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P62399 (RL5_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 110. 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·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
50S ribosomal protein L5
Gene names
Name:rplE
Ordered Locus Names:b3308, JW3270
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length179 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. Its 5S rRNA binding is significantly enhanced in the presence of L18. HAMAP-Rule MF_01333_B

In the 70S ribosome in the initiation state (Ref.13) was modeled to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; the protein-protein contacts between S13 and L5 in B1b change in the model with bound EF-G implicating this bridge in subunit movement (Ref.13 and Ref.12). In the two 3.5 A resolved ribosome structures (Ref.15) the contacts between L5, S13 and S19 are different, confirming the dynamic nature of this interaction. HAMAP-Rule MF_01333_B

Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. HAMAP-Rule MF_01333_B

Subunit structure

Part of the 50S ribosomal subunit; part of the 5S rRNA/L5/L18/L25 subcomplex. Contacts the 5S rRNA; cross-links to the P site tRNA. Forms a bridge to the 30S subunit in the 70S ribosome, contacting protein S13 and S19. Ref.7 Ref.13 Ref.15

Sequence similarities

Belongs to the ribosomal protein L5P family.

Mass spectrometry

Molecular mass is 20169.8 Da from positions 2 - 179. Determined by MALDI. Ref.11

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.4
Chain2 – 17917850S ribosomal protein L5 HAMAP-Rule MF_01333_B
PRO_0000124925

Amino acid modifications

Modified residue31N6-acetyllysine Ref.12

Experimental info

Sequence conflict941E → Q AA sequence Ref.4
Sequence conflict1271N → D AA sequence Ref.4

Secondary structure

.......................................... 179
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P62399 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: B2E95A8BE4B8D2A7

FASTA17920,302
        10         20         30         40         50         60 
MAKLHDYYKD EVVKKLMTEF NYNSVMQVPR VEKITLNMGV GEAIADKKLL DNAAADLAAI 

        70         80         90        100        110        120 
SGQKPLITKA RKSVAGFKIR QGYPIGCKVT LRGERMWEFF ERLITIAVPR IRDFRGLSAK 

