RegulonDB

Gene
Name:	rplY
Synonym(s):	ECK2179, EG10885, b2185
Genome position(nucleotides):	2282517 --> 2282801 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	50.53
External database links:

ASAP:	ABE-0007231
CGSC:	242
ECHOBASE:	EB0878
ECOLIHUB:	rplY
OU-MICROARRAY:	b2185
STRING:	511145.b2185
COLOMBOS:	rplY

Product

Name:

50S ribosomal subunit protein L25

Synonym(s):

RplY

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

ribosome,cytosol

Molecular weight:

10.693

Isoelectric point:

10.218

Motif(s):

Type	Positions	Sequence
	86 -> 94	LQHIDFVRA
	4 -> 91	INAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEVLTIVVDGKEIKVKAQDVQRHPYKPKLQHIDF

Classification:

Multifun Terms (GenProtEC)
		2 - information transfer --> 2.3 - protein related --> 2.3.2 - translation
		2 - information transfer --> 2.3 - protein related --> 2.3.8 - ribosomal proteins
		6 - cell structure --> 6.6 - ribosomes
Gene Ontology Terms (GO)
	cellular_component	GO:0005829 - cytosol GO:0005840 - ribosome GO:0022625 - cytosolic large ribosomal subunit
	molecular_function	GO:0003735 - structural constituent of ribosome GO:0003723 - RNA binding GO:0019843 - rRNA binding GO:0008097 - 5S rRNA binding
	biological_process	GO:0006412 - translation GO:0000027 - ribosomal large subunit assembly GO:0017148 - negative regulation of translation GO:0009314 - response to radiation

Note(s):

Note(s): ...[more].

Reference(s):

[1] Abdel-Meguid SS., et al., 1983
[2] Bausk EV., et al., 1985
[3] Bear DG., et al., 1977
[4] Bitar KG., et al., 1975
[5] Branlant C., et al., 1976
[6] Branlant C., et al., 1977
[7] Chen-Schmeisser U., et al., 1977
[8] Chigradze IuN. 2008
[9] Chu FK., et al., 1976
[10] Dontsova OA., et al., 1990
[11] Douthwaite S., et al., 1982
[12] Dovgas NV., et al., 1975
[13] Fox JW., et al., 1988
[14] Fox JW., et al., 1978
[15] Fuenteun J., et al., 1975
[16] Gast WH., et al., 1976
[17] Gaunt-Klopfer M., et al., 1975
[18] Gewirth DT., et al., 1987
[19] Gimautdinova OI., et al., 1985
[20] Gimautdinova OI., et al., 1982
[21] Gray PN., et al., 1973
[22] Guerin MF., et al., 1981
[23] Herfurth E., et al., 1995
[24] Hernandez F., et al., 1977
[25] Kime MJ., et al., 1981
[26] Krassnigg F., et al., 1978
[27] Lotti M., et al., 1989
[28] Maimets TO., et al., 1981
[29] Metspalu E., et al., 1982
[30] Moore PB., et al., 1983
[31] Morrison CA., et al., 1977
[32] Newberry V., et al., 1980
[33] Osterberg R., et al., 1976
[34] Parker KK., et al., 1983
[35] Pieler T., et al., 1982
[36] Reblova K., et al., 2004
[37] Sander G., et al., 1975
[38] Schnier J., et al., 1979
[39] Silberklang M., et al., 1983
[40] Tate WP., et al., 1983
[41] Tewari DS., et al., 1983
[42] Tumanova LG., et al., 1984
[43] Tumanova LG., et al., 1983
[44] Ulbrich B., et al., 1975
[45] Willumeit R., et al., 2001
[46] Zimmermann J., et al., 1978
[47] van de Ven FJ., et al., 1983

External database links:

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Operon

Name:

rplY

Operon arrangement:

Transcription unit	Promoter
	rplVp

RNA cis-regulatory element

Attenuation:	Translational

Elements in the selected gene context region unrelated to any object in RegulonDB

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	rplYp3	2282433	forward	nd	[ICWHO]	[48]
promoter	rplYp5	2282437	forward	nd	[ICWHO]	[48]
promoter	rplYp6	2282438	forward	nd	[ICWHO]	[48]
promoter	TSS_2480	2283645	reverse	nd	[RS-EPT-CBR]	[49]

