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P60723 (RL4_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 120. 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 L4
Gene names
Name:rplD
Synonyms:eryA
Ordered Locus Names:b3319, JW3281
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length201 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. Ref.11

Protein L4 is a both a transcriptional repressor and a translational repressor protein; these two functions are independent of each other. It regulates transcription of the S10 operon (to which L4 belongs) by causing premature termination of transcription within the S10 leader; termination absolutely requires the NusA protein. L4 controls the translation of the S10 operon by binding to its mRNA. The regions of L4 that control regulation (residues 131-210) are different from those required for ribosome assembly (residues 89-103). Ref.11

Forms part of the polypeptide exit tunnel. Ref.11

Can regulate expression from Citrobacter freundii, Haemophilus influenzae, Morganella morganii, Salmonella typhimurium, Serratia marcescens, Vibrio cholerae and Yersinia enterocolitica (but not Pseudomonas aeruginosa) S10 leaders in vitro. Ref.11

Subunit structure

Part of the 50S ribosomal subunit. Ref.10

Miscellaneous

The erythromycin sensitive allele is dominant over the resistant allele.

Sequence similarities

Belongs to the ribosomal protein L4P family.

Mass spectrometry

Molecular mass is 22086.2 Da from positions 1 - 201. Determined by MALDI. Ref.19

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 20120150S ribosomal protein L4 HAMAP-Rule MF_01328_B
PRO_0000129215

Natural variations

Natural variant631K → E in strain: N282; confers erythromycin resistance. Ribosomes bind erythromycin poorly and have reduced peptidyltransferase activity. 50S subunits assemble normally, even in the presence of drug, but assembly is cold-sensitive at 20 degrees Celsius.

Experimental info

Mutagenesis40 – 8849Missing: Regulates the S10 operon normally. Assembles into ribosomes in vivo.
Mutagenesis67 – 10337Missing: Regulates the S10 operon normally. Does not assemble into ribosomes in vivo.
Mutagenesis93 – 1019Missing: Regulates the S10 operon normally. Not stably associated with the ribosome in vivo.
Mutagenesis1311T → I: Does not regulate the S10 operon; assembles into ribosomes in vivo.
Mutagenesis1341L → P: Does not regulate the S10 operon in vivo.
Mutagenesis1601A → V: Does not regulate the S10 operon; assembles into ribosomes in vivo.
Mutagenesis1671V → D: Does not regulate the S10 operon in vivo.
Mutagenesis171 – 20131DATGI…EEMLA → RRSK: Loss of S10 operon regulation. Assembles into ribosomes in vivo.

Secondary structure

............................................ 201
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P60723 [UniParc].

Last modified July 21, 1986. Version 1.
Checksum: 3A953206B0F083B5

FASTA20122,087
        10         20         30         40         50         60 
MELVLKDAQS ALTVSETTFG RDFNEALVHQ VVVAYAAGAR QGTRAQKTRA EVTGSGKKPW 

        70         80         90        100        110        120 
RQKGTGRARS GSIKSPIWRS GGVTFAARPQ DHSQKVNKKM YRGALKSILS ELVRQDRLIV 

       130        140        150        160        170        180 
VEKFSVEAPK TKLLAQKLKD MALEDVLIIT GELDENLFLA ARNLHKVDVR DATGIDPVSL 

