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MetaCyc Polypeptide: 50S ribosomal subunit protein L6

Gene: rplF Accession Numbers: EG10869 (MetaCyc), b3305, ECK3292

Species: Escherichia coli K-12 substr. MG1655

Component of:
50S ribosomal subunit
ribosome

Summary:
The L6 protein is a component of the 50S subunit of the ribosome.

L6 interacts with 23S rRNA [Urlaub95, Osswald90, Uchiumi99]. Interaction appears to be cooperative with L3 [Uchiumi99]. L6 crosslinks to the stem-loop structure in domain V of 23S rRNA [Wower81], but assembles to domain VI [Leffers88]. The L6 binding site within domain VI has been identified [Stelzl00].

L6 is altered in a gentamicin-resistant mutant [Buckel77]. Ribosomes of gentamicin-resistant L6 mutants have altered misreading properties; the L6 alteration is thought to change a parameter of the ribosome function involved in codon recognition [Kuhberger79]. L6 also participates in the binding of dibekacin to ribosomes [Akiyama81].

Mutations in L6 cause a cold-sensitive growth defect as well as defective assembly and maturation of the 30S and 50S subunits of the ribosome at low temperature [Bosl81].

Locations: cytosol, ribosome

Map Position: [3,443,629 <- 3,444,162]

Unification Links: ASAP:ABE-0010827, CGSC:258, DIP:DIP-35860N, EchoBASE:EB0862, EcoGene:EG10869, EcoliWiki:b3305, Mint:MINT-1244940, OU-Microarray:b3305, PortEco:rplF, PR:PRO_000023814, Pride:P0AG55, Protein Model Portal:P0AG55, RefSeq:NP_417764, RegulonDB:EG10869, SMR:P0AG55, String:511145.b3305, Swiss-Model:P0AG55, UniProt:P0AG55

Relationship Links: InterPro:IN-FAMILY:IPR000702, InterPro:IN-FAMILY:IPR002358, InterPro:IN-FAMILY:IPR019906, InterPro:IN-FAMILY:IPR020040, Panther:IN-FAMILY:PTHR11655, PDB:Structure:1EG0, PDB:Structure:1ML5, PDB:Structure:2J28, PDB:Structure:2RDO, PDB:Structure:3BBX, PDB:Structure:3J5L, PDB:Structure:3J7Z, PDB:Structure:3J9Y, PDB:Structure:487D, PDB:Structure:4CSU, PDB:Structure:4U1U, PDB:Structure:4U1V, PDB:Structure:4U20, PDB:Structure:4U24, PDB:Structure:4U25, PDB:Structure:4U26, PDB:Structure:4U27, PDB:Structure:4UY8, PDB:Structure:4V6E, PDB:Structure:4V6K, PDB:Structure:4V6L, PDB:Structure:4V6M, PDB:Structure:4V6N, PDB:Structure:4V6O, PDB:Structure:4V6P, PDB:Structure:4V6Q, PDB:Structure:4V6R, PDB:Structure:4V6S, PDB:Structure:4V6T, PDB:Structure:4V6V, PDB:Structure:4V6Y, PDB:Structure:4V6Z, PDB:Structure:4V7V, PDB:Structure:4V9C, PDB:Structure:4V9D, PDB:Structure:4V9O, PDB:Structure:4V9P, PDB:Structure:4V47, PDB:Structure:4V48, PDB:Structure:4V4H, PDB:Structure:4V4Q, PDB:Structure:4V4V, PDB:Structure:4V4W, PDB:Structure:4V50, PDB:Structure:4V52, PDB:Structure:4V53, PDB:Structure:4V54, PDB:Structure:4V55, PDB:Structure:4V56, PDB:Structure:4V57, PDB:Structure:4V5B, PDB:Structure:4V5H, PDB:Structure:4V5Y, PDB:Structure:4V64, PDB:Structure:4V65, PDB:Structure:4V66, PDB:Structure:4V69, PDB:Structure:4V6C, PDB:Structure:4V6D, PDB:Structure:4V70, PDB:Structure:4V71, PDB:Structure:4V72, PDB:Structure:4V73, PDB:Structure:4V74, PDB:Structure:4V75, PDB:Structure:4V76, PDB:Structure:4V77, PDB:Structure:4V78, PDB:Structure:4V79, PDB:Structure:4V7A, PDB:Structure:4V7B, PDB:Structure:4V7C, PDB:Structure:4V7D, PDB:Structure:4V7I, PDB:Structure:4V7S, PDB:Structure:4V7T, PDB:Structure:4V7U, PDB:Structure:4V85, PDB:Structure:4V89, PDB:Structure:4WF1, PDB:Structure:4WWW, PDB:Structure:4YBB, PDB:Structure:5AFI, PDB:Structure:5AKA, Pfam:IN-FAMILY:PF00347, Prints:IN-FAMILY:PR00059, Prosite:IN-FAMILY:PS00525

