – 1443
Beta strandi145 – 1473
Beta strandi148 – 1503
Beta strandi152 – 1543
Beta strandi159 – 1635
Beta strandi167 – 1693
Beta strandi172 – 1754
Helixi180 – 1823
Helixi183 – 1864
Beta strandi188 – 1958
Beta strandi199 – 2013

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1GIYX-ray5.50V1-206[»]
2HGJX-ray5.00Y1-206[»]
2HGQX-ray5.50Y1-206[»]
2HGUX-ray4.51Y1-206[»]
2J01X-ray2.80Z1-206[»]
2J03X-ray2.80Z1-206[»]
2V47X-ray3.80Z1-206[»]
2V49X-ray3.80Z1-206[»]
2WDIX-ray3.30Z1-206[»]
2WDJX-ray3.30Z1-206[»]
2WDLX-ray3.50Z1-206[»]
2WDNX-ray3.50Z1-206[»]
2WH2X-ray3.45Z1-206[»]
2WH4X-ray3.45Z1-206[»]
2WRJX-ray3.60Z1-206[»]
2WRLX-ray3.60Z1-206[»]
2WROX-ray3.60Z1-206[»]
2WRRX-ray3.60Z1-206[»]
2X9SX-ray3.10Z1-206[»]
2X9UX-ray3.10Z1-206[»]
2XG0X-ray3.20Z1-206[»]
2XG2X-ray3.20Z1-206[»]
2XQEX-ray3.10Z1-206[»]
2XTGelectron microscopy7.80Z1-206[»]
2XUXelectron microscopy7.60Z1-206[»]
2Y0VX-ray3.10Z1-206[»]
2Y0XX-ray3.10Z1-206[»]
2Y0ZX-ray3.10Z1-206[»]
2Y11X-ray3.10Z1-206[»]
2Y13X-ray3.10Z1-206[»]
2Y15X-ray3.10Z1-206[»]
2Y17X-ray3.10Z1-206[»]
2Y19X-ray3.10Z1-206[»]
3FINelectron microscopy6.40Z3-179[»]
3HUXX-ray3.10Z1-206[»]
3HUZX-ray3.10Z1-206[»]
3I8FX-ray3.10V1-206[»]
3I8IX-ray3.10V1-206[»]
3I9CX-ray3.50V1-206[»]
3I9EX-ray3.50V1-206[»]
3KIRX-ray3.30Z1-206[»]
3KITX-ray3.30Z1-206[»]
3KIWX-ray3.60Z1-206[»]
3KIYX-ray3.60Z1-206[»]
3KNIX-ray3.00Z1-206[»]
3KNKX-ray3.00Z1-206[»]
3KNMX-ray3.45Z1-206[»]
3KNOX-ray3.45Z1-206[»]
3TVEX-ray3.10V1-175[»]
3TVHX-ray3.10V1-179[»]
3UXQX-ray3.20Z1-206[»]
3UXRX-ray3.20Z1-206[»]
3UYEX-ray3.00V1-206[»]
3UYGX-ray3.00V1-206[»]
3UZ1X-ray3.30V1-206[»]
3UZ2X-ray3.30V1-206[»]
3UZ8X-ray3.00V1-206[»]
3UZ9X-ray3.00V1-206[»]
3UZFX-ray3.30V1-206[»]
3UZHX-ray3.30V1-206[»]
3UZKX-ray3.30V1-206[»]
3UZNX-ray3.30V1-206[»]
3V23X-ray3.00Z1-206[»]
3V25X-ray3.00Z1-206[»]
3V27X-ray3.10Z1-206[»]
3V29X-ray3.10Z1-206[»]
3V2DX-ray2.70Z1-206[»]
3V2FX-ray2.70Z1-206[»]
3V6WX-ray3.90Z1-206[»]
3V6XX-ray3.90Z1-206[»]
3ZN9X-ray3.10Z1-206[»]
3ZNEX-ray3.10Z1-206[»]
3ZVPX-ray3.80Z1-206[»]
4ABSX-ray3.10Z1-206[»]
4B8GX-ray3.70Z1-206[»]
4B8IX-ray3.70Z1-206[»]
4BTDX-ray2.95Z2-206[»]
4BYCX-ray3.35Z1-206[»]
4BYEX-ray3.35Z1-206[»]
4DHAX-ray3.20Z1-206[»]
4DHCX-ray3.20Z1-206[»]
4EJBX-ray3.52Z1-206[»]
4EJCX-ray3.52Z1-206[»]
4G5LX-ray3.30V1-206[»]
4G5NX-ray3.30V1-206[»]
4G5UX-ray3.10V1-206[»]
4G5WX-ray3.10V1-206[»]
4JUXX-ray2.86Z1-206[»]
4K0MX-ray3.30Z3-178[»]
4K0QX-ray3.30Z3-178[»]
4NVVX-ray3.00Z1-206[»]
4NVXX-ray3.00Z1-206[»]
4NVZX-ray3.10Z1-206[»]
4NW1X-ray3.10Z1-206[»]
ProteinModelPortaliQ5SHZ1.
SMRiQ5SHZ1. Positions 1-185.

