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P68919 (RL25_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 97. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
50S ribosomal protein L25
Gene names
Name:rplY
Ordered Locus Names:b2185, JW2173
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length94 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Binds to the 5S rRNA independently of L5 and L18. Not required for binding of the 5S rRNA/L5/L18 subcomplex to 23S rRNA. HAMAP-Rule MF_01336

Subunit structure

Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S rRNA. Ref.11

Sequence similarities

Belongs to the ribosomal protein L25P family.

Mass spectrometry

Molecular mass is 10693.4 Da from positions 1 - 94. Determined by MALDI. Ref.15

Binary interactions

With

Entry

#Exp.

IntAct

Notes

dnaKP0A6Y81EBI-553087,EBI-542092

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 949450S ribosomal protein L25 HAMAP-Rule MF_01336
PRO_0000181478

Experimental info

Sequence conflict86 – 949LQHIDFVRA → CSTSTSFALNC in AAA16413. Ref.6

Secondary structure

........................ 94
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P68919 [UniParc].

Last modified July 21, 1986. Version 1.
Checksum: 85DAF5ACBA1C5F86

FASTA9410,693
        10         20         30         40         50         60 
MFTINAEVRK EQGKGASRRL RAANKFPAII YGGKEAPLAI ELDHDKVMNM QAKAEFYSEV 

