Reviewed, UniProtKB/Swiss-Prot P0AG55 (RL6_ECOLI)

Names and origin

Protein names

Recommended name:
    50S ribosomal protein L6

Gene names

Name:	rplF
Ordered Locus Names:	b3305, JW3267

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	177 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	This protein binds directly to at least 2 domains of the 23S ribosomal RNA, thus is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center. HAMAP MF_01365 Gentamicin-resistant mutations in this protein affect translation fidelity. HAMAP MF_01365
Subunit structure	Part of the 50S ribosomal subunit. HAMAP MF_01365
Sequence similarities	Belongs to the ribosomal protein L6P family.
Mass spectrometry	Molecular mass is 18772.7 Da from positions 2 - 177. Determined by MALDI. Ref.9

Ontologies

Keywords
Biological process	Antibiotic resistance
Ligand	RNA-binding rRNA-binding
Molecular function	Ribonucleoprotein Ribosomal protein
PTM	Acetylation
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	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	protein binding Inferred from physical interaction. Source: IntAct rRNA binding Inferred from electronic annotation. Source: HAMAP structural constituent of ribosome Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
gadE	P63204	1	EBI-546389,EBI-562022

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.1 Ref.5

Chain

2 – 177

176

50S ribosomal protein L6 HAMAP MF_01365

PRO_0000131048

Amino acid modifications

Modified residue

44

1

N6-acetyllysine Ref.10

Natural variations

Natural variant

152 – 177

26

RRPEP…EAKKK → AL in gentamicin resistant strain: GS50-15. HAMAP MF_01365

Natural variant

158 – 177

20

KGKGV…EAKKK → TL in gentamicin resistant strain: GS20-8. HAMAP MF_01365

Experimental info

Sequence conflict

82

1

G → D in CAA25720. Ref.2

Sequence conflict

88

1

Q → E AA sequence Ref.1

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

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177

Helix Strand Turn

Details...

Beta strand

16 – 20

5

Beta strand

23 – 27

5

Beta strand

46 – 49

4

Turn

59 – 61

3

Helix

62 – 80

19

Beta strand

83 – 89

7

Beta strand

100 – 105

6

Beta strand

108 – 111

4

Beta strand

113 – 116

4

Beta strand

132 – 136

5

Helix

138 – 150

13

Beta strand

161 – 164

4

Sequences

	Sequence		Length	Mass (Da)
	P0AG55-1 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: 946B64E9FA42FE61	FASTA	177	18,904
	10 20 30 40 50 60 MSRVAKAPVV VPAGVDVKIN GQVITIKGKN GELTRTLNDA VEVKHADNTL TFGPRDGYAD 70 80 90 100 110 120 GWAQAGTARA LLNSMVIGVT EGFTKKLQLV GVGYRAAVKG NVINLSLGFS HPVDHQLPAG 130 140 150 160 170 ITAECPTQTE IVLKGADKQV IGQVAADLRA YRRPEPYKGK GVRYADEVVR TKEAKKK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The primary structure of protein L6 from the aminoacyl-tRNA binding site of the Escherichia coli ribosome." Chen R., Arfsten U., Chen-Schmeisser U. Hoppe-Seyler's Z. Physiol. Chem. 358:531-535(1977) [PubMed: 324885] [Abstract] Cited for: PRELIMINARY PROTEIN SEQUENCE OF 2-177. Strain: K.
[2]	"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: 6222285] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[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: 9278503] [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: 16738553] [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: 9298646] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-13. Strain: K12 / EMG2.
[6]	"Alteration of ribosomal protein L6 in gentamicin-resistant strains of Escherichia coli. Effects on fidelity of protein synthesis." Kuehberger R., Piepersberg W., Petzet A., Buckel P., Boeck A. Biochemistry 18:187-193(1979) [PubMed: 369594] [Abstract] Cited for: ISOLATION, CHARACTERIZATION OF VARIANTS GENTAMICIN-RESISTANT GE20-8; GS20-10 AND GS50-15. Strain: K12 / A19.
[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: 6170935] [Abstract] Cited for: CROSS-LINKING TO 23S RRNA. Strain: MRE-600.
[8]	"Ribosomal proteins S5 and L6: high-resolution crystal structures and roles in protein synthesis and antibiotic resistance." Davies C., Bussiere D.E., Golden B.L., Porter S.J., Ramakrishnan V., White S.W. J. Mol. Biol. 279:873-888(1998) [PubMed: 9642068] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF VARIANTS GENTAMICIN-RESISTANT.
[9]	"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: 10094780] [Abstract] Cited for: MASS SPECTROMETRY. Strain: K12 / ATCC 25404 / DSM 5698 / NCIMB 11290.
[10]	"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: 18723842] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-44, MASS SPECTROMETRY.
[11]	"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: 10756104] [Abstract] Cited for: 3D-STRUCTURE MODELING.
[12]	"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: 12809609] [Abstract] Cited for: STRUCTURE BY ELECTRON MICROSCOPY (11.50 ANGSTROMS). Strain: MRE-600.
[13]	"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: 16272117] [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

