RegulonDB RegulonDB 10.8: Gene Form
   

infB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

infB nusA rbfA anti-anti-terminator anti-terminator terminator TSS_3466 TSS_3466 infBp infBp TSS_3465 TSS_3465 TSS_3464 (cluster) TSS_3464 (cluster) TSS_3463 TSS_3463 TSS_3462 TSS_3462 TSS_3461 TSS_3461 TSS_3460 TSS_3460 TSS_3459 TSS_3459 TSS_3458 TSS_3458 TSS_3457 TSS_3457 TSS_3456 TSS_3456 TSS_3455 TSS_3455

Gene      
Name: infB    Texpresso search in the literature
Synonym(s): ECK3157, EG10505, b3168, ssyG
Genome position(nucleotides): 3313342 <-- 3316014 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.42
External database links:  
ASAP:
ABE-0010410
CGSC:
597
ECHOBASE:
EB0500
OU-MICROARRAY:
b3168
PortEco:
infB
STRING:
511145.b3168
COLOMBOS: infB


Product      
Name: translation initiation factor IF-2
Synonym(s): IF-2, InfB, SsyG, protein chain initiation factor IF2
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 97.35
Isoelectric point: 5.906
Motif(s):
 
Type Positions Sequence
158 -> 158 V
165 -> 165 M
394 -> 550 VTIMGHVDHGKTSLLDYIRSTKVASGEAGGITQHIGAYHVETENGMITFLDTPGHAAFTSMRARGAQATDIVVLVVAADDGVMPQTIEAIQHAKAAQVPVVVAVNKIDKPEADPDRVKNELSQYGILPEEWGGESQFVHVSAKAGTGIDELLDAILL
398 -> 405 GHVDHGKT
541 -> 668 IDELLDAILLQAEVLELKAVRKGMASGAVIESFLDKGRGPVATVLVREGTLHKGDIVLCGFEYGRVRAMRNELGQEVLEAGPSIPVEILGLSGVPAAGDEVTVVRDEKKAREVALYRQGKFREVKLAR

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.3 - protein related --> 2.3.2 - translation
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0005515 - protein binding
GO:0003743 - translation initiation factor activity
GO:0000166 - nucleotide binding
GO:0003924 - GTPase activity
GO:0005525 - GTP binding
GO:0043024 - ribosomal small subunit binding
GO:0097216 - guanosine tetraphosphate binding
biological_process GO:0006412 - translation
GO:0006413 - translational initiation
Note(s): Note(s): ...[more].
Evidence: [IDA] Inferred from direct assay
Reference(s): [1] Beaudry P., et al., 1979
[2] Benne R., et al., 1973
[3] Berthelot F., et al., 1977
[4] Boileau G., et al., 1983
[5] Brandi L., et al., 2004
[6] Burakovskii DE., et al., 2007
[7] Canonaco MA., et al., 1986
[8] Cenatiempo Y., et al., 1987
[9] Cole JR., et al., 1987
[10] Dubnoff JS., et al., 1969
[11] Fakunding JL., et al., 1973
[12] Guillon JM., et al., 1996
[13] Hamel E. 1975
[14] Hartz D., et al., 1989
[15] Heimark RL., et al., 1976
[16] Iwasaki K., et al., 1968
[17] Karimi R., et al., 1998
[18] Krauss SW., et al., 1975
[19] La Teana A., et al., 2001
[20] La Teana A., et al., 1993
[21] Larigauderie G., et al., 2000
[22] Mangroo D., et al., 1995
[23] Mayer C., et al., 2003
[24] Mazumder R. 1972
[25] Milon P., et al., 2007
[26] Moreno JM., et al., 1998
[27] Naaktgeboren N., et al., 1975
[28] Petersen HU., et al., 1979
[29] Plumbridge JA., et al., 1982
[30] Plumbridge JA., et al., 1983
[31] Qin H., et al., 2009
[32] Revel M., et al., 1968
[33] Romby P., et al., 1990
[34] Sacerdot C., et al., 1984
[35] Schmitt M., et al., 1980
[36] Steffensen SA., et al., 1997
[37] Thanedar S., et al., 2000
[38] Travers AA., et al., 1980
[39] Vachon G., et al., 1990
[40] Wakao H., et al., 1991
[41] Wakao H., et al., 1990
[42] Wakao H., et al., 1989
[43] Weiel J., et al., 1982
[44] Wintermeyer W., et al., 1983
[45] Wu XQ., et al., 1997
[46] Yusupova G., et al., 1996
[47] van der Hofstad GA., et al., 1978
[48] van der Hofstad GA., et al., 1976
[49] van der Laken K., et al., 1980
External database links:  
DIP:
DIP-36182N
ECOCYC:
EG10505-MONOMER
ECOLIWIKI:
b3168
INTERPRO:
IPR005225
INTERPRO:
IPR036925
INTERPRO:
IPR027417
INTERPRO:
IPR023115
INTERPRO:
IPR015760
INTERPRO:
IPR013575
INTERPRO:
IPR009061
INTERPRO:
IPR009000
INTERPRO:
IPR006847
INTERPRO:
IPR000795
INTERPRO:
IPR000178
MINT:
MINT-1235405
MODBASE:
P0A705
PANTHER:
PTHR43381
PDB:
1ZO1
PDB:
3JCN
PDB:
3JCJ
PDB:
5ME0
PDB:
5ME1
PDB:
1ND9
PFAM:
PF11987
PFAM:
PF08364
PFAM:
PF04760
PFAM:
PF00009
PRIDE:
P0A705
PRODB:
PRO_000023013
PROSITE:
PS51722
PROSITE:
PS01176
REFSEQ:
NP_417637
SMR:
P0A705
UNIPROT:
P0A705