        70         80         90 
LTIVVDGKEI KVKAQDVQRH PYKPKLQHID FVRA 

« Hide

References

« Hide 'large scale' references
[1]"The primary structure of the 5S RNA binding protein L25 from Escherichia coli ribosomes."
Dovgas N.V., Markova L.F., Mednikova T.A., Vinokurov L.M., Alakhov Y.B., Ovchinnikov Y.A.
FEBS Lett. 53:351-354(1975) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE.
Strain: MRE-600.
[2]Erratum
Dovgas N.V., Markova L.F., Mednikova T.A., Vinokurov L.M., Alakhov Y.B., Ovchinnikov Y.A.
FEBS Lett. 57:305-305(1975)
Cited for: SEQUENCE REVISION.
[3]"The primary structure of the 5s rRNA binding protein L25 of Escherichia coli ribosomes."
Bitar K.G., Wittmann-Liebold B.
Hoppe-Seyler's Z. Physiol. Chem. 356:1343-1352(1975) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE.
Strain: K12.
[4]"Primary structure of the protein L25 from the ribosomes of E. coli MRE-600 forming part of the 5S-RNA-protein complex."
Alakhov Y.B., Vinokurov L.M., Dovgas N.V., Markova L.F., Mednikova T.A., Motuz L.P., Kashparov I.A., Ovchinnikov Y.A.
Bioorg. Khim. 2:5-18(1976)
Cited for: PROTEIN SEQUENCE.
Strain: MRE-600.
[5]"Cloning, characterization, and physical location of the rplY gene which encodes ribosomal protein L25 in Escherichia coli K12."
Uemura Y., Isono S., Isono K.
Mol. Gen. Genet. 226:341-344(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12.
[6]"Automated multiplex sequencing of the E.coli genome."
Richterich P., Lakey N., Gryan G., Jaehn L., Mintz L., Robison K., Church G.M.
Submitted (OCT-1993) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / BHB2600.
[7]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[8]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[9]"Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12."
Link A.J., Robison K., Church G.M.
Electrophoresis 18:1259-1313(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 1-12.
Strain: K12 / EMG2.
[10]"Small genes/gene-products in Escherichia coli K-12."
Wasinger V.C., Humphery-Smith I.
FEMS Microbiol. Lett. 169:375-382(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 1-10.
Strain: K12.
[11]"Incorporation of six additional proteins to complete the assembly map of the 50 S subunit from Escherichia coli ribosomes."
Herold M., Nierhaus K.H.
J. Biol. Chem. 262:8826-8833(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: ASSEMBLY MAP OF THE 50S SUBUNIT, BINDING TO 5S RRNA.
Strain: K12.
[12]"Stoichiometry, cooperativity, and stability of interactions between 5S RNA and proteins L5, L18, and L25 from the 50S ribosomal subunit of Escherichia coli."
Spierer P., Zimmermann R.A.
Biochemistry 17:2474-2479(1978) [PubMed] [Europe PMC] [Abstract]
Cited for: FORMATION OF THE 5S RRNA/L5/L18/L25 SUBCOMPLEX.
Strain: MRE-600.
[13]"5S rRNA sugar-phosphate backbone protection in complexes with specific ribosomal proteins."
Shpanchenko O.V., Zvereva M.I., Dontsova O.A., Nierhaus K.H., Bogdanov A.A.
FEBS Lett. 394:71-75(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION OF THE 5S RRNA/L5/L18/L25 SUBCOMPLEX.
Strain: K12 / A19.
[14]"Escherichia coli proteome analysis using the gene-protein database."
VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY 2D-GEL.
[15]"Observation of Escherichia coli ribosomal proteins and their posttranslational modifications by mass spectrometry."
Arnold R.J., Reilly J.P.
Anal. Biochem. 269:105-112(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: MASS SPECTROMETRY.
Strain: K12 / ATCC 25404 / DSM 5698 / NCIMB 11290.
[16]"The NMR structure of Escherichia coli ribosomal protein L25 shows homology to general stress proteins and glutaminyl-tRNA synthetases."
Stoldt M., Woehnert J., Goerlach M., Brown L.R.
EMBO J. 17:6377-6384(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR IN COMPLEX WITH A FRAGMENT OF 5S RRNA.
Strain: MRE-600.
[17]"The NMR structure of the 5S rRNA E-domain-protein L25 complex shows preformed and induced recognition."
Stoldt M., Woehnert J., Ohlenschlaeger O., Goerlach M., Brown L.R.
EMBO J. 18:6508-6521(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR IN COMPLEX WITH A FRAGMENT OF 5S RRNA.
[18]"Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution."
Lu M., Steitz T.A.
Proc. Natl. Acad. Sci. U.S.A. 97:2023-2028(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) BOUND TO A FRAGMENT OF 5S RRNA.
[19]"The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo-electron microscopic reconstruction at 7.5 A resolution."
Mueller F., Sommer I., Baranov P., Matadeen R., Stoldt M., Woehnert J., Goerlach M., van Heel M., Brimacombe R.
J. Mol. Biol. 298:35-59(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: 3D-STRUCTURE MODELING.
[20]"Study of the structural dynamics of the E. coli 70S ribosome using real-space refinement."
Gao H., Sengupta J., Valle M., Korostelev A., Eswar N., Stagg S.M., Van Roey P., Agrawal R.K., Harvey S.C., Sali A., Chapman M.S., Frank J.
Cell 113:789-801(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY ELECTRON MICROSCOPY (11.50 ANGSTROMS).
Strain: MRE-600.
[21]"Structures of the bacterial ribosome at 3.5 A resolution."
Schuwirth B.S., Borovinskaya M.A., Hau C.W., Zhang W., Vila-Sanjurjo A., Holton J.M., Cate J.H.D.
Science 310:827-834(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.46 ANGSTROMS) OF 2 DIFFERENT RIBOSOME STRUCTURES.
Strain: MRE-600.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
D13326 Genomic DNA. Translation: BAA02585.1.
U00008 Genomic DNA. Translation: AAA16413.1.
U00096 Genomic DNA. Translation: AAC75246.1.
AP009048 Genomic DNA. Translation: BAE76650.1.
PIRR5EC25. S16002.
RefSeqNP_416690.1. NC_000913.3.
YP_490425.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1B75NMR-A1-94[»]
1D6KNMR-A1-94[»]
1DFUX-ray1.80P1-94[»]
1ML5electron microscopy14.00v1-94[»]
1P85electron microscopy12.30T1-94[»]
1P86electron microscopy11.50T1-94[»]
1VS6X-ray3.46V1-94[»]
1VS8X-ray3.46V1-94[»]
1VT2X-ray3.30V1-94[»]
2AW4X-ray3.46V1-94[»]
2AWBX-ray3.46V1-94[»]
2GYAelectron microscopy15.00T1-94[»]
2GYCelectron microscopy15.00T1-94[»]
2I2TX-ray3.22V1-94[»]
2I2VX-ray3.22V1-94[»]
2J28electron microscopy8.00V1-94[»]
2QAMX-ray3.21V1-94[»]
2QAOX-ray3.21V1-94[»]
2QBAX-ray3.54V1-94[»]
2QBCX-ray3.54V1-94[»]
2QBEX-ray3.30V1-94[»]
2QBGX-ray3.30V1-94[»]
2QBIX-ray4.00V1-94[»]
2QBKX-ray4.00V1-94[»]
2QOVX-ray3.93V1-94[»]
2QOXX-ray3.93V1-94[»]
2QOZX-ray3.50V1-94[»]
2QP1X-ray3.50V1-94[»]
2RDOelectron microscopy9.10V1-94[»]
2VHMX-ray3.74V1-94[»]
2VHNX-ray3.74V1-94[»]
2WWQelectron microscopy5.80W1-94[»]
2Z4LX-ray4.45V1-94[»]
2Z4NX-ray4.45V1-94[»]
3BBXelectron microscopy10.00V1-94[»]
3DF2X-ray3.50V1-94[»]
3DF4X-ray3.50V1-94[»]
3E1Belectron microscopy-C1-94[»]
3E1Delectron microscopy-C1-94[»]
3FIKelectron microscopy6.70V1-94[»]
3I1NX-ray3.19V1-94[»]
3I1PX-ray3.19V1-94[»]
3I1RX-ray3.81V1-94[»]
3I1TX-ray3.81V1-94[»]
3I20X-ray3.71V1-94[»]
3I22X-ray3.71V1-94[»]
3IZTelectron microscopy-W1-94[»]
3IZUelectron microscopy-W1-94[»]
3J01electron microscopy-V1-94[»]
3J0Telectron microscopy12.10X1-94[»]
3J0Welectron microscopy14.70X1-94[»]
3J0Yelectron microscopy13.50X1-94[»]
3J11electron microscopy13.10X1-94[»]
3J12electron microscopy11.50X1-94[»]
3J14electron microscopy11.50X1-94[»]
3J19electron microscopy8.30V1-94[»]
3J37electron microscopy9.80Z1-94[»]
3J4Xelectron microscopy12.00V1-94[»]
3J50electron microscopy20.00V1-94[»]
3J51electron microscopy17.00V1-94[»]
3J52electron microscopy12.00V1-94[»]
3J54electron microscopy13.00V1-94[»]
3J56electron microscopy15.00V1-94[»]
3J58electron microscopy17.00V1-94[»]
3J5Aelectron microscopy12.00V1-94[»]
3J5Celectron microscopy17.00V1-94[»]
3J5Eelectron microscopy17.00V1-94[»]
3J5Gelectron microscopy20.00V1-94[»]
3J5Ielectron microscopy15.00V1-94[»]
3J5Kelectron microscopy9.00V1-94[»]
3J5Oelectron microscopy6.80V1-94[»]
3J5Uelectron microscopy7.60X1-94[»]
3J5Welectron microscopy7.60Y1-94[»]
3KCRelectron microscopy-V1-94[»]
3OASX-ray3.25V1-94[»]
3OATX-ray3.25V1-94[»]
3OFCX-ray3.19V1-94[»]
3OFDX-ray3.19V1-94[»]
3OFQX-ray3.10V1-94[»]
3OFRX-ray3.10V1-94[»]
3OFZX-ray3.29V1-94[»]
3OG0X-ray3.29V1-94[»]
3ORBX-ray3.30V1-94[»]
3R8SX-ray3.00V1-94[»]
3R8TX-ray3.00V1-94[»]
3SGFX-ray3.20Z1-94[»]
3UOSX-ray3.70Z1-94[»]
487Delectron microscopy7.50N1-94[»]
4GARX-ray3.30V1-94[»]
4GAUX-ray3.30V1-94[»]
4KIXX-ray2.90V1-94[»]
4KIZX-ray2.90V1-94[»]
4KJ1X-ray2.90V1-94[»]
4KJ3X-ray2.90V1-94[»]
4KJ5X-ray2.90V1-94[»]
4KJ7X-ray2.90V1-94[»]
4KJ9X-ray2.90V1-94[»]
4KJBX-ray2.90V1-94[»]
ProteinModelPortalP68919.
SMRP68919. Positions 1-94.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-35885N.
IntActP68919. 13 interactions.
MINTMINT-1261165.
STRING511145.b2185.

