P60723 (RL4_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
50S ribosomal protein L4

Gene names

Name:	rplD
Synonyms:	eryA
Ordered Locus Names:	b3319, JW3281

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	201 AA.
Sequence status	Complete.
Protein existence	Evidence 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. HAMAP-Rule MF_01328_B
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

Ontologies

Keywords
Biological process	Antibiotic resistance Transcription Transcription regulation Transcription termination Translation regulation
Ligand	RNA-binding rRNA-binding
Molecular function	Repressor Ribonucleoprotein Ribosomal protein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	DNA-dependent transcription, termination Inferred from electronic annotation. Source: UniProtKB-KW regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW response to antibiotic Inferred from electronic annotation. Source: UniProtKB-KW translation Inferred from electronic annotation. Source: HAMAP
Cellular_component	ribosome Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	rRNA binding Inferred from electronic annotation. Source: HAMAP structural constituent of ribosome Inferred from electronic annotation. Source: InterPro translation repressor activity Inferred from direct assay PubMed 6996835. Source: EcoliWiki
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 201

201

50S ribosomal protein L4 HAMAP-Rule MF_01328_B

PRO_0000129215

Natural variations

Natural variant

63

1

K → 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

Mutagenesis

40 – 88

49

Missing: Regulates the S10 operon normally. Assembles into ribosomes in vivo.

Mutagenesis

67 – 103

37

Missing: Regulates the S10 operon normally. Does not assemble into ribosomes in vivo.

Mutagenesis

93 – 101

9

Missing: Regulates the S10 operon normally. Not stably associated with the ribosome in vivo.

Mutagenesis

131

1

T → I: Does not regulate the S10 operon; assembles into ribosomes in vivo.

Mutagenesis

134

1

L → P: Does not regulate the S10 operon in vivo.

Mutagenesis

160

1

A → V: Does not regulate the S10 operon; assembles into ribosomes in vivo.

Mutagenesis

167

1

V → D: Does not regulate the S10 operon in vivo.

Mutagenesis

171 – 201

31

DATGI…EEMLA → RRSK: Loss of S10 operon regulation. Assembles into ribosomes in vivo.

Secondary structure

1

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201

Helix Strand Turn

Details...

Turn

6 – 8

3

Helix

16 – 19

4

Beta strand

22 – 24

3

Helix

25 – 36

12

Turn

37 – 39

3

Turn

49 – 51

3

Beta strand

52 – 54

3

Beta strand

62 – 67

6

Beta strand

78 – 81

4

Beta strand

83 – 85

3

Helix

98 – 114

17

Beta strand

118 – 120

3

Beta strand

121 – 123

3

Beta strand

127 – 129

3

Helix

131 – 141

11

Beta strand

144 – 152

9

Helix

155 – 159

5

Beta strand

160 – 163

4

Beta strand

165 – 171

7

Helix

172 – 174

3

Helix

177 – 182

6

Beta strand

183 – 188

6

Helix

190 – 200

11

Sequences

	Sequence		Length	Mass (Da)
	P60723 [UniParc]. Last modified July 21, 1986. Version 1. Checksum: 3A953206B0F083B5	FASTA	201	22,087
	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

References

	« Hide 'large scale' referencesShow '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 277:1453-1474(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.

PIR

R5EC4. C23129.