Gene-Reaction Schematic

Gene-Reaction Schematic


GO Terms:
Biological Process:
Inferred by computational analysisGO:0006412 - translation [GOA06, GOA01a]
Inferred by computational analysisGO:0046677 - response to antibiotic [UniProtGOA11a]
Molecular Function:
Inferred by computational analysisGO:0003723 - RNA binding [UniProtGOA11a]
Inferred by computational analysisGO:0003735 - structural constituent of ribosome [GOA01a]
Inferred by computational analysisGO:0019843 - rRNA binding [UniProtGOA11a, GOA06, GOA01a]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005829 - cytosol [DiazMejia09, Ishihama08]
Inferred from experimentGO:0022625 - cytosolic large ribosomal subunit [Hindennach71]
Inferred by computational analysisGO:0005622 - intracellular [GOA01a]
Inferred by computational analysisGO:0005840 - ribosome [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0030529 - ribonucleoprotein complex [UniProtGOA11a]

MultiFun Terms: cell structureribosomes
information transferprotein relatedribosomal proteins
information transferprotein relatedtranslation

Credits:
Last-Curated 03-Apr-2006 by Keseler I, SRI International


Subunit of: 50S ribosomal subunit

Synonyms: ribosome, large subunit

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of 50S ribosomal subunit = [RplA][RplB][RplC][RplD][RplE][RplF][(RplJ)([RplL]2)2][RplI][RplJ][RplK][RplM][RplN][RplO][RplP][RplQ][RplR][RplS][RplT][RplU][RplV][RplW][RplX][RplY][RpmA][RpmB][RpmC][RpmD][RpmE][RpmF][RpmG][RpmH][RpmI][RpmJ][5S ribosomal RNA (rrfA)][23S ribosomal RNA (rrlA)]
         50S ribosomal subunit protein L1 = RplA (extended summary available)
         50S ribosomal subunit protein L2 = RplB (summary available)
         50S ribosomal subunit protein L3 = RplC (summary available)
         50S ribosomal subunit protein L4 = RplD (extended summary available)
         50S ribosomal subunit protein L5 = RplE (extended summary available)
         50S ribosomal subunit protein L6 = RplF (summary available)
         50S ribosomal protein complex L8 = (RplJ)([RplL]2)2
                 50S ribosomal subunit protein L10 = RplJ (extended summary available)
                 50S ribosomal subunit protein L7/L12 dimer = (RplL)2
                         50S ribosomal subunit protein L12 = RplL
         50S ribosomal subunit protein L9 = RplI (extended summary available)
         50S ribosomal subunit protein L10 = RplJ (extended summary available)
         50S ribosomal subunit protein L11 = RplK (extended summary available)
         50S ribosomal subunit protein L13 = RplM (extended summary available)
         50S ribosomal subunit protein L14 = RplN (extended summary available)
         50S ribosomal subunit protein L15 = RplO (summary available)
         50S ribosomal subunit protein L16 = RplP (extended summary available)
         50S ribosomal subunit protein L17 = RplQ (summary available)
         50S ribosomal subunit protein L18 = RplR (extended summary available)
         50S ribosomal subunit protein L19 = RplS (extended summary available)
         50S ribosomal subunit protein L20 = RplT (extended summary available)
         50S ribosomal subunit protein L21 = RplU (summary available)
         50S ribosomal subunit protein L22 = RplV (extended summary available)
         50S ribosomal subunit protein L23 = RplW (extended summary available)
         50S ribosomal subunit protein L24 = RplX (summary available)
         50S ribosomal subunit protein L25 = RplY (extended summary available)
         50S ribosomal subunit protein L27 = RpmA (extended summary available)
         50S ribosomal subunit protein L28 = RpmB (summary available)
         50S ribosomal subunit protein L29 = RpmC (summary available)
         50S ribosomal subunit protein L30 = RpmD (summary available)
         50S ribosomal subunit protein L31 = RpmE (summary available)
         50S ribosomal subunit protein L32 = RpmF (summary available)
         50S ribosomal subunit protein L33 = RpmG (summary available)
         50S ribosomal subunit protein L34 = RpmH (summary available)
         50S ribosomal subunit protein L35 = RpmI (summary available)
         50S ribosomal subunit protein L36 = RpmJ (extended summary available)