Chemistry

ChEMBLCHEMBL2363135.

2D gel databases

SWISS-2DPAGEP68919.

Proteomic databases

PaxDbP68919.
PRIDEP68919.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC75246; AAC75246; b2185.
BAE76650; BAE76650; BAE76650.
GeneID12934501.
945618.
KEGGecj:Y75_p2148.
eco:b2185.
PATRIC32119725. VBIEscCol129921_2273.

Organism-specific databases

EchoBASEEB0878.
EcoGeneEG10885. rplY.

Phylogenomic databases

eggNOGCOG1825.
HOGENOMHOG000277629.
KOK02897.
OMASIELDHD.
OrthoDBEOG6SZ1PC.
ProtClustDBPRK05943.

Enzyme and pathway databases

BioCycEcoCyc:EG10885-MONOMER.
ECOL316407:JW2173-MONOMER.

Gene expression databases

GenevestigatorP68919.

Family and domain databases

Gene3D2.40.240.10. 1 hit.
HAMAPMF_01336. Ribosomal_L25.
InterProIPR020056. Rbsml_L25/Gln-tRNA_synth_b-brl.
IPR011035. Ribosomal_L25/Gln-tRNA_synth.
IPR020055. Ribosomal_L25_short.
[Graphical view]
PfamPF01386. Ribosomal_L25p. 1 hit.
[Graphical view]
ProDomPD012503. Ribosomal_L25. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMSSF50715. SSF50715. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP68919.
PROP68919.

Entry information

Entry nameRL25_ECOLI
AccessionPrimary (citable) accession number: P68919
Secondary accession number(s): P02426, Q2MAQ6
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: March 19, 2014
This is version 97 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

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene