RegulonDB RegulonDB 10.8: Gene Form
   

der gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

der bamB yfgJ xseA anti-anti-terminator anti-terminator terminator terminator TSS_2794 TSS_2794 TSS_2793 TSS_2793 TSS_2792 TSS_2792

Gene      
Name: der    Texpresso search in the literature
Synonym(s): ECK2507, G7319, b2511, engA, yfgK
Genome position(nucleotides): 2635884 <-- 2637356 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.21
External database links:  
ASAP:
ABE-0008270
ECHOBASE:
EB3959
OU-MICROARRAY:
b2511
PortEco:
der
STRING:
511145.b2511
COLOMBOS: der


Product      
Name: 50S ribosomal subunit stability factor
Synonym(s): Der, EngA, YfgK
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 55.036
Isoelectric point: 5.588
Motif(s):
 
Type Positions Sequence
203 -> 376 IKLAIVGRPNVGKSTLTNRILGEERVVVYDMPGTTRDSIYIPMERDGREYVLIDTAGVRKRGKITDAVEKFSVIKTLQAIEDANVVMLVIDAREGISDQDLSLLGFILNSGRSLVIVVNKWDGLSQEVKEQVKETLDFRLGFIDFARVHFISALHGSGVGNLFESVREAYDSST
377 -> 461 RRVGTSMLTRIMTMAVEDHQPPLVRGRRVKLKYAHAGGYNPPIVVIHGNQVKDLPDSYKRYLMNYFRKSLDVMGSPIRIQFKEGE
469 -> 469 N
15 -> 15 K
205 -> 322 LAIVGRPNVGKSTLTNRILGEERVVVYDMPGTTRDSIYIPMERDGREYVLIDTAGVRKRGKITDAVEKFSVIKTLQAIEDANVVMLVIDAREGISDQDLSLLGFILNSGRSLVIVVNK

 

Classification:
Multifun Terms (GenProtEC)  
  6 - cell structure --> 6.6 - ribosomes
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0005515 - protein binding
GO:0043022 - ribosome binding
GO:0000166 - nucleotide binding
GO:0003924 - GTPase activity
GO:0005525 - GTP binding
GO:0043023 - ribosomal large subunit binding
GO:0032794 - GTPase activating protein binding
GO:0097216 - guanosine tetraphosphate binding
biological_process GO:0042254 - ribosome biogenesis
GO:0000027 - ribosomal large subunit assembly
Note(s): Note(s): ...[more].
Evidence: [IGI] Inferred from genetic interaction
[IMP] Inferred from mutant phenotype
Reference(s): [1] Ash MR., et al., 2012
[2] Hwang J., et al., 2001
[3] Hwang J., et al., 2006
[4] Luo Y., et al., 2010
[5] Majumdar S., et al., 2017
[6] Naganathan A., et al., 2015
[7] Tan J., et al., 2002
External database links:  
DIP:
DIP-48272N
ECOCYC:
G7319-MONOMER
ECOLIWIKI:
b2511
INTERPRO:
IPR006073
INTERPRO:
IPR032859
INTERPRO:
IPR031166
INTERPRO:
IPR027417
INTERPRO:
IPR016484
INTERPRO:
IPR015946
INTERPRO:
IPR005225
MODBASE:
P0A6P5
PANTHER:
PTHR11649:SF5
PDB:
3J8G
PFAM:
PF01926
PFAM:
PF14714
PRIDE:
P0A6P5
PRINTS:
PR00326
PRODB:
PRO_000022516
PROSITE:
PS51712
REFSEQ:
NP_417006
SMR:
P0A6P5
UNIPROT:
P0A6P5


Operon      
Name: bamB-der         
Operon arrangement:
Transcription unit        Promoter
bamB-der


RNA cis-regulatory element    
Attenuation: Transcriptional


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_2792 2636300 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_2793 2636452 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_2794 2637789 reverse nd [RS-EPT-CBR] [8]


Evidence    

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



Reference(s)    

 [1] Ash MR., Maher MJ., Mitchell Guss J., Jormakka M., 2012, The cation-dependent G-proteins: In a class of their own., FEBS Lett 586(16):2218-24

 [2] Hwang J., Inouye M., 2001, An essential GTPase, der, containing double GTP-binding domains from Escherichia coli and Thermotoga maritima., J Biol Chem 276(33):31415-21

 [3] Hwang J., Inouye M., 2006, The tandem GTPase, Der, is essential for the biogenesis of 50S ribosomal subunits in Escherichia coli., Mol Microbiol 61:1660-1672

 [4] Luo Y., Fischer JJ., Baessler OY., Schrey AK., Ungewiss J., Glinski M., Sefkow M., Dreger M., Koester H., 2010, GDP-capture compound--a novel tool for the profiling of GTPases in pro- and eukaryotes by capture compound mass spectrometry (CCMS)., J Proteomics 73(4):815-9

 [5] Majumdar S., Acharya A., Tomar SK., Prakash B., 2017, Disrupting domain-domain interactions is indispensable for EngA-ribosome interactions., Biochim Biophys Acta 1865(3):289-303

 [6] Naganathan A., Wood MP., Moore SD., 2015, The Large Ribosomal Subunit Protein L9 Enables the Growth of EF-P Deficient Cells and Enhances Small Subunit Maturation., PLoS One 10(4):e0120060

 [7] Tan J., Jakob U., Bardwell JC., 2002, Overexpression of two different GTPases rescues a null mutation in a heat-induced rRNA methyltransferase., J Bacteriol 184(10):2692-8

 [8] 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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