Operon      
Name: metY-rimP-nusA-infB-rbfA-truB-rpsO-pnp         
Operon arrangement:
Transcription unit        Promoter
pnp
rpsO
rpsO-pnp
infB
nusA-infB
rimP-nusA-infB
metY
metY-yhbC-nusA-infB
metY-yhbC-nusA-infB-rbfA-truB-rpsO-pnp
metY
metY-yhbC-nusA-infB-rbfA-truB-rpsO-pnp


Transcriptional Regulation      
Display Regulation             
Activated by: Fis
Repressed by: CRP, ArgR


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_3455 3314593 reverse nd [RS-EPT-CBR] [50]
  promoter TSS_3456 3315518 reverse nd [RS-EPT-CBR] [50]
  promoter TSS_3457 3315522 reverse nd [RS-EPT-CBR] [50]
  promoter TSS_3458 3315577 reverse nd [RS-EPT-CBR] [50]
  promoter TSS_3459 3315601 reverse nd [RS-EPT-CBR] [50]
  promoter TSS_3460 3315649 reverse nd [RS-EPT-CBR] [50]
  promoter TSS_3461 3315652 reverse nd [RS-EPT-CBR] [50]
  promoter TSS_3462 3315673 reverse nd [RS-EPT-CBR] [50]
  promoter TSS_3463 3315804 reverse nd [RS-EPT-CBR] [50]
  promoter TSS_3464 (cluster) 3315809 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [50]
  promoter TSS_3465 3315884 reverse nd [RS-EPT-CBR] [50]
  promoter TSS_3466 3316378 reverse nd [RS-EPT-CBR] [50]


Evidence    

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



Reference(s)    

 [1] Beaudry P., Sander G., Grunberg-Manago M., Douzou P., 1979, Cation-induced regulatory mechanism of GTPase activity dependent on polypeptide initiation factor 2., Biochemistry 18(1):202-7

 [2] Benne R., Naaktgeboren N., Gubbens J., Voorma HO., 1973, Recycling of initiation factors IF-1, IF-2 and IF-3., Eur J Biochem 32(2):372-80

 [3] Berthelot F., Bogdanovsky D., Schapira G., Gros F., 1977, Comparative nature of the reactions catalysed by reticulocyte initiation factor IF-M1 and Escherichia coli factor IF2 on Escherichia coli ribosomes., FEBS Lett 74(1):91-4