Miscellaneous databases

EvolutionaryTraceiQ5SHZ1.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG1825.
HOGENOMiHOG000214906.
KOiK02897.
OMAiCIGVKLG.
OrthoDBiEOG6SZ1PC.
PhylomeDBiQ5SHZ1.

Family and domain databases

Gene3Di2.170.120.20. 1 hit.
2.40.240.10. 1 hit.
HAMAPiMF_01334. Ribosomal_L25_CTC.
InterProiIPR020056. Rbsml_L25/Gln-tRNA_synth_b-brl.
IPR011035. Ribosomal_L25/Gln-tRNA_synth.
IPR020057. Ribosomal_L25_b-dom.
IPR001021. Ribosomal_L25_long.
[Graphical view]
PfamiPF14693. Ribosomal_TL5_C. 1 hit.
[Graphical view]
SUPFAMiSSF50715. SSF50715. 1 hit.
TIGRFAMsiTIGR00731. ctc_TL5. 1 hit.

Sequencei

Sequence statusi: Complete.

Q5SHZ1-1 [UniParc]FASTAAdd to Basket

« Hide

MEYRLKAYYR EGEKPSALRR AGKLPGVMYN RHLNRKVYVD LVEFDKVFRQ    50
ASIHHVIVLE LPDGQSLPTL VRQVNLDKRR RRPEHVDFFV LSDEPVEMYV 100
PLRFVGTPAG VRAGGVLQEI HRDILVKVSP RNIPEFIEVD VSGLEIGDSL 150
HASDLKLPPG VELAVSPEET IAAVVPPEDV EKLAEEAAAE VAEPEVIKKG 200
KEEEEE 206
Length:206
Mass (Da):23,205
Last modified:December 21, 2004 - v1
Checksum:iACC20EC1279181CD
GO

Mass spectrometryi

Molecular mass is 23207 Da from positions 1 - 206. Determined by MALDI. 1 Publication

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti43 – 453EFD → QRF AA sequence 1 Publication
Sequence conflicti60 – 7011ELPDGQSLPTL → QLRRGTRLSPE AA sequence 1 Publication
Add
BLAST

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AP008226 Genomic DNA. Translation: BAD71412.1.
RefSeqiYP_144855.1. NC_006461.1.