       190        200 
IAFDKVVMTA DAVKQVEEML A 

« Hide

References

« Hide 'large scale' references
[1]"The primary structure of protein L4 from the large subunit of the Escherichia coli ribosome."
Kimura M., Wittmann-Liebold B.
FEBS Lett. 121:317-322(1980)
Cited for: PROTEIN SEQUENCE.
[2]"Structure of the Escherichia coli S10 ribosomal protein operon."
Zurawski G., Zurawski S.M.
Nucleic Acids Res. 13:4521-4526(1985) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]"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.
[4]"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.
[5]"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.
[6]"Protein-rRNA binding features and their structural and functional implications in ribosomes as determined by cross-linking studies."
Urlaub H., Kruft V., Bischof O., Mueller E.-C., Wittmann-Liebold B.
EMBO J. 14:4578-4588(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 26-50, CROSS-LINKING TO RRNA.
Strain: MRE-600.
[7]"The use of 2-iminothiolane as an RNA-protein cross-linking agent in Escherichia coli ribosomes, and the localisation on 23S RNA of sites cross-linked to proteins L4, L6, L21, L23, L27 and L29."
Wower I., Wower J., Meinke M., Brimacombe R.
Nucleic Acids Res. 9:4285-4302(1981) [PubMed] [Europe PMC] [Abstract]
Cited for: CROSS-LINKING TO 23S RRNA.
Strain: MRE-600.
[8]"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.
[9]"Biochemical and genetic studies on two different types of erythromycin resistant mutants of Escherichia coli with altered ribosomal proteins."
Wittmann H.G., Stoffler G., Apirion D., Rosen L., Tanaka K., Tamaki M., Takata R., Dekio S., Otaka E.
Mol. Gen. Genet. 127:175-189(1973) [PubMed] [Europe PMC] [Abstract]
Cited for: BIOCHEMICAL CHARACTERIZATION OF AN ERYTHROMYCIN-RESISTANT VARIANT.
Strain: N282.
[10]"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.
Strain: K12.
[11]"Autogenous control of the S10 ribosomal protein operon of Escherichia coli: genetic dissection of transcriptional and posttranscriptional regulation."
Freedman L.P., Zengel J.M., Archer R.H., Lindahl L.
Proc. Natl. Acad. Sci. U.S.A. 84:6516-6520(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN TRANSCRIPTION/TRANSLATION REGULATION.
Strain: K12 / LL308.
[12]"Escherichia coli ribosomal protein L4 stimulates transcription termination at a specific site in the leader of the S10 operon independent of L4-mediated inhibition of translation."
Zengel J.M., Lindahl L.
J. Mol. Biol. 213:67-78(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: MECHANISM OF TRANSCRIPTIONAL REGULATION.
Strain: K12 / LL308.
[13]"Ribosomal protein L4 stimulates in vitro termination of transcription at a NusA-dependent terminator in the S10 operon leader."
Zengel J.M., Lindahl L.
Proc. Natl. Acad. Sci. U.S.A. 87:2675-2679(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: REQUIREMENT FOR NUSA IN TRANSCRIPTION TERMINATION CONTROL.
[14]"Ribosomal protein gene sequence changes in erythromycin-resistant mutants of Escherichia coli."
Chittum H.S., Champney W.S.
J. Bacteriol. 176:6192-6198(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION OF CHANGES IN AN ERYTHROMYCIN-RESISTANT VARIANT.
Strain: N282.
[15]"Erythromycin inhibits the assembly of the large ribosomal subunit in growing Escherichia coli cells."
Chittum H.S., Champney W.S.
Curr. Microbiol. 30:273-279(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: ERYTHROMYCIN AND RIBOSOME ASSEMBLY.
Strain: N282 and SK901.
[16]"Ribosomal protein L4 from Escherichia coli utilizes nonidentical determinants for its structural and regulatory functions."
Li X., Lindahl L., Zengel J.M.
RNA 2:24-37(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: REQUIREMENT FOR RNA-BINDING, MUTAGENESIS, REGULATION-DEFECTIVE MUTANTS.
Strain: K12 / LL308.
[17]"Phylogenetic analysis of L4-mediated autogenous control of the S10 ribosomal protein operon."
Allen T., Shen P., Samsel L., Liu R., Lindahl L., Zengel J.M.
J. Bacteriol. 181:6124-6132(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: ABILITY TO REGULATE S10 OPERON EXPRESSION IN OTHER BACTERIA.
Strain: K12 / LL308.
[18]"The extended loops of ribosomal proteins L4 and L22 are not required for ribosome assembly or L4-mediated autogenous control."
Zengel J.M., Jerauld A., Walker A., Wahl M.C., Lindahl L.
RNA 9:1188-1197(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: REQUIREMENT FOR RIBOSOME ASSEMBLY, S10 OPERON REGULATION.
Strain: K12 / LL308.
[19]"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.
[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]"The polypeptide tunnel system in the ribosome and its gating in erythromycin resistance mutants of L4 and L22."