 [4] Boileau G., Butler P., Hershey JW., Traut RR., 1983, Direct cross-links between initiation factors 1, 2, and 3 and ribosomal proteins promoted by 2-iminothiolane., Biochemistry 22(13):3162-70

 [5] Brandi L., Marzi S., Fabbretti A., Fleischer C., Hill WE., Gualerzi CO., Stephen Lodmell J., 2004, The translation initiation functions of IF2: targets for thiostrepton inhibition., J Mol Biol 335(4):881-94

 [6] Burakovskii DE., Smirnova AS., Lesniak DV., Kiparisov SV., Leonov AA., Sergiev PV., Bogdanov AA., Dontsova OA., 2007, [Interaction of 23S ribosomal RNA helices 89 and 91 of Escherichia coli contributes to the activity of IF2 but is insignificant for elongation factors functioning]., Mol Biol (Mosk) 41(6):1031-41

 [7] Canonaco MA., Calogero RA., Gualerzi CO., 1986, Mechanism of translational initiation in prokaryotes. Evidence for a direct effect of IF2 on the activity of the 30 S ribosomal subunit., FEBS Lett 207(2):198-204

 [8] Cenatiempo Y., Deville F., Dondon J., Grunberg-Manago M., Sacerdot C., Hershey JW., Hansen HF., Petersen HU., Clark BF., Kjeldgaard M., 1987, The protein synthesis initiation factor 2 G-domain. Study of a functionally active C-terminal 65-kilodalton fragment of IF2 from Escherichia coli., Biochemistry 26(16):5070-6

 [9] Cole JR., Olsson CL., Hershey JW., Grunberg-Manago M., Nomura M., 1987, Feedback regulation of rRNA synthesis in Escherichia coli. Requirement for initiation factor IF2., J Mol Biol 198(3):383-92

 [10] Dubnoff JS., Maitra U., 1969, Protein factors involved in polypeptide chain initiation in Escherichia coli., Cold Spring Harb Symp Quant Biol 34:301-6

 [11] Fakunding JL., Hershey JW., 1973, The interaction of radioactive initiation factor IF-2 with ribosomes during initiation of protein synthesis., J Biol Chem 248(12):4206-12

 [12] Guillon JM., Heiss S., Soutourina J., Mechulam Y., Laalami S., Grunberg-Manago M., Blanquet S., 1996, Interplay of methionine tRNAs with translation elongation factor Tu and translation initiation factor 2 in Escherichia coli., J Biol Chem 271(37):22321-5

 [13] Hamel E., 1975, Activities of guanosine triphosphate analogues in reactions catalyzed by elongation factor Tu and initiation factor 2 of Escherichia coli., Biochim Biophys Acta 414(3):326-40

 [14] Hartz D., McPheeters DS., Gold L., 1989, Selection of the initiator tRNA by Escherichia coli initiation factors., Genes Dev 3(12A):1899-912

 [15] Heimark RL., Hershey JW., Traut RR., 1976, Cross-linking of initiation factor IF2 to proteins L7/L12 in 70 S ribosomes of Escherichia coli., J Biol Chem 251(24):7779-84

 [16] Iwasaki K., Sabol S., Wahba AJ., Ochoa S., 1968, Translation of the genetic message. VII. Role of initiation factors in formation of the chain initiation complex with Escherichia coli ribosomes., Arch Biochem Biophys 125(2):542-7

 [17] Karimi R., Pavlov MY., Heurgue-Hamard V., Buckingham RH., Ehrenberg M., 1998, Initiation factors IF1 and IF2 synergistically remove peptidyl-tRNAs with short polypeptides from the P-site of translating Escherichia coli ribosomes., J Mol Biol 281(2):241-52

 [18] Krauss SW., Leder P., 1975, Regulation of initiation and elongation factor levels in Escherichia coli as assessed by a quantitative immunoassay., J Biol Chem 250(10):3752-8

 [19] La Teana A., Gualerzi CO., Dahlberg AE., 2001, Initiation factor IF 2 binds to the alpha-sarcin loop and helix 89 of Escherichia coli 23S ribosomal RNA., RNA 7(8):1173-9