       130        140        150        160        170 
SFDGRGNYSM GVREQIIFPE IDYDKVDRVR GLDITITTTA KSDEEGRALL AAFDFPFRK 

« Hide

References

« Hide 'large scale' references
[1]"The spc ribosomal protein operon of Escherichia coli: sequence and cotranscription of the ribosomal protein genes and a protein export gene."
Cerretti D.P., Dean D., Davis G.R., Bedwell D.M., Nomura M.
Nucleic Acids Res. 11:2599-2616(1983) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12.
[2]"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.
[3]"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.
[4]"The primary structure of the 5 S RNA binding protein L5 of Escherichia coli ribosomes."
Chen R., Ehrke G.
FEBS Lett. 69:240-245(1976) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 2-179.
Strain: K.
[5]"Translational regulation by ribosomal protein S8 in Escherichia coli: structural homology between rRNA binding site and feedback target on mRNA."
Olins P.O., Nomura M.
Nucleic Acids Res. 9:1757-1764(1981) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-18.
Strain: K12 / JM105 / ATCC 47016.
[6]"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.
[7]"Assembly map of the large subunit (50S) of Escherichia coli ribosomes."
Rohl R., Nierhaus K.H.
Proc. Natl. Acad. Sci. U.S.A. 79:729-733(1982) [PubMed] [Europe PMC] [Abstract]
Cited for: REQUIREMENT FOR INCORPORATION OF 5S RRNA INTO THE 50S SUBUNIT.
Strain: MRE-600.
[8]"The ribosomal neighbourhood of the central fold of tRNA: cross-links from position 47 of tRNA located at the A, P or E site."
Osswald M., Doering T., Brimacombe R.
Nucleic Acids Res. 23:4635-4641(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: CROSS-LINKING TO THE TRNA CENTRAL FOLD.
Strain: MRE-600.
[9]"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 A 5S RRNA/L5/L18/L25 SUBCOMPLEX.
Strain: K12 / A19.
[10]"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.
[11]"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.
[12]"Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli."
Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y.
Mol. Cell. Proteomics 8:215-225(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-3, IDENTIFICATION BY MASS SPECTROMETRY.
Strain: K12 / JW1106 and K12 / MG1655 / ATCC 47076.
[13]"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), INTERSUBUNIT BRIDGE FORMATION.
Strain: MRE-600.
[14]"Locking and unlocking of ribosomal motions."
Valle M., Zavialov A., Sengupta J., Rawat U., Ehrenberg M., Frank J.
Cell 114:123-134(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: 3D-STRUCTURE MODELING OF RIBOSOMAL COMPLEXES INCLUDING BRIDGE CHANGES UPON TRANSLOCATION.
[15]"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 INCLUDING 2 CONFORMATIONS OF INTERSUBUNIT BRIDGE B1B.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X01563 Genomic DNA. Translation: CAA25717.1.
U18997 Genomic DNA. Translation: AAA58105.1.
U00096 Genomic DNA. Translation: AAC76333.1.
AP009048 Genomic DNA. Translation: BAE77983.1.
M10195 Genomic DNA. Translation: AAA24051.1.
PIRR5EC5. G65123.
RefSeqNP_417767.1. NC_000913.3.
YP_492124.1. NC_007779.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1ML5electron microscopy14.00g2-177[»]
1P85electron microscopy12.30D2-179[»]
1P86electron microscopy11.50D2-179[»]
1VS6X-ray3.46F1-179[»]
1VS8X-ray3.46F1-179[»]
1VT2X-ray3.30F1-179[»]
2AW4X-ray3.46F2-179[»]
2AWBX-ray3.46F2-179[»]
2GYAelectron microscopy15.00D3-179[»]
2GYCelectron microscopy15.00D3-179[»]
2I2TX-ray3.22F2-179[»]
2I2VX-ray3.22F2-179[»]
2J28electron microscopy8.00F2-179[»]
2QAMX-ray3.21F2-179[»]
2QAOX-ray3.21F2-179[»]
2QBAX-ray3.54F2-179[»]
2QBCX-ray3.54F2-179[»]
2QBEX-ray3.30F2-179[»]
2QBGX-ray3.30F2-179[»]
2QBIX-ray4.00F2-179[»]
2QBKX-ray4.00F2-179[»]
2QOVX-ray3.93F2-179[»]
2QOXX-ray3.93F2-179[»]
2QOZX-ray3.50F2-179[»]
2QP1X-ray3.50F2-179[»]
2RDOelectron microscopy9.10F2-179[»]
2VHMX-ray3.74F2-179[»]
2VHNX-ray3.74F2-179[»]
2WWQelectron microscopy5.80F2-179[»]
2Z4LX-ray4.45F2-179[»]
2Z4NX-ray4.45F2-179[»]
3BBXelectron microscopy10.00F2-179[»]
3DF2X-ray3.50F2-178[»]
3DF4X-ray3.50F2-178[»]
3E1Belectron microscopy-22-179[»]
3E1Delectron microscopy-22-179[»]
3FIKelectron microscopy6.70F2-179[»]
3I1NX-ray3.19F1-179[»]
3I1PX-ray3.19F1-179[»]
3I1RX-ray3.81F1-179[»]
3I1TX-ray3.81F1-179[»]
3I20X-ray3.71F1-179[»]
3I22X-ray3.71F1-179[»]
3IZTelectron microscopy-G1-179[»]
3IZUelectron microscopy-G1-179[»]
3J01electron microscopy-F2-179[»]
3J0Telectron microscopy12.10G2-179[»]
3J0Welectron microscopy14.70G2-179[»]
3J0Yelectron microscopy13.50G2-179[»]
3J11electron microscopy13.10G2-179[»]
3J12electron microscopy11.50G2-179[»]
3J14electron microscopy11.50G2-179[»]
3J19electron microscopy8.30F2-178[»]
3J37electron microscopy9.80G2-179[»]
3J4Xelectron microscopy12.00F1-179[»]
3J50electron microscopy20.00F1-179[»]
3J51electron microscopy17.00F1-179[»]
3J52electron microscopy12.00F1-179[»]
3J54electron microscopy13.00F1-179[»]
3J56electron microscopy15.00F1-179[»]
3J58electron microscopy17.00F1-179[»]
3J5Aelectron microscopy12.00F1-179[»]
3J5Celectron microscopy17.00F1-179[»]
3J5Eelectron microscopy17.00F1-179[»]
3J5Gelectron microscopy20.00F1-179[»]
3J5Ielectron microscopy15.00F1-179[»]
3J5Kelectron microscopy9.00F1-179[»]
3J5Lelectron microscopy6.60F2-178[»]
3J5Oelectron microscopy6.80F1-179[»]
3J5Selectron microscopy7.50G2-179[»]
3J5Uelectron microscopy7.60G2-179[»]
3J5Welectron microscopy7.60G2-179[»]
3KCRelectron microscopy-F1-179[»]
3OASX-ray3.25F2-179[»]
3OATX-ray3.25F2-178[»]
3OFCX-ray3.19F2-178[»]
3OFDX-ray3.19F2-179[»]
3OFQX-ray3.10F2-179[»]
3OFRX-ray3.10F2-178[»]
3OFZX-ray3.29F2-178[»]
3OG0X-ray3.29F2-179[»]
3ORBX-ray3.30F1-179[»]
3R8SX-ray3.00F2-178[»]
3R8TX-ray3.00F2-178[»]
3SGFX-ray3.20F1-179[»]
3UOSX-ray3.70F1-179[»]
4GARX-ray3.30F1-179[»]
4GAUX-ray3.30F1-179[»]
4KIXX-ray2.90F1-179[»]
4KIZX-ray2.90F1-179[»]
4KJ1X-ray2.90F1-179[»]
4KJ3X-ray2.90F1-179[»]
4KJ5X-ray2.90F1-179[»]
4KJ7X-ray2.90F1-179[»]
4KJ9X-ray2.90F1-179[»]
4KJBX-ray2.90F1-179[»]
ProteinModelPortalP62399.
SMRP62399. Positions 2-178.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid852112. 1 interaction.
DIPDIP-35914N.
IntActP62399. 71 interactions.
MINTMINT-1238892.
STRING511145.b3308.