Genome annotation databases

EnsemblBacteriaiBAD71412; BAD71412; BAD71412.
GeneIDi3169859.
KEGGittj:TTHA1589.
PATRICi23958133. VBITheThe93045_1559.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AP008226 Genomic DNA. Translation: BAD71412.1 .
RefSeqi YP_144855.1. 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 V 1-206 [» ]
2HGJ X-ray 5.00 Y 1-206 [» ]
2HGQ X-ray 5.50 Y 1-206 [» ]
2HGU X-ray 4.51 Y 1-206 [» ]
2J01 X-ray 2.80 Z 1-206 [» ]
2J03 X-ray 2.80 Z 1-206 [» ]
2V47 X-ray 3.80 Z 1-206 [» ]
2V49 X-ray 3.80 Z 1-206 [» ]
2WDI X-ray 3.30 Z 1-206 [» ]
2WDJ X-ray 3.30 Z 1-206 [» ]
2WDL X-ray 3.50 Z 1-206 [» ]
2WDN X-ray 3.50 Z 1-206 [» ]
2WH2 X-ray 3.45 Z 1-206 [» ]
2WH4 X-ray 3.45 Z 1-206 [» ]
2WRJ X-ray 3.60 Z 1-206 [» ]
2WRL X-ray 3.60 Z 1-206 [» ]
2WRO X-ray 3.60 Z 1-206 [» ]
2WRR X-ray 3.60 Z 1-206 [» ]
2X9S X-ray 3.10 Z 1-206 [» ]
2X9U X-ray 3.10 Z 1-206 [» ]
2XG0 X-ray 3.20 Z 1-206 [» ]
2XG2 X-ray 3.20 Z 1-206 [» ]
2XQE X-ray 3.10 Z 1-206 [» ]
2XTG electron microscopy 7.80 Z 1-206 [» ]
2XUX electron microscopy 7.60 Z 1-206 [» ]
2Y0V X-ray 3.10 Z 1-206 [» ]
2Y0X X-ray 3.10 Z 1-206 [» ]
2Y0Z X-ray 3.10 Z 1-206 [» ]
2Y11 X-ray 3.10 Z 1-206 [» ]
2Y13 X-ray 3.10 Z 1-206 [» ]
2Y15 X-ray 3.10 Z 1-206 [» ]
2Y17 X-ray 3.10 Z 1-206 [» ]
2Y19 X-ray 3.10 Z 1-206 [» ]
3FIN electron microscopy 6.40 Z 3-179 [» ]
3HUX X-ray 3.10 Z 1-206 [» ]
3HUZ X-ray 3.10 Z 1-206 [» ]
3I8F X-ray 3.10 V 1-206 [» ]
3I8I X-ray 3.10 V 1-206 [» ]
3I9C X-ray 3.50 V 1-206 [» ]
3I9E X-ray 3.50 V 1-206 [» ]
3KIR X-ray 3.30 Z 1-206 [» ]
3KIT X-ray 3.30 Z 1-206 [» ]
3KIW X-ray 3.60 Z 1-206 [» ]
3KIY X-ray 3.60 Z 1-206 [» ]
3KNI X-ray 3.00 Z 1-206 [» ]
3KNK X-ray 3.00 Z 1-206 [» ]
3KNM X-ray 3.45 Z 1-206 [» ]
3KNO X-ray 3.45 Z 1-206 [» ]
3TVE X-ray 3.10 V 1-175 [» ]
3TVH X-ray 3.10 V 1-179 [» ]
3UXQ X-ray 3.20 Z 1-206 [» ]
3UXR X-ray 3.20 Z 1-206 [» ]
3UYE X-ray 3.00 V 1-206 [» ]
3UYG X-ray 3.00 V 1-206 [» ]
3UZ1 X-ray 3.30 V 1-206 [» ]
3UZ2 X-ray 3.30 V 1-206 [» ]
3UZ8 X-ray 3.00 V 1-206 [» ]
3UZ9 X-ray 3.00 V 1-206 [» ]
3UZF X-ray 3.30 V 1-206 [» ]
3UZH X-ray 3.30 V 1-206 [» ]
3UZK X-ray 3.30 V 1-206 [» ]
3UZN X-ray 3.30 V 1-206 [» ]
3V23 X-ray 3.00 Z 1-206 [» ]
3V25 X-ray 3.00 Z 1-206 [» ]
3V27 X-ray 3.10 Z 1-206 [» ]
3V29 X-ray 3.10 Z 1-206 [» ]
3V2D X-ray 2.70 Z 1-206 [» ]
3V2F X-ray 2.70 Z 1-206 [» ]
3V6W X-ray 3.90 Z 1-206 [» ]
3V6X X-ray 3.90 Z 1-206 [» ]
3ZN9 X-ray 3.10 Z 1-206 [» ]
3ZNE X-ray 3.10 Z 1-206 [» ]
3ZVP X-ray 3.80 Z 1-206 [» ]
4ABS X-ray 3.10 Z 1-206 [» ]
4B8G X-ray 3.70 Z 1-206 [» ]
4B8I X-ray 3.70 Z 1-206 [» ]
4BTD X-ray 2.95 Z 2-206 [» ]
4BYC X-ray 3.35 Z 1-206 [» ]
4BYE X-ray 3.35 Z 1-206 [» ]
4DHA X-ray 3.20 Z 1-206 [» ]
4DHC X-ray 3.20 Z 1-206 [» ]
4EJB X-ray 3.52 Z 1-206 [» ]
4EJC X-ray 3.52 Z 1-206 [» ]
4G5L X-ray 3.30 V 1-206 [» ]
4G5N X-ray 3.30 V 1-206 [» ]
4G5U X-ray 3.10 V 1-206 [» ]
4G5W X-ray 3.10 V 1-206 [» ]
4JUX X-ray 2.86 Z 1-206 [» ]
4K0M X-ray 3.30 Z 3-178 [» ]
4K0Q X-ray 3.30 Z 3-178 [» ]
4NVV X-ray 3.00 Z 1-206 [» ]
4NVX X-ray 3.00 Z 1-206 [» ]
4NVZ X-ray 3.10 Z 1-206 [» ]
4NW1 X-ray 3.10 Z 1-206 [» ]
ProteinModelPortali Q5SHZ1.
SMRi Q5SHZ1. Positions 1-185.
ModBasei Search...