Evidence
[ICWHO] Inferred computationally without human oversight
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Reference(s)
[1] 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
[2] Bausk EV., Graifer DM., Karpova GG., 1985, [Study of the photoaffinity modification of Escherichia coli ribosomes near the donor tRNA-binding center]., Mol Biol (Mosk) 19(2):545-52
[3] 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
[4] 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
[5] 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
[6] 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
[7] Chen-Schmeisser U., Garrett RA., 1977, A new method for the isolation of a 5 S RNA complex with proteins L5, L18 and L25 from Escherichia coli ribosomes., FEBS Lett 74(2):287-91
[8] Chigradze IuN., 2008, [Structural behavior of RNA-binding proteins in free and complex states: ribosomal protein L25 and 5S RNA from Escherichia coli]., Mol Biol (Mosk) 42(4):685-92
[9] Chu FK., Maeba PY., 1976, Protein binding and subunit association activity in particles reconstituted from Escherichia coli MRE600 50S ribosomal components., Can J Biochem 54(5):470-6
[10] Dontsova OA., Efimov AV., Kopylov AM., 1990, [The 5S rRNA-protein complex of Escherichia coli studied by carbodiimide modification]., Nauchnye Doki Vyss Shkoly Biol Nauki (2):22-30
[11] Douthwaite S., Christensen A., Garrett RA., 1982, Binding site of ribosomal proteins on prokaryotic 5S ribonucleic acids: a study with ribonucleases., Biochemistry 21(10):2313-20
[12] 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
[13] 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
[14] Fox JW., Wong KP., 1978, Changes in the conformation and stability of 5 S RNA upon the binding of ribosomal proteins., J Biol Chem 253(1):18-20
[15] Fuenteun J., Monier R., Garrett R., Le Bret M., Le Pecq JB., 1975, Effect of 50 S subunit proteins L5, L18 and L25 on the fluorescence of 5 S RNA-bound ethidium bromide., J Mol Biol 93(4):535-41
[16] 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
[17] Gaunt-Klopfer M., Erdmann VA., 1975, ATPase and GTPase activities associated with the 5-S RNA-protein complex of Escherichia coli ribosomes., Biochim Biophys Acta 390(2):226-30
[18] Gewirth DT., Abo SR., Leontis NB., Moore PB., 1987, Secondary structure of 5S RNA: NMR experiments on RNA molecules partially labeled with nitrogen-15., Biochemistry 26(16):5213-20
[19] Gimautdinova OI., Karpova GG., Knorre DG., Frolova SB., 1985, Direct cross-linking of heptauridilate to E. coli ribosomes by water-soluble carbodiimide in the complex stabilized by codon-anticodon interaction at both A- and P-sites., FEBS Lett 185(2):221-5
[20] Gimautdinova OI., Karpova GG., Kozyreva NA., 1982, [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
[21] Gray PN., Bellemare G., Monier R., Garrett RA., Stoffler G., 1973, Identification of the nucleotide sequences involved in the interaction between Escherichia coli 5 RNA and specific 50 S subunit proteins., J Mol Biol 77(1):133-52
[22] Guerin MF., Hayes DH., Nierhaus KH., 1981, Effects of partial deproteinization on the functional properties of 50S ribosomal subunits of E. coli., Biochimie 63(8-9):699-707
[23] 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
[24] Hernandez F., Vazquez D., Ballesta JP., 1977, Functional roles of 50-S ribosomal proteins., Eur J Biochem 78(1):267-72
[25] Kime MJ., Ratcliffe RG., Moore PB., Williams RJ., 1981, A proton NMR study of ribosomal protein L25 from Escherichia coli., Eur J Biochem 116(2):269-76
[26] Krassnigg F., Erdmann VA., Fasold H., 1978, The synthesis of a photoreactive puromycin analogue and its application for labeling proteins in the 50-S subunit of Escherichia coli ribosomes., Eur J Biochem 87(3):439-43
[27] 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
[28] Maimets TO., Ustav MB., Villems RL., Saarma MIu., Lind AIa., 1981, [Binding of Escherichia coli 50S ribosomal subunit proteins with two large 5S RNA fragments]., Mol Biol (Mosk) 15(3):569-74
[29] Metspalu E., Ustav M., Maimets T., Villems R., 1982, The composition and properties of the Escherichia coli 5-S RNA-protein complex., Eur J Biochem 121(2):383-9
[30] Moore PB., Kime MJ., Leontis NB., Abdel-Meguid SS., 1983, Physical studies on a nucleoprotein from the ribosome of E. coli., J Biomol Struct Dyn 1(2):383-94
[31] Morrison CA., Tischendorf G., Stoffler G., Garrett RA., 1977, Accessibility of proteins in 50S ribosomal subunits of Escherichia coli to antibodies: an ultracentrifugation study., Mol Gen Genet 151(3):245-52
[32] Newberry V., Garrett RA., 1980, The role of the basic N-terminal region of protein L18 in 5S RNA-23S RNA complex formation., Nucleic Acids Res 8(18):4131-42
[33] Osterberg R., Sjoberg B., 1976, Small-angle x-ray scattering study of the 5S RNA binding proteins L18 and L25 from Escherichia coli ribosomes., FEBS Lett 65(1):73-6
[34] Parker KK., Wickstrom E., 1983, Crosslinking of Escherichia coli 50S ribosomal subunits with chlorambucilyl oligoprolyl phenylalanyl-tRNA molecular rulers., Nucleic Acids Res 11(2):515-24
[35] Pieler T., Erdmann VA., 1982, Three-dimensional structural model of eubacterial 5S RNA that has functional implications., Proc Natl Acad Sci U S A 79(15):4599-603
[36] Reblova K., Spackova N., Koca J., Leontis NB., Sponer J., 2004, Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex., Biophys J 87(5):3397-412
[37] Sander G., Marsh RC., Voigt J., Parmeggiani A., 1975, A comparative study of the 50S ribosomal subunit and several 50S subparticles in EF-T-and EF-G-dependent activities., Biochemistry 14(9):1805-14
[38] Schnier J., Isono K., 1979, The gene for ribosomal protein L25 (rplY) maps at 47.3 min near nalA in Escherichia coli K-12., Mol Gen Genet 176(3):313-8
[39] Silberklang M., RajBhandary UL., Luck A., Erdmann VA., 1983, Chemical reactivity of E. coli 5S RNA in situ in the 50S ribosomal subunit., Nucleic Acids Res 11(3):605-17
[40] Tate WP., Schulze H., Nierhaus KH., 1983, The importance of the Escherichia coli ribosomal protein L16 for the reconstitution of the peptidyl-tRNA hydrolysis activity of peptide chain termination., J Biol Chem 258(21):12810-5
[41] Tewari DS., Burma DP., 1983, Incorporation of 5S RNA into 16S-23S RNA complex., Biochem Biophys Res Commun 114(1):348-54
[42] Tumanova LG., Gongadze GM., Ven'iaminov SIu., Gudkov AT., Bushuev VN., 1984, [Comparison of the physical properties of ribosomal proteins from Escherichia coli 50S subparticles isolated by different methods]., Mol Biol (Mosk) 18(3):751-8
[43] Tumanova LG., Gongadze GM., Venyaminov SYu., Gudkov AT., Bushuev VN., 1983, Physical properties of ribosomal proteins isolated under different conditions from the Escherichia coli 50 S subunit., FEBS Lett 157(1):85-90
[44] Ulbrich B., Nierhaus KH., 1975, Pools of ribosomal proteins in Escherichia coli. Studies on the exchange of proteins between pools and ribosomes., Eur J Biochem 57(1):49-54
[45] Willumeit R., Diedrich G., Forthmann S., Beckmann J., May RP., Stuhrmann HB., Nierhaus KH., 2001, Mapping proteins of the 50S subunit from Escherichia coli ribosomes., Biochim Biophys Acta 1520(1):7-20
[46] Zimmermann J., Erdmann VA., 1978, Identification of Escherichia coli and Bacillus stearothermophilus ribosomal protein binding sites on Escherichia coli 5S RNA., Mol Gen Genet 160(3):247-57
[47] van de Ven FJ., de Bruin SH., Hilbers CW., 1983, 500-MHz 1H-NMR studies of ribosomal proteins isolated from 70-S ribosomes of Escherichia coli., Eur J Biochem 134(3):429-38
[48] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78
[49] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.