RegulonDB RegulonDB 10.8: Gene Form
   

rpmF gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

plsX yceD rpmF FadR DksA-ppGpp DksA-ppGpp fabHp fabHp TSS_1388 TSS_1388 TSS_1387 TSS_1387 plsXp plsXp TSS_1386 (cluster) TSS_1386 (cluster) TSS_1385 TSS_1385 rpmFp rpmFp TSS_1384 (cluster) TSS_1384 (cluster) TSS_1383 TSS_1383 TSS_1382 (cluster) TSS_1382 (cluster) TSS_1381 TSS_1381 TSS_1380 TSS_1380 TSS_1379 (cluster) TSS_1379 (cluster) TSS_1378 TSS_1378 TSS_1377 TSS_1377 TSS_1376 (cluster) TSS_1376 (cluster) TSS_1375 (cluster) TSS_1375 (cluster) TSS_1374 TSS_1374 TSS_1373 TSS_1373 TSS_1372 TSS_1372 TSS_1371 TSS_1371 TSS_1370 TSS_1370

Gene      
Name: rpmF    Texpresso search in the literature
Synonym(s): ECK1075, EG10890, b1089
Genome position(nucleotides): 1147367 --> 1147540 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
54.02
External database links:  
ASAP:
ABE-0003686
CGSC:
17605
ECHOBASE:
EB0883
OU-MICROARRAY:
b1089
PortEco:
rpmF
STRING:
511145.b1089
COLOMBOS: rpmF


Product      
Name: 50S ribosomal subunit protein L32
Synonym(s): RpmF
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol,ribosome
Molecular weight: 6.446
Isoelectric point: 11.623
Motif(s):
 
Type Positions Sequence
2 -> 57 AVQQNKPTRSKRGMRRSHDALTAVTSLSVDKTSGEKHLRHHITADGYYRGRKVIAK

 

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:0015934 - large ribosomal subunit
GO:0022625 - cytosolic large ribosomal subunit
molecular_function GO:0003735 - structural constituent of ribosome
GO:0005515 - protein binding
biological_process GO:0006412 - translation
GO:0000027 - ribosomal large subunit assembly
GO:0000302 - response to reactive oxygen species
GO:0009314 - response to radiation
Note(s): Note(s): ...[more].
Reference(s): [1] Andrieux E., et al., 1984
[2] Barritault D., et al., 1975
[3] Bausk EV., et al., 1985
[4] Dzionara M., et al., 1977
[5] Gimautdinova OI., et al., 1981
[6] Gimautdinova OI., et al., 1982
[7] Gimautdinova OI., et al., 1984
[8] Graifer DM., et al., 1989
[9] Isono S., et al., 1978
[10] Janda I., et al., 1985
[11] Laughrea M., et al., 1987
[12] Oh W., et al., 1992
[13] Pichon JL., et al., 1977
[14] Podkovyrov S., et al., 1995
[15] Tanaka Y., et al., 1989
[16] Tejedor F., et al., 1985
[17] Wittmann-Liebold B., et al., 1975
[18] Zhang Y., et al., 1998
External database links:  
DIP:
DIP-35782N
ECOCYC:
EG10890-MONOMER
ECOLIWIKI:
b1089
INTERPRO:
IPR002677
INTERPRO:
IPR011332
MODBASE:
P0A7N4
PANTHER:
PTHR35534
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:
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:
6ENF
PDB:
6ENJ
PDB:
6ENU
PDB:
6GBZ
PDB:
6GC0
PDB:
6GC4
PDB:
6GC6
PDB:
6GC7
PDB:
6GC8
PDB:
6GWT
PDB:
6GXM
PDB:
6GXN
PDB:
6GXO
PDB:
6GXP
PDB:
6H4N
PDB:
6H58
PDB:
6HRM
PDB:
6I0Y
PDB:
6I7V
PDB:
6OFX
PDB:
6OG7
PDB:
6Q98
PDB:
6Q9A
PDB:
6QUL
PFAM:
PF01783
PRIDE:
P0A7N4
PRODB:
PRO_000023838
REFSEQ:
NP_415607
SMR:
P0A7N4
UNIPROT:
P0A7N4


Operon      
Name: yceD-rpmF-plsX-fabHDG-acpP-fabF         
Operon arrangement:
Transcription unit        Promoter
yceD-rpmF
yceD-rpmF
rpmF-plsX-fabHDG
plsX-fabHDG
fabHDG
acpP
acpP-fabF
fabDG-acpP
fabF
fabG-acpP


