RegulonDB RegulonDB 10.9: Gene Form
   

hybD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

hybC hybB hybD hybE hybF hybA TSS_3306 TSS_3306

Gene      
Name: hybD    Texpresso search in the literature
Synonym(s): ECK2987, EG11802, b2993
Genome position(nucleotides): 3140792 <-- 3141286 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
54.75
External database links:  
ASAP:
ABE-0009826
CGSC:
33421
ECHOBASE:
EB1750
ECOLIHUB:
hybD
OU-MICROARRAY:
b2993
STRING:
511145.b2993
COLOMBOS: hybD


Product      
Name: hydrogenase 2 maturation protease
Synonym(s): HybD
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 17.751
Isoelectric point: 4.368
Motif(s):
 
Type Positions Sequence
160 -> 164 EAIHD
20 -> 147 VRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKKNAPGTMMILRDEEVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQVLA

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.7 - anaerobic respiration
  2 - information transfer --> 2.3 - protein related --> 2.3.3 - posttranslational modification
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0005515 - protein binding
GO:0008047 - enzyme activator activity
GO:0008233