Component of: ribosome

Credits:
Created 02-Jun-2006 by Keseler I, SRI International


Subunit of: ribosome

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of ribosome = [(RpsA)(RpsB)(RpsC)(RpsD)(RpsE)(RpsF)(RpsG)(RpsH)(RpsI)(RpsJ)(RpsK)(RpsL)(RpsM)(RpsN)(RpsO)(RpsP)(RpsQ)(RpsR)(RpsS)(RpsT)(RpsU)(Sra)(16S ribosomal RNA (rrsA))][(RplA)(RplB)(RplC)(RplD)(RplE)(RplF)([RplJ][(RplL)2]2)(RplI)(RplJ)(RplK)(RplM)(RplN)(RplO)(RplP)(RplQ)(RplR)(RplS)(RplT)(RplU)(RplV)(RplW)(RplX)(RplY)(RpmA)(RpmB)(RpmC)(RpmD)(RpmE)(RpmF)(RpmG)(RpmH)(RpmI)(RpmJ)(5S ribosomal RNA (rrfA))(23S ribosomal RNA (rrlA))]
         30S ribosomal subunit = (RpsA)(RpsB)(RpsC)(RpsD)(RpsE)(RpsF)(RpsG)(RpsH)(RpsI)(RpsJ)(RpsK)(RpsL)(RpsM)(RpsN)(RpsO)(RpsP)(RpsQ)(RpsR)(RpsS)(RpsT)(RpsU)(Sra)(16S ribosomal RNA (rrsA))
                 30S ribosomal subunit protein S1 = RpsA (extended summary available)
                 30S ribosomal subunit protein S2 = RpsB (summary available)
                 30S ribosomal subunit protein S3 = RpsC (summary available)
                 30S ribosomal subunit protein S4 = RpsD (extended summary available)
                 30S ribosomal subunit protein S5 = RpsE (extended summary available)
                 30S ribosomal subunit protein S6 = RpsF (extended summary available)
                 30S ribosomal subunit protein S7 = RpsG (extended summary available)
                 30S ribosomal subunit protein S8 = RpsH (extended summary available)
                 30S ribosomal subunit protein S9 = RpsI (extended summary available)
                 30S ribosomal subunit protein S10 = RpsJ (extended summary available)
                 30S ribosomal subunit protein S11 = RpsK (summary available)
                 30S ribosomal subunit protein S12 = RpsL (extended summary available)
                 30S ribosomal subunit protein S13 = RpsM (extended summary available)
                 30S ribosomal subunit protein S14 = RpsN (summary available)
                 30S ribosomal subunit protein S15 = RpsO (extended summary available)
                 30S ribosomal subunit protein S16 = RpsP (summary available)
                 30S ribosomal subunit protein S17 = RpsQ (summary available)
                 30S ribosomal subunit protein S18 = RpsR (extended summary available)
                 30S ribosomal subunit protein S19 = RpsS (summary available)
                 30S ribosomal subunit protein S20 = RpsT (extended summary available)
                 30S ribosomal subunit protein S21 = RpsU (summary available)
                 30S ribosomal subunit protein S22 = Sra (summary available)
         50S ribosomal subunit = (RplA)(RplB)(RplC)(RplD)(RplE)(RplF)([RplJ][(RplL)2]2)(RplI)(RplJ)(RplK)(RplM)(RplN)(RplO)(RplP)(RplQ)(RplR)(RplS)(RplT)(RplU)(RplV)(RplW)(RplX)(RplY)(RpmA)(RpmB)(RpmC)(RpmD)(RpmE)(RpmF)(RpmG)(RpmH)(RpmI)(RpmJ)(5S ribosomal RNA (rrfA))(23S ribosomal RNA (rrlA))