EMBLGenBankDDBJ

X01563 Genomic DNA. Translation: CAA25720.1.
U18997 Genomic DNA. Translation: AAA58102.1.
U00096 Genomic DNA. Translation: AAC76330.1.
AP009048 Genomic DNA. Translation: BAE77986.1.

PIR

R5EC6. D65123.

RefSeq

AP_004485.1.
NP_417764.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1P85	electron microscopy	-	E	2-177	[»]
1P86	electron microscopy	11.50	E	1-177	[»]
1VS6	X-ray	3.46	G	1-177	[»]
1VS8	X-ray	3.46	G	1-177	[»]
2AW4	X-ray	3.46	G	1-177	[»]
2AWB	X-ray	3.46	G	1-177	[»]
2GYA	electron microscopy	-	E	6-171	[»]
2GYC	electron microscopy	2.00	E	6-172	[»]
2I2T	X-ray	3.22	G	2-176	[»]
2I2V	X-ray	3.22	G	2-176	[»]
2J28	electron microscopy	8.00	G	2-176	[»]
2QAM	X-ray	3.21	G	2-177	[»]
2QAO	X-ray	3.21	G	2-177	[»]
2QBA	X-ray	3.54	G	2-177	[»]
2QBC	X-ray	3.54	G	2-177	[»]
2QBE	X-ray	3.30	G	2-177	[»]
2QBG	X-ray	3.30	G	2-177	[»]
2QBI	X-ray	4.00	G	2-177	[»]
2QBK	X-ray	4.00	G	2-177	[»]
2QOV	X-ray	3.93	G	2-177	[»]
2QOX	X-ray	3.93	G	2-177	[»]
2QOZ	X-ray	3.50	G	2-177	[»]
2QP1	X-ray	3.50	G	2-177	[»]
2RDO	electron microscopy	9.10	G	2-177	[»]
2VHM	X-ray	3.74	G	2-177	[»]
2VHN	X-ray	3.74	G	2-177	[»]
2Z4L	X-ray	4.45	G	2-177	[»]
2Z4N	X-ray	4.45	G	2-177	[»]
3BBX	electron microscopy	-	G	2-177	[»]
3FIK	electron microscopy	-	G	2-177	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P0AG55. 83 interactions.

2-D gel databases

ECO2DBASE

I017.2. 6TH EDITION.

Proteomic databases

PRIDE

P0AG55.

Genome annotation databases

GeneID

947803.

GenomeReviews

Gene locus JW3267 in contig AP009048_GR.
Gene locus b3305 in contig U00096_GR.

KEGG

ecj:JW3267.
eco:b3305.

Organism-specific databases

EchoBASE

EB0862.

EcoGene

EG10869. rplF.

CMR

Search...

Phylogenomic databases

HOGENOM

P0AG55.

OMA

P0AG55. RTLVANM.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10869-MON.

Family and domain databases

HAMAP

MF_01365.
[Tree]

InterPro

IPR000702. Ribosomal_L6.
IPR020040. Ribosomal_L6_a/b-dom.
IPR002358. Ribosomal_L6_CS.
IPR019906. Ribosomal_L6_sg.
[Graphical view]

Gene3D

G3DSA:3.90.930.12. Ribosomal_L6. 2 hits.

PANTHER

PTHR11655. Ribosomal_L6. 1 hit.

Pfam

PF00347. Ribosomal_L6. 2 hits.
[Graphical view]

PIRSF

PIRSF002162. Ribosomal_L6. 1 hit.

PRINTS

PR00059. RIBOSOMALL6.

ProDom

PD002236. Ribosomal_L6. 1 hit.
[Graphical view] [Entries sharing at least one domain]

TIGRFAMs

TIGR03654. L6_bact. 1 hit.

PROSITE

PS00525. RIBOSOMAL_L6_1. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

RL6_ECOLI

Accession

Primary (citable) accession number: P0AG55
Secondary accession number(s): P02390, Q2M6X0

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	January 23, 2007
Last modified:	June 16, 2009
This is version 42 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)