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MetaCyc Polypeptide: 50S ribosomal subunit protein L25

Gene: rplY Accession Numbers: EG10885 (MetaCyc), b2185, ECK2179

Species: Escherichia coli K-12 substr. MG1655

Component of:
50S ribosomal subunit
ribosome

Summary:
The L25 protein is a component of the 50S subunit of the ribosome and binds to 5S rRNA. L25 is not an essential protein [Korepanov07].

Binding of L25 to 5S rRNA has been studied in detail [Spierer78, Spierer78a, Douthwaite79, Osterberg79, Garrett79, Speek82, Huber84, Kime83, Kime84, Kime84a, Szymkowiak85, Goringer86, Leontis86, Leontis86a, Shpanchenko96]. Solution structures of L25 alone and in complex with a segment of 5S rRNA has been determined [Stoldt98, Wohnert99, Stoldt99], and a crystal structure of L25 bound to a loop E-containing fragment of 5S rRNA has been solved at 1.8 Å resolution [Lu00a]. The interaction of L25 with 5S rRNA is not required for incorporation of L25 into the ribosome, although it is important for its retention [Anikaev14].

L25 can be crosslinked to 23 S rRNA in the initiation complex [Chistyakov89] and to ribosomal protein L19 [Walleczek89, Redl89, Walleczek89a].

A truncated form of L25 can be detected in 2-D gels [Wasinger98]. L25 is not posttranslationally modified [Arnold99].

An rplY deletion mutant is viable, but has a slower growth rate than wild type. Mutant ribosomes lack only L25 and are impaired in protein biosynthesis [Korepanov07].

Citations: [Fuenteun75, GauntKlopfer75, Sander75, Dovgas75, Ulbrich75, Bitar75, Gast76, Chu76, Osterberg76, Branlant76, ChenSchmeisser77, Morrison77, Bear77, Gray73, Hernandez77, Branlant77, Fox78, Zimmermann78, Krassnigg78, Schnier79, Newberry80, Maimets, Kime81, Guerin, Metspalu82, Douthwaite82, Gimautdinova, Pieler82, Parker83, Silberklang83, Tumanova83, Tewari83, vandeVen83, Moore83, Tate83, AbdelMeguid83, Tumanova, Bausk, Gimautdinova85, Gewirth87, Fox88, Lotti89, Dontsova90, Herfurth95, Willumeit01, Reblova04, Chigradze]

Locations: cytosol, ribosome

Map Position: [2,280,539 -> 2,280,823]

Molecular Weight of Polypeptide: 12.0 kD (experimental) [Giri79 ]

Unification Links: ASAP:ABE-0007231 , CGSC:242 , DIP:DIP-35885N , EchoBASE:EB0878 , EcoGene:EG10885 , EcoliWiki:b2185 , Mint:MINT-1261165 , ModBase:P68919 , OU-Microarray:b2185 , PortEco:b2185 , PR:PRO_000023831 , Pride:P68919 , Protein Model Portal:P68919 , RefSeq:NP_416690 , RegulonDB:EG10885 , SMR:P68919 , String:511145.b2185 , UniProt:P68919

Relationship Links: InterPro:IN-FAMILY:IPR011035 , InterPro:IN-FAMILY:IPR020055 , InterPro:IN-FAMILY:IPR020056 , PDB:Structure:1B75 , PDB:Structure:1D6K , PDB:Structure:1DFU , 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:3DF2 , PDB:Structure:3DF4 , 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:3J4X , 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:3J50 , PDB:Structure:3J51 , PDB:Structure:3J52 , PDB:Structure:3J54 , PDB:Structure:3J56 , PDB:Structure:3J58 , PDB:Structure:3J5A , PDB:Structure:3J5C , PDB:Structure:3J5E , PDB:Structure:3J5G , PDB:Structure:3J5I , PDB:Structure:3J5K , PDB:Structure:3J5L , PDB:Structure:3J5O , PDB:Structure:3J5U , PDB:Structure:3J5W , 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:PF01386 , ProDom:IN-FAMILY:PD012503

Ortholog Links: Ecol199310Cyc (Escherichia coli CFT073):C2722 , EcoO157Cyc (Escherichia coli O157:H7 str. EDL933):RPLY , ShigellaCyc (Shigella flexneri 2a str. 2457T):RPLY

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01a]
Molecular Function: GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01a]
GO:0008097 - 5S rRNA binding Inferred by computational analysis [GOA01a]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a]
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 ? 19-May-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 (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 (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 (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 (summary available)

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


Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 86 -> 94
[Richterich93, UniProt10a]
UniProt: (in Ref. 6; AAA16413);

History:
10/20/97 Gene b2185 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10885; confirmed by SwissProt match.