                 50S ribosomal subunit protein L1 = RplA (extended summary available)
                 50S ribosomal subunit protein L2 = RplB (summary available)
                 50S ribosomal subunit protein L3 = RplC (summary available)
                 50S ribosomal subunit protein L4 = RplD (extended summary available)
                 50S ribosomal subunit protein L5 = RplE (extended summary available)
                 50S ribosomal subunit protein L6 = RplF (summary available)
                 50S ribosomal protein complex L8 = (RplJ)([RplL]2)2
                         50S ribosomal subunit protein L10 = RplJ (extended summary available)
                         50S ribosomal subunit protein L7/L12 dimer = (RplL)2
                                 50S ribosomal subunit protein L12 = RplL
                 50S ribosomal subunit protein L9 = RplI (extended summary available)
                 50S ribosomal subunit protein L10 = RplJ (extended summary available)
                 50S ribosomal subunit protein L11 = RplK (extended summary available)
                 50S ribosomal subunit protein L13 = RplM (extended summary available)
                 50S ribosomal subunit protein L14 = RplN (extended summary available)
                 50S ribosomal subunit protein L15 = RplO (summary available)
                 50S ribosomal subunit protein L16 = RplP (extended summary available)
                 50S ribosomal subunit protein L17 = RplQ (summary available)
                 50S ribosomal subunit protein L18 = RplR (extended summary available)
                 50S ribosomal subunit protein L19 = RplS (extended summary available)
                 50S ribosomal subunit protein L20 = RplT (extended summary available)
                 50S ribosomal subunit protein L21 = RplU (summary available)
                 50S ribosomal subunit protein L22 = RplV (extended summary available)
                 50S ribosomal subunit protein L23 = RplW (extended summary available)
                 50S ribosomal subunit protein L24 = RplX (summary available)
                 50S ribosomal subunit protein L25 = RplY (extended summary available)
                 50S ribosomal subunit protein L27 = RpmA (extended summary available)
                 50S ribosomal subunit protein L28 = RpmB (summary available)
                 50S ribosomal subunit protein L29 = RpmC (summary available)
                 50S ribosomal subunit protein L30 = RpmD (summary available)
                 50S ribosomal subunit protein L31 = RpmE (summary available)
                 50S ribosomal subunit protein L32 = RpmF (summary available)
                 50S ribosomal subunit protein L33 = RpmG (summary available)
                 50S ribosomal subunit protein L34 = RpmH (summary available)
                 50S ribosomal subunit protein L35 = RpmI (summary available)
                 50S ribosomal subunit protein L36 = RpmJ (extended summary available)

