Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

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:b3305 , 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 , Panther:IN-FAMILY:PTHR11655:SF6 , PDB:Structure:1EG0 , PDB:Structure:1ML5 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2VHM , PDB:Structure:2VHN , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:487D , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF00347 , Prints:IN-FAMILY:PR00059 , Prosite:IN-FAMILY:PS00525

Ortholog Links: Ecol199310Cyc (Escherichia coli CFT073):C4068 , EcoO157Cyc (Escherichia coli O157:H7 str. EDL933):RPLF , ShigellaCyc (Shigella flexneri 2a str. 2457T):RPLF

Gene-Reaction Schematic: ?

GO Terms:

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

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

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 (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 (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 (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 (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 (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 (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 (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 (summary available)

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


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Chen77a, Link97, UniProt11]
UniProt: Removed.
Chain 2 -> 177
[UniProt09]
UniProt: 50S ribosomal protein L6;
Acetylation-Modification 44
[Zhang09, UniProt11]
UniProt: N6-acetyllysine.
Sequence-Conflict 82
[Cerretti83, UniProt10]
Alternate sequence: D; UniProt: (in Ref. 2; CAA25720);
Sequence-Conflict 88
[Chen77a, UniProt10]
Alternate sequence: E; UniProt: (in Ref. 1; AA sequence);
Extrinsic-Sequence-Variant 152 -> 177
[UniProt10]
Alternate sequence: AL; UniProt: (in gentamicin resistant strain: GS50-15);
Extrinsic-Sequence-Variant 158 -> 177
[UniProt10]
Alternate sequence: TL; 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

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

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." 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

Zhang09: 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


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Sat Nov 22, 2014, BIOCYC13A.