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 TSS_1370 1146794 forward nd [RS-EPT-CBR] [19]
  promoter TSS_1371 1146809 forward nd [RS-EPT-CBR] [19]
  promoter TSS_1372 1147056 forward nd [RS-EPT-CBR] [19]
  promoter TSS_1373 1147094 forward nd [RS-EPT-CBR] [19]
  promoter TSS_1374 1147132 forward nd [RS-EPT-CBR] [19]
  promoter TSS_1375 (cluster) 1147141 forward For this promoter, there
Read more >
[RS-EPT-CBR] [19]
  promoter TSS_1376 (cluster) 1147146 forward For this promoter, there
Read more >
[RS-EPT-CBR] [19]
  promoter TSS_1377 1147188 forward nd [RS-EPT-CBR] [19]
  promoter TSS_1378 1147194 forward nd [RS-EPT-CBR] [19]
  promoter TSS_1379 (cluster) 1147206 forward For this promoter, there
Read more >
[RS-EPT-CBR] [19]
  promoter TSS_1380 1147213 forward nd [RS-EPT-CBR] [19]
  promoter TSS_1381 1147215 forward nd [RS-EPT-CBR] [19]
  promoter TSS_1382 (cluster) 1147300 forward For this promoter, there
Read more >
[RS-EPT-CBR] [19]
  promoter TSS_1383 1147307 forward nd [RS-EPT-CBR] [19]
  promoter TSS_1384 (cluster) 1147313 forward For this promoter, there
Read more >
[RS-EPT-CBR] [19]
  promoter TSS_1385 1147350 forward nd [RS-EPT-CBR] [19]
  promoter TSS_1386 (cluster) 1147395 forward For this promoter, there
Read more >
[RS-EPT-CBR] [19]
  promoter TSS_1387 1147771 forward nd [RS-EPT-CBR] [19]
  promoter TSS_1388 1148362 forward nd [RS-EPT-CBR] [19]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates



Reference(s)    

 [1] Andrieux E., Cozzone AJ., 1984, Conformational changes in bacterial polysomes induced by amino acid starvation., Int J Biochem 16(1):113-6

 [2] Barritault D., Expert-Bezancon A., Milet M., 1975, [Nearest-neighbor relationships among 50S ribosomal proteins of E. coli]., C R Acad Sci Hebd Seances Acad Sci D 281(14):1043-6

 [3] 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

 [4] Dzionara M., Robinson SM., Wittmann-Liebold B., 1977, Prediction for secondary structures of ten proteins from the 50S subunit of the Escherichia coli ribosome., J Supramol Struct 7(2):191-204

 [5] Gimautdinova OI., Karpova GG., Knorre DG., Kobetz ND., 1981, The proteins of the messenger RNA binding site of Escherichia coli ribosomes., Nucleic Acids Res 9(14):3465-81

 [6] 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

 [7] Gimautdinova OI., Zenkova MA., Karpova GG., Podust LM., 1984, [Affinity modification of Escherichia coli ribosomes with photoactivated analogs of mRNA]., Mol Biol (Mosk) 18(4):907-18

 [8] Graifer DM., Babkina GT., Matasova NB., Vladimirov SN., Karpova GG., Vlassov VV., 1989, Structural arrangement of tRNA binding sites on Escherichia coli ribosomes, as revealed from data on affinity labelling with photoactivatable tRNA derivatives., Biochim Biophys Acta 1008(2):146-56

 [9] Isono S., Isono K., 1978, Mutations affecting the structural genes and the genes coding for modifying enzymes for ribosomal proteins in Escherichia coli., Mol Gen Genet 165(1):15-20

 [10] Janda I., Kitakawa M., Isono K., 1985, Gene rpmF for ribosomal protein L32 and gene rimJ for a ribosomal protein acetylating enzyme are located near pyrC (23.4 min) in Escherichia coli., Mol Gen Genet 201(3):433-6

 [11] Laughrea M., Latulippe J., Filion AM., Boulet L., 1987, Mistranslation in twelve Escherichia coli ribosomal proteins. Cysteine misincorporation at neutral amino acid residues other than tryptophan., Eur J Biochem 169(1):59-64

 [12] Oh W., Larson TJ., 1992, Physical locations of genes in the rne (ams)-rpmF-plsX-fab region of the Escherichia coli K-12 chromosome., J Bacteriol 174(23):7873-4

 [13] Pichon JL., Coeroli C., Marchis-Mouren G., 1977, Studies on ribosomal protein biosynthesis in an RNA polymerase temperature sensitive E. coli mutant., Mol Gen Genet 150(3):257-64

 [14] Podkovyrov S., Larson TJ., 1995, Lipid biosynthetic genes and a ribosomal protein gene are cotranscribed., FEBS Lett 368(3):429-31

 [15] Tanaka Y., Tsujimura A., Fujita N., Isono S., Isono K., 1989, Cloning and analysis of an Escherichia coli operon containing the rpmF gene for ribosomal protein L32 and the gene for a 30-kilodalton protein., J Bacteriol 171(10):5707-12

 [16] Tejedor F., Ballesta JP., 1985, Ribosome structure: binding site of macrolides studied by photoaffinity labeling., Biochemistry 24(2):467-72

 [17] Wittmann-Liebold B., Greuer B., Pannenbecker R., 1975, The primary structure of protein L32 from the 50S subunit of Escherichia coli ribosomes., Hoppe Seylers Z Physiol Chem 356(12):1977-9

 [18] Zhang Y., Cronan JE., 1998, Transcriptional analysis of essential genes of the Escherichia coli fatty acid biosynthesis gene cluster by functional replacement with the analogous Salmonella typhimurium gene cluster., J Bacteriol 180(13):3295-303

 [19] 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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