Gabashvili I.S., Gregory S.T., Valle M., Grassucci R., Worbs M., Wahl M.C., Dahlberg A.E., Frank J.
Mol. Cell 8:181-188(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY ELECTRON MICROSCOPY (17.8 ANGSTROMS), EFFECT OF THE ERYTHROMYCIN-RESISTANT VARIANT ON THE POLYPEPTIDE EXIT TUNNEL.
Strain: N282.
[22]"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
X02613 Genomic DNA. Translation: CAA26461.1.
U18997 Genomic DNA. Translation: AAA58116.1.
U00096 Genomic DNA. Translation: AAC76344.1.
AP009048 Genomic DNA. Translation: BAE77972.1.
PIRR5EC4. C23129.
RefSeqNP_417778.1. NC_000913.3.
YP_492113.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1P85electron microscopy12.30C1-201[»]
1P86electron microscopy11.50C1-201[»]
1VS6X-ray3.46E1-201[»]
1VS8X-ray3.46E1-201[»]
1VT2X-ray3.30E1-201[»]
2AW4X-ray3.46E1-201[»]
2AWBX-ray3.46E1-201[»]
2GYAelectron microscopy15.00C1-198[»]
2GYCelectron microscopy15.00C1-198[»]
2I2TX-ray3.22E1-201[»]
2I2VX-ray3.22E1-201[»]
2J28electron microscopy8.00E1-201[»]
2QAMX-ray3.21E1-201[»]
2QAOX-ray3.21E1-201[»]
2QBAX-ray3.54E1-201[»]
2QBCX-ray3.54E1-201[»]
2QBEX-ray3.30E1-201[»]
2QBGX-ray3.30E1-201[»]
2QBIX-ray4.00E1-201[»]
2QBKX-ray4.00E1-201[»]
2QOVX-ray3.93E1-201[»]
2QOXX-ray3.93E1-201[»]
2QOZX-ray3.50E1-201[»]
2QP1X-ray3.50E1-201[»]
2RDOelectron microscopy9.10E1-201[»]
2VHMX-ray3.74E1-201[»]
2VHNX-ray3.74E1-201[»]
2WWQelectron microscopy5.80E1-201[»]
2Z4LX-ray4.45E1-201[»]
2Z4NX-ray4.45E1-201[»]
3BBXelectron microscopy10.00E1-201[»]
3DF2X-ray3.50E1-201[»]
3DF4X-ray3.50E1-201[»]
3E1Belectron microscopy-11-201[»]
3E1Delectron microscopy-11-201[»]
3FIKelectron microscopy6.70E1-201[»]
3I1NX-ray3.19E1-201[»]
3I1PX-ray3.19E1-201[»]
3I1RX-ray3.81E1-201[»]
3I1TX-ray3.81E1-201[»]
3I20X-ray3.71E1-201[»]
3I22X-ray3.71E1-201[»]
3IZTelectron microscopy-F1-201[»]
3IZUelectron microscopy-F1-201[»]
3J01electron microscopy-E1-201[»]
3J0Telectron microscopy12.10F1-201[»]
3J0Welectron microscopy14.70F1-201[»]
3J0Yelectron microscopy13.50F1-201[»]
3J11electron microscopy13.10F1-201[»]
3J12electron microscopy11.50F1-201[»]
3J14electron microscopy11.50F1-201[»]
3J19electron microscopy8.30E1-201[»]
3J37electron microscopy9.80F1-201[»]
3J4Xelectron microscopy12.00E1-201[»]
3J50electron microscopy20.00E1-201[»]
3J51electron microscopy17.00E1-201[»]
3J52electron microscopy12.00E1-201[»]
3J54electron microscopy13.00E1-201[»]
3J56electron microscopy15.00E1-201[»]
3J58electron microscopy17.00E1-201[»]
3J5Aelectron microscopy12.00E1-201[»]
3J5Celectron microscopy17.00E1-201[»]
3J5Eelectron microscopy17.00E1-201[»]
3J5Gelectron microscopy20.00E1-201[»]
3J5Ielectron microscopy15.00E1-201[»]
3J5Kelectron microscopy9.00E1-201[»]
3J5Oelectron microscopy6.80E1-201[»]
3J5Uelectron microscopy7.60F1-201[»]
3J5Welectron microscopy7.60F1-201[»]
3KCRelectron microscopy-E1-201[»]
3OASX-ray3.25E1-201[»]
3OATX-ray3.25E1-201[»]
3OFCX-ray3.19E1-201[»]
3OFDX-ray3.19E1-201[»]
3OFQX-ray3.10E1-201[»]
3OFRX-ray3.10E1-201[»]
3OFZX-ray3.29E1-201[»]
3OG0X-ray3.29E1-201[»]
3ORBX-ray3.30E1-201[»]
3R8SX-ray3.00E1-201[»]
3R8TX-ray3.00E1-201[»]
3SGFX-ray3.20E1-201[»]
3UOSX-ray3.70E1-201[»]
4GARX-ray3.30E1-201[»]
4GAUX-ray3.30E1-201[»]
4KIXX-ray2.90E1-201[»]
4KIZX-ray2.90E1-201[»]
4KJ1X-ray2.90E1-201[»]
4KJ3X-ray2.90E1-201[»]
4KJ5X-ray2.90E1-201[»]
4KJ7X-ray2.90E1-201[»]
4KJ9X-ray2.90E1-201[»]
4KJBX-ray2.90E1-201[»]
DisProtDP00600.
ProteinModelPortalP60723.
SMRP60723. Positions 1-201.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-35791N.
IntActP60723. 214 interactions.
MINTMINT-1219709.
STRING511145.b3319.

Chemistry

ChEMBLCHEMBL2363135.

Proteomic databases

PaxDbP60723.
PRIDEP60723.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC76344; AAC76344; b3319.
BAE77972; BAE77972; BAE77972.
GeneID12932297.
947818.
KEGGecj:Y75_p3857.
eco:b3319.
PATRIC32122070. VBIEscCol129921_3412.

Organism-specific databases

EchoBASEEB0860.
EcoGeneEG10867. rplD.

Phylogenomic databases

eggNOGCOG0088.
HOGENOMHOG000248766.
KOK02926.
OMAFTQKINK.
OrthoDBEOG6M0T9G.
PhylomeDBP60723.
ProtClustDBPRK05319.

Enzyme and pathway databases

BioCycEcoCyc:EG10867-MONOMER.
ECOL316407:JW3281-MONOMER.

Gene expression databases

GenevestigatorP60723.

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

EvolutionaryTraceP60723.
PROP60723.

Entry information

Entry nameRL4_ECOLI
AccessionPrimary (citable) accession number: P60723
Secondary accession number(s): P02388, Q2M6Y4
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: April 16, 2014
This is version 120 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