Protein-protein interaction databases

STRINGi 300852.TTHA1589.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAD71412 ; BAD71412 ; BAD71412 .
GeneIDi 3169859.
KEGGi ttj:TTHA1589.
PATRICi 23958133. VBITheThe93045_1559.

Phylogenomic databases

eggNOGi COG1825.
HOGENOMi HOG000214906.
KOi K02897.
OMAi CIGVKLG.
OrthoDBi EOG6SZ1PC.
PhylomeDBi Q5SHZ1.

Enzyme and pathway databases

BioCyci TTHE300852:GH8R-1628-MONOMER.

Miscellaneous databases

EvolutionaryTracei Q5SHZ1.

Family and domain databases

Gene3Di 2.170.120.20. 1 hit.
2.40.240.10. 1 hit.
HAMAPi MF_01334. Ribosomal_L25_CTC.
InterProi IPR020056. Rbsml_L25/Gln-tRNA_synth_b-brl.
IPR011035. Ribosomal_L25/Gln-tRNA_synth.
IPR020057. Ribosomal_L25_b-dom.
IPR001021. Ribosomal_L25_long.
[Graphical view ]
Pfami PF14693. Ribosomal_TL5_C. 1 hit.
[Graphical view ]
SUPFAMi SSF50715. SSF50715. 1 hit.
TIGRFAMsi TIGR00731. ctc_TL5. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "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.
  2. "The isolation and complete amino acid sequence of the ribosomal protein L36 from Thermus thermophilus and its zinc-binding motif."
    Boysen R.I., Lorenz S., Kim J.S., Schroeder W.F.K.J., Erdmann V.A.
    Endocyt. Cell Res. 11:41-58(1995)
    Cited for: PROTEIN SEQUENCE OF 1-70.
  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 1-30.
  4. "Identification, purification and partial sequence of four Thermus thermophilus 5S rRNA binding proteins."
    Kim J.-S., Boysen R.I., Schroeder W., Erdmann V.A., Gessner R.V.
    Endocyt. Cell Res. 11:177-194(1996)
    Cited for: PROTEIN SEQUENCE OF 1-22, ISOLATION OF 5S RRNA-ASSOCIATED COMPLEXES.
  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 nameiRL25_THET8
AccessioniPrimary (citable) accession number: Q5SHZ1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 29, 2005
Last sequence update: December 21, 2004
Last modified: September 3, 2014
This is version 85 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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