 [20] La Teana A., Pon CL., Gualerzi CO., 1993, Translation of mRNAs with degenerate initiation triplet AUU displays high initiation factor 2 dependence and is subject to initiation factor 3 repression., Proc Natl Acad Sci U S A 90(9):4161-5

 [21] Larigauderie G., Laalami S., Nyengaard NR., Grunberg-Manago M., Cenatiempo Y., Mortensen KK., Sperling-Petersen HU., 2000, Mutation of Thr445 and Ile500 of initiation factor 2 G-domain affects Escherichia coli growth rate at low temperature., Biochimie 82(12):1091-8

 [22] Mangroo D., RajBhandary UL., 1995, Mutants of Escherichia coli initiator tRNA defective in initiation. Effects of overproduction of methionyl-tRNA transformylase and the initiation factors IF2 and IF3., J Biol Chem 270(20):12203-9

 [23] Mayer C., Kohrer C., Kenny E., Prusko C., RajBhandary UL., 2003, Anticodon sequence mutants of Escherichia coli initiator tRNA: effects of overproduction of aminoacyl-tRNA synthetases, methionyl-tRNA formyltransferase, and initiation factor 2 on activity in initiation., Biochemistry 42(17):4787-99

 [24] Mazumder R., 1972, Initiation factor 2-dependent ribosomal binding of N-formylmethionyl-transfer RNA without added guanosine triphosphate., Proc Natl Acad Sci U S A 69(10):2770-3

 [25] Milon P., Konevega AL., Peske F., Fabbretti A., Gualerzi CO., Rodnina MV., 2007, Transient kinetics, fluorescence, and FRET in studies of initiation of translation in bacteria., Methods Enzymol 430:1-30

 [26] Moreno JM., Kildsgaard J., Siwanowicz I., Mortensen KK., Sperling-Petersen HU., 1998, Binding of Escherichia coli initiation factor IF2 to 30S ribosomal subunits: a functional role for the N-terminus of the factor., Biochem Biophys Res Commun 252(2):465-71

 [27] Naaktgeboren N., Vermaas A., Voorma HO., 1975, The joining of the 30-S initiation complex with the 50-S subunit, the main target for thiostrepton., Eur J Biochem 57(2):493-51

 [28] Petersen HU., Roll T., Grunberg-Manago M., Clark BF., 1979, Specific interaction of initiation factor IF2 of E. coli with formylmethionyl-tRNA f Met., Biochem Biophys Res Commun 91(3):1068-74

 [29] Plumbridge JA., Howe JG., Springer M., Touati-Schwartz D., Hershey JW., Grunberg-Manago M., 1982, Cloning and mapping of a gene for translational initiation factor IF2 in Escherichia coli., Proc Natl Acad Sci U S A 79(16):5033-7

 [30] Plumbridge JA., Springer M., 1983, Organization of the Escherichia coli chromosome around the genes for translation initiation factor IF2 (infB) and a transcription termination factor (nusA)., J Mol Biol 167(2):227-43

 [31] Qin H., Grigoriadou C., Cooperman BS., 2009, Interaction of IF2 with the ribosomal GTPase-associated center during 70S initiation complex formation., Biochemistry 48(22):4699-706

 [32] Revel M., Lelong JC., Brawerman G., Gros F., 1968, Function of three protein factors and ribosomal subunits in the initiation of protein synthesis in E. coli., Nature 219(5158):1016-21

 [33] Romby P., Wakao H., Westhof E., Grunberg-Manago M., Ehresmann B., Ehresmann C., Ebel JP., 1990, The conformation of the initiator tRNA and of the 16S rRNA from Escherichia coli during the formation of the 30S initiation complex., Biochim Biophys Acta 1050(1-3):84-92

 [34] Sacerdot C., Dessen P., Hershey JW., Plumbridge JA., Grunberg-Manago M., 1984, Sequence of the initiation factor IF2 gene: unusual protein features and homologies with elongation factors., Proc Natl Acad Sci U S A 81(24):7787-91

