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
OU-MICROARRAY:	b2185
PortEco:	rplY
STRING:	511145.b2185
COLOMBOS:	rplY

Product

Name:

50S ribosomal subunit protein L25

Synonym(s):

RplY

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol,ribosome

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	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: 3.113. P-value: 9.611e-5 Read more >	[ICWHO]	[48]
promoter	rplYp5	2282437	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.81. P-value: 4.918e-5 Read more >	[ICWHO]	[48]
promoter	rplYp6	2282438	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.923. P-value: 1.314e-5 Read more >	[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.