Enzymes activated by ribosome, sorted by the type of activation, are:

Activator (Mechanism unknown) of: ATPase [Becker12]

Credits:
Created 15-Jun-2006 by Keseler I, SRI International


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
Inferred from experiment[Link97, Chen77a]
UniProt: Removed.
Chain 2 -> 177
Author statement[UniProt15]
UniProt: 50S ribosomal protein L6.
N6-acetyllysine-Modification 44
Inferred from experiment[Zhang09c]
UniProt: N6-acetyllysine.
Sequence-Conflict 82
Inferred by curator[Cerretti83, UniProt15]
UniProt: (in Ref. 2; CAA25720).
Sequence-Conflict 88
Inferred by curator[Chen77a, UniProt15]
UniProt: (in Ref. 1; AA sequence).
Extrinsic-Sequence-Variant 152 -> 177
Inferred from experiment[Kuhberger79]
UniProt: In gentamicin resistant strain: GS50-15..
Extrinsic-Sequence-Variant 158 -> 177
Inferred from experiment[Kuhberger79]
UniProt: In gentamicin resistant strain: GS20-8..

History:
10/20/97 Gene b3305 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10869.


References

Akiyama81: Akiyama T, Tanaka N (1981). "Ribosomal proteins S9 and L6 participate in the binding of [3H]dibekacin to E. coli ribosomes." J Antibiot (Tokyo) 34(6);763-9. PMID: 6268595

Becker12: Becker M, Gzyl KE, Altamirano AM, Vuong A, Urban K, Wieden HJ (2012). "The 70S ribosome modulates the ATPase activity of Escherichia coli YchF." RNA Biol 9(10);1288-301. PMID: 22995830

Bosl81: Bosl A, Bock A (1981). "Ribosomal mutation in Escherichia coli affecting membrane stability." Mol Gen Genet 182(2);358-60. PMID: 7026977

Buckel77: Buckel P, Buchberger A, Bock A, Wittmann HG (1977). "Alteration of ribosomal protein L6 in mutants of Escherichia coli resistant to gentamicin." Mol Gen Genet 158(1);47-54. PMID: 342908

Cerretti83: Cerretti DP, Dean D, Davis GR, Bedwell DM, Nomura M (1983). "The spc ribosomal protein operon of Escherichia coli: sequence and cotranscription of the ribosomal protein genes and a protein export gene." Nucleic Acids Res 11(9);2599-616. PMID: 6222285

Chen77a: Chen R, Arfsten U, Chen-Schmeisser U (1977). "The primary structure of protein L6 from the aminoacyl-tRNA binding site of the Escherichia coli ribosome." Hoppe Seylers Z Physiol Chem 358(4);531-5. PMID: 324885

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Hindennach71: Hindennach I, Kaltschmidt E, Wittmann HG (1971). "Ribosomal proteins. Isolation of proteins from 50S ribosomal subunits of Escherichia coli." Eur J Biochem 23(1);12-6. PMID: 4942547

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Kuhberger79: Kuhberger R, Piepersberg W, Petzet A, Buckel P, Bock A (1979). "Alteration of ribosomal protein L6 in gentamicin-resistant strains of Escherichia coli. Effects on fidelity of protein synthesis." Biochemistry 18(1);187-93. PMID: 369594

Leffers88: Leffers H, Egebjerg J, Andersen A, Christensen T, Garrett RA (1988). "Domain VI of Escherichia coli 23 S ribosomal RNA. Structure, assembly and function." J Mol Biol 204(3);507-22. PMID: 2465415

Link97: Link AJ, Robison K, Church GM (1997). "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Electrophoresis 18(8);1259-313. PMID: 9298646

Osswald90: Osswald M, Greuer B, Brimacombe R (1990). "Localization of a series of RNA-protein cross-link sites in the 23S and 5S ribosomal RNA from Escherichia coli, induced by treatment of 50S subunits with three different bifunctional reagents." Nucleic Acids Res 18(23);6755-60. PMID: 1702198

Stelzl00: Stelzl U, Spahn CM, Nierhaus KH (2000). "Selecting rRNA binding sites for the ribosomal proteins L4 and L6 from randomly fragmented rRNA: application of a method called SERF." Proc Natl Acad Sci U S A 97(9);4597-602. PMID: 10781065

Uchiumi99: Uchiumi T, Sato N, Wada A, Hachimori A (1999). "Interaction of the sarcin/ricin domain of 23 S ribosomal RNA with proteins L3 and L6." J Biol Chem 274(2);681-6. PMID: 9873002

UniProt15: UniProt Consortium (2015). "UniProt version 2015-08 released on 2015-07-22." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Urlaub95: Urlaub H, Kruft V, Bischof O, Muller EC, Wittmann-Liebold B (1995). "Protein-rRNA binding features and their structural and functional implications in ribosomes as determined by cross-linking studies." EMBO J 14(18);4578-88. PMID: 7556101

Wower81: Wower I, Wower J, Meinke M, Brimacombe R (1981). "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." Nucleic Acids Res 9(17);4285-302. PMID: 6170935

Zhang09c: Zhang J, Sprung R, Pei J, Tan X, Kim S, Zhu H, Liu CF, Grishin NV, Zhao Y (2009). "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Mol Cell Proteomics 8(2);215-25. PMID: 18723842


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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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