 [35] Schmitt M., Manderschied U., Kyriatsoulis A., Brinckmann U., Gassen HG., 1980, Tetranucleotides as effectors for the binding of initiator tRNA to Escherichia coli ribosomes., Eur J Biochem 109(1):291-9

 [36] Steffensen SA., Poulsen AB., Mortensen KK., Sperling-Petersen HU., 1997, E. coli translation initiation factor IF2--an extremely conserved protein. Comparative sequence analysis of the infB gene in clinical isolates of E. coli., FEBS Lett 419(2-3):281-4

 [37] Thanedar S., Kumar NV., Varshney U., 2000, The fate of the initiator tRNAs is sensitive to the critical balance between interacting proteins., J Biol Chem 275(27):20361-7

 [38] Travers AA., Debenham PG., Pongs O., 1980, Translation initiation factor 2 alters transcriptional selectivity of Escherichia coli ribonucleic acid polymerase., Biochemistry 19(8):1651-6

 [39] Vachon G., Laalami S., Grunberg-Manago M., Julien R., Cenatiempo Y., 1990, Purified internal G-domain of translational initiation factor IF-2 displays guanine nucleotide binding properties., Biochemistry 29(41):9728-33

 [40] Wakao H., Romby P., Ebel JP., Grunberg-Manago M., Ehresmann C., Ehresmann B., 1991, Topography of the Escherichia coli ribosomal 30S subunit-initiation factor 2 complex., Biochimie 73(7-8):991-1000

 [41] Wakao H., Romby P., Laalami S., Ebel JP., Ehresmann C., Ehresmann B., 1990, Binding of initiation factor 2 and initiator tRNA to the Escherichia coli 30S ribosomal subunit induces allosteric transitions in 16S rRNA., Biochemistry 29(35):8144-51

 [42] Wakao H., Romby P., Westhof E., Laalami S., Grunberg-Manago M., Ebel JP., Ehresmann C., Ehresmann B., 1989, The solution structure of the Escherichia coli initiator tRNA and its interactions with initiation factor 2 and the ribosomal 30 S subunit., J Biol Chem 264(34):20363-71

 [43] Weiel J., Hershey JW., 1982, The binding of fluorescein-labeled protein synthesis initiation factor 2 to Escherichia coli 30 S ribosomal subunits determined by fluorescence polarization., J Biol Chem 257(3):1215-20

 [44] Wintermeyer W., Gualerzi C., 1983, Effect of Escherichia coli initiation factors on the kinetics of N-Acphe-tRNAPhe binding to 30S ribosomal subunits. A fluorescence stopped-flow study., Biochemistry 22(3):690-4

 [45] Wu XQ., RajBhandary UL., 1997, Effect of the amino acid attached to Escherichia coli initiator tRNA on its affinity for the initiation factor IF2 and on the IF2 dependence of its binding to the ribosome., J Biol Chem 272(3):1891-5

 [46] Yusupova G., Reinbolt J., Wakao H., Laalami S., Grunberg-Manago M., Romby P., Ehresmann B., Ehresmann C., 1996, Topography of the Escherichia coli initiation factor 2/fMet-tRNA(f)(Met) complex as studied by cross-linking., Biochemistry 35(9):2978-84

 [47] van der Hofstad GA., Buitenhek A., Bosch L., Voorma HO., 1978, Initiation factor IF-3 and the binary complex between initiation factor IF-2 and formylmethionyl-tRNA are mutually exclusive on the 30-S ribosomal subunit., Eur J Biochem 89(1):213-20

 [48] van der Hofstad GA., Foekens JA., Van Den Elsen PJ., Voorma HO., 1976, Cooperative effects of initiation factors and fMet-tRNA in the formation of the 40-S initiation complex., Eur J Biochem 66(1):181-92

 [49] van der Laken K., Bakker-Steeneveld H., Berkhout B., van Knippenberg PH., 1980, The role of the codon and the initiation factor IF-2 in the selection of N-blocked aminoacyl-tRNA for initiation., Eur J Biochem 104(1):19-33

 [50] 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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