RegulonDB RegulonDB 10.9: Gene Form
   

rplY gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

radD yejK rplY DksA-ppGpp DksA-ppGpp terminator TSS_2480 TSS_2480 rplVp rplVp rplYp6 rplYp6 rplYp5 rplYp5 rplYp3 rplYp3

Gene      
Name: rplY    Texpresso search in the literature
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:  
DIP:
DIP-35885N
ECOCYC:
EG10885-MONOMER
ECOLIWIKI:
b2185
INTERPRO:
IPR011035
INTERPRO:
IPR020055
INTERPRO:
IPR020056
INTERPRO:
IPR029751
MODBASE:
P68919
PDB:
1B75
PDB:
1D6K
PDB:
1DFU
PDB:
1ML5
PDB:
2J28
PDB:
2RDO
PDB:
3BBX
PDB:
3J5L
PDB:
3J7Z
PDB:
3J8G
PDB:
3J9Y
PDB:
3J9Z
PDB:
3JA1
PDB:
3JBU
PDB:
3JBV
PDB:
3JCD
PDB:
3JCE
PDB:
3JCJ
PDB:
3JCN
PDB:
487D
PDB:
4CSU
PDB:
4U1U
PDB:
4U1V
PDB:
4U20
PDB:
4U24
PDB:
4U25
PDB:
4U26
PDB:
4U27
PDB:
4UY8
PDB:
4V47
PDB:
4V48
PDB:
4V4H
PDB:
4V4Q
PDB:
4V4V
PDB:
4V4W
PDB:
4V50
PDB:
4V52
PDB:
4V53
PDB:
4V54
PDB:
4V55
PDB:
4V56
PDB:
4V57
PDB:
4V5B
PDB:
4V5H
PDB:
4V5Y
PDB:
4V64
PDB:
4V65
PDB:
4V66
PDB:
4V69
PDB:
4V6C
PDB:
4V6D
PDB:
4V6E
PDB:
4V6K
PDB:
4V6L
PDB:
4V6M
PDB:
4V6N
PDB:
4V6O
PDB:
4V6P
PDB:
4V6Q
PDB:
4V6R
PDB:
4V6S
PDB:
4V6T
PDB:
4V6V
PDB:
4V6Y
PDB:
4V6Z
PDB:
4V70
PDB:
4V71
PDB:
4V72
PDB:
4V73
PDB:
4V74
PDB:
4V75
PDB:
4V76
PDB:
4V77
PDB:
4V78
PDB:
4V79
PDB:
4V7A
PDB:
4V7B
PDB:
4V7C
PDB:
4V7D
PDB:
4V7I
PDB:
4V7S
PDB:
4V7T
PDB:
4V7U
PDB:
4V7V
PDB:
4V85
PDB:
4V89
PDB:
4V9C
PDB:
4V9D
PDB:
4V9O
PDB:
4V9P
PDB:
4WF1
PDB:
4WOI
PDB:
4WWW
PDB:
4YBB
PDB:
5ADY
PDB:
5AFI
PDB:
5AKA
PDB:
5GAD
PDB:
5GAE
PDB:
5GAF
PDB:
5GAG
PDB:
5GAH
PDB:
5H5U
PDB:
5IQR
PDB:
5IT8
PDB:
5J5B
PDB:
5J7L
PDB:
5J88
PDB:
5J8A
PDB:
5J91
PDB:
5JC9
PDB:
5JTE
PDB:
5JU8
PDB:
5KCR
PDB:
5KCS
PDB:
5KPS
PDB:
5KPV
PDB:
5KPW
PDB:
5KPX
PDB:
5L3P
PDB:
5LZA
PDB:
5LZB
PDB:
5LZC
PDB:
5LZD
PDB:
5LZE
PDB:
5LZF
PDB:
5MDV
PDB:
5MDW
PDB:
5MDY
PDB:
5MDZ
PDB:
5MGP
PDB:
5NCO
PDB:
5NP6
PDB:
5NWY
PDB:
5O2R
PDB:
5U4I
PDB:
5U9F
PDB:
5U9G
PDB:
5UYK
PDB:
5UYL
PDB:
5UYM
PDB:
5UYN
PDB:
5UYP
PDB:
5UYQ
PDB:
5WDT
PDB:
5WE4
PDB:
5WE6
PDB:
5WFK
PDB:
6BU8
PDB:
6BY1
PDB:
6C4I
PDB:
6DNC
PDB:
6ENF
PDB:
6ENJ
PDB:
6ENU
PDB:
6GBZ
PDB:
6GC0
PDB:
6GC4
PDB:
6GC8
PDB:
6GWT
PDB:
6GXM
PDB:
6GXN
PDB:
6GXO
PDB:
6GXP
PDB:
6H4N
PDB:
6H58
PDB:
6HRM
PDB:
6I0Y
PDB:
6I7V
PDB:
6O9J
PDB:
6O9K
PDB:
6OFX
PDB:
6OG7
PDB:
6ORE
PDB:
6ORL
PDB:
6OST
PDB:
6OT3
PDB:
6OUO
PDB:
6Q97
PDB:
6Q98
PDB:
6Q9A
PDB:
6QUL
PDB:
6S0K
PDB:
6SZS
PDB:
6TBV
PDB:
6TC3
PFAM:
PF01386
PRIDE:
P68919
PRODB:
PRO_000023831
REFSEQ:
NP_416690
SMR:
P68919
UNIPROT:
P68919


Operon      
Name: rplY         
Operon arrangement:
Transcription unit        Promoter
 


RNA cis-regulatory element    
Attenuation: Translational


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

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter rplYp3 2282433 forward Similarity to the consensus
Read more >
[ICWHO] [48]
  promoter rplYp5 2282437 forward Similarity to the consensus
Read more >
[ICWHO] [48]
  promoter rplYp6 2282438 forward Similarity to the consensus
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.


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