References

AbdelMeguid83: Abdel-Meguid SS, Moore PB, Steitz TA (1983). "Crystallization of a ribonuclease-resistant fragment of Escherichia coli 5 S ribosomal RNA and its complex with protein L25." J Mol Biol 171(2);207-15. PMID: 6197527

Anikaev14: Anikaev AY, Korepanov AP, Korobeinikova AV, Kljashtorny VG, Piendl W, Nikonov SV, Garber MB, Gongadze GM (2014). "Mutant forms of Escherichia coli protein L25 unable to bind to 5S rRNA are incorporated efficiently into the ribosome in vivo." Biochemistry (Mosc) 79(8);826-35. PMID: 25365493

Arnold99: Arnold RJ, Reilly JP (1999). "Observation of Escherichia coli ribosomal proteins and their posttranslational modifications by mass spectrometry." Anal Biochem 269(1);105-12. PMID: 10094780

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Bear77: Bear DG, Schleich T, Noller HF, Garrett RA (1977). "Alteration of 5S RNA conformation by ribosomal proteins L18 and L25." Nucleic Acids Res 4(7);2511-26. PMID: 333392

Bitar75: Bitar KG, Wittmann-Liebold B (1975). "The primary structure of the 5s rRNA binding protein L25 of Escherichia coli ribosomes." Hoppe Seylers Z Physiol Chem 356(9);1343-52. PMID: 1100506

Branlant76: Branlant C, Krol A, Sriwidada J, Brimacombe R (1976). "RNA sequences associated with proteins L1, L9, and L5, L18, L25, in ribonucleoprotein fragments isolated from the 50-S subunit of Escherichia coli ribosomes." Eur J Biochem 70(2);483-92. PMID: 827440

Branlant77: Branlant C, Widada JS, Krol A, Ebel JP (1977). "Studies on the primary structure of the ribosomal 23S RNA of Escherichia coli: II. A characterisation and an alignment of 24 sections spanning the entire molecule and its application to the localisation of specific fragments." Nucleic Acids Res 4(12);4323-45. PMID: 414209

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Dovgas75: Dovgas NV, Markova LF, Mednikova TA, Vinokurov LM, Alakhov YB, Ovhinnikov YA (1975). "The primary structure of the 5 S RNA binding protein L25 from Escherichia coli ribosomes." FEBS Lett 53(3);351-4. PMID: 1093874

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Fox88: Fox JW, Owens DP, Wong KP (1988). "Purification and conformation of ribosomal protein L25 from E. coli ribosome." Int J Pept Protein Res 31(3);255-64. PMID: 3286550

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Garrett79: Garrett RA, Noller HF (1979). "Structures of complexes of 5S RNA with ribosomal proteins L5, L18 and L25 from Escherichia coli: identification of kethoxal-reactive sites on the 5S RNA." J Mol Biol 132(4);637-48. PMID: 393829

Gast76: Gast WH, Leberman R (1976). "Release of certain ribosomal proteins from 70-S Escherichia coli ribosomes by mild ribonuclease digestion." Biochim Biophys Acta 432(1);98-103. PMID: 769834

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Gimautdinova: Gimautdinova OI, Karpova GG, Kozyreva NA "[Affinity labeling of ribosomes from Escherichia coli with 4-(N-2-chloroethyl-N-methylamino) benzyl-5'-phosphamides of oligouridylates of different length]." Mol Biol (Mosk) 16(4);752-62. PMID: 6750359

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Herfurth95: Herfurth E, Wittmann-Liebold B (1995). "Determination of peptide regions exposed at the surface of the bacterial ribosome with antibodies against synthetic peptides." Biol Chem Hoppe Seyler 376(2);81-90. PMID: 7794529

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Huber84: Huber PW, Wool IG (1984). "Nuclease protection analysis of ribonucleoprotein complexes: use of the cytotoxic ribonuclease alpha-sarcin to determine the binding sites for Escherichia coli ribosomal proteins L5, L18, and L25 on 5S rRNA." Proc Natl Acad Sci U S A 81(2);322-6. PMID: 6364140

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

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Kime83: Kime MJ, Moore PB (1983). "Nuclear Overhauser experiments at 500 MHz on the downfield proton spectra of 5S ribonucleic acid and its complex with ribosomal protein L25." Biochemistry 22(11);2622-9. PMID: 6347250

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Leontis86a: Leontis NB, Ghosh P, Moore PB (1986). "Effect of magnesium ion on the structure of the 5S RNA from Escherichia coli. An imino proton magnetic resonance study of the helix I, IV, and V regions of the molecule." Biochemistry 25(23);7386-92. PMID: 3542026

Lotti89: Lotti M, Noah M, Stoffler-Meilicke M, Stoffler G (1989). "Localization of proteins L4, L5, L20 and L25 on the ribosomal surface by immuno-electron microscopy." Mol Gen Genet 216(2-3);245-53. PMID: 2664451

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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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