Chemistry

ChEMBLCHEMBL2363135.

Proteomic databases

PaxDbP62399.
PRIDEP62399.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC76333; AAC76333; b3308.
BAE77983; BAE77983; BAE77983.
GeneID12934390.
947800.
KEGGecj:Y75_p3868.
eco:b3308.
PATRIC32122048. VBIEscCol129921_3401.

Organism-specific databases

EchoBASEEB0861.
EcoGeneEG10868. rplE.

Phylogenomic databases

eggNOGCOG0094.
HOGENOMHOG000231311.
KOK02931.
OMATEQLIFP.
OrthoDBEOG6M9F1R.
PhylomeDBP62399.

Enzyme and pathway databases

BioCycEcoCyc:EG10868-MONOMER.
ECOL316407:JW3270-MONOMER.

Gene expression databases

GenevestigatorP62399.

Family and domain databases

Gene3D3.30.1440.10. 1 hit.
HAMAPMF_01333_B. Ribosomal_L5_B.
InterProIPR002132. Ribosomal_L5.
IPR020930. Ribosomal_L5_bac-type.
IPR020929. Ribosomal_L5_CS.
IPR022803. Ribosomal_L5_domain.
[Graphical view]
PANTHERPTHR11994. PTHR11994. 1 hit.
PfamPF00281. Ribosomal_L5. 1 hit.
PF00673. Ribosomal_L5_C. 1 hit.
[Graphical view]
PIRSFPIRSF002161. Ribosomal_L5. 1 hit.
SUPFAMSSF55282. SSF55282. 1 hit.
PROSITEPS00358. RIBOSOMAL_L5. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP62399.
PROP62399.

Entry information

Entry nameRL5_ECOLI
AccessionPrimary (citable) accession number: P62399
Secondary accession number(s): P02389, Q2M6X3
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: July 9, 2014
This is version 110 of the entry and version 2 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