RefSeq

NP_417778.1. NC_000913.2.
YP_492113.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1P85	electron microscopy	12.30	C	1-201	[»]
1P86	electron microscopy	11.50	C	1-201	[»]
1VS6	X-ray	3.46	E	1-201	[»]
1VS8	X-ray	3.46	E	1-201	[»]
1VT2	X-ray	3.30	E	1-201	[»]
2AW4	X-ray	3.46	E	1-201	[»]
2AWB	X-ray	3.46	E	1-201	[»]
2GYA	electron microscopy	15.00	C	1-198	[»]
2GYC	electron microscopy	15.00	C	1-198	[»]
2I2T	X-ray	3.22	E	1-201	[»]
2I2V	X-ray	3.22	E	1-201	[»]
2J28	electron microscopy	8.00	E	1-201	[»]
2QAM	X-ray	3.21	E	1-201	[»]
2QAO	X-ray	3.21	E	1-201	[»]
2QBA	X-ray	3.54	E	1-201	[»]
2QBC	X-ray	3.54	E	1-201	[»]
2QBE	X-ray	3.30	E	1-201	[»]
2QBG	X-ray	3.30	E	1-201	[»]
2QBI	X-ray	4.00	E	1-201	[»]
2QBK	X-ray	4.00	E	1-201	[»]
2QOV	X-ray	3.93	E	1-201	[»]
2QOX	X-ray	3.93	E	1-201	[»]
2QOZ	X-ray	3.50	E	1-201	[»]
2QP1	X-ray	3.50	E	1-201	[»]
2RDO	electron microscopy	9.10	E	1-201	[»]
2VHM	X-ray	3.74	E	1-201	[»]
2VHN	X-ray	3.74	E	1-201	[»]
2WWQ	electron microscopy	5.80	E	1-201	[»]
2Z4L	X-ray	4.45	E	1-201	[»]
2Z4N	X-ray	4.45	E	1-201	[»]
3BBX	electron microscopy	10.00	E	1-201	[»]
3DF2	X-ray	3.50	E	1-201	[»]
3DF4	X-ray	3.50	E	1-201	[»]
3E1B	electron microscopy	-	1	1-201	[»]
3E1D	electron microscopy	-	1	1-201	[»]
3FIK	electron microscopy	6.70	E	1-201	[»]
3I1N	X-ray	3.19	E	1-201	[»]
3I1P	X-ray	3.19	E	1-201	[»]
3I1R	X-ray	3.81	E	1-201	[»]
3I1T	X-ray	3.81	E	1-201	[»]
3I20	X-ray	3.71	E	1-201	[»]
3I22	X-ray	3.71	E	1-201	[»]
3IZT	electron microscopy	-	F	1-201	[»]
3IZU	electron microscopy	-	F	1-201	[»]
3J01	electron microscopy	-	E	1-201	[»]
3J0T	electron microscopy	12.10	F	1-201	[»]
3J0W	electron microscopy	14.70	F	1-201	[»]
3J0Y	electron microscopy	13.50	F	1-201	[»]
3J11	electron microscopy	13.10	F	1-201	[»]
3J12	electron microscopy	11.50	F	1-201	[»]
3J14	electron microscopy	11.50	F	1-201	[»]
3J19	electron microscopy	8.30	E	1-201	[»]
3KCR	electron microscopy	-	E	1-201	[»]
3OAS	X-ray	3.25	E	1-201	[»]
3OAT	X-ray	3.25	E	1-201	[»]
3OFC	X-ray	3.19	E	1-201	[»]
3OFD	X-ray	3.19	E	1-201	[»]
3OFQ	X-ray	3.10	E	1-201	[»]
3OFR	X-ray	3.10	E	1-201	[»]
3OFZ	X-ray	3.29	E	1-201	[»]
3OG0	X-ray	3.29	E	1-201	[»]
3ORB	X-ray	3.30	E	1-201	[»]
3R8S	X-ray	3.00	E	1-201	[»]
3R8T	X-ray	3.00	E	1-201	[»]
3SGF	X-ray	3.20	E	1-201	[»]
3UOS	X-ray	3.70	E	1-201	[»]
4GAR	X-ray	3.30	E	1-201	[»]
4GAU	X-ray	3.30	E	1-201	[»]

ProteinModelPortal

P60723.

SMR

P60723. Positions 1-201.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-35791N.

IntAct

P60723. 213 interactions.

MINT

MINT-1219709.

STRING

511145.b3319.

Proteomic databases

PaxDb

P60723.

PRIDE

P60723.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76344; AAC76344; b3319.
BAE77972; BAE77972; BAE77972.

GeneID

12932297.
947818.

KEGG

ecj:Y75_p3857.
eco:b3319.

PATRIC

32122070. VBIEscCol129921_3412.

Organism-specific databases

EchoBASE

EB0860.

EcoGene

EG10867. rplD.

Phylogenomic databases

eggNOG

COG0088.

HOGENOM

HOG000248766.

KO

K02926.

OMA

FDILNAN.

ProtClustDB

PRK05319.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10867-MONOMER.
ECOL316407:JW3281-MONOMER.

Gene expression databases

Genevestigator

P60723.

Family and domain databases

Gene3D

3.40.1370.10. 1 hit.

HAMAP

MF_01328_B. Ribosomal_L4_B.

InterPro

IPR002136. Ribosomal_L4/L1e.
IPR013005. Ribosomal_L4/L1e_bac-type.
IPR023574. Ribosomal_L4_dom.
[Graphical view]

PANTHER

PTHR10746. PTHR10746. 1 hit.

Pfam

PF00573. Ribosomal_L4. 1 hit.
[Graphical view]

SUPFAM

SSF52166. Ribosomal_L4/L1E. 1 hit.

TIGRFAMs

TIGR03953. rplD_bact. 1 hit.

ProtoNet

Search...

Other

ChEMBL

CHEMBL1931.

EvolutionaryTrace

P60723.

Entry information

Entry name

RL4_ECOLI

Accession

Primary (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:	May 1, 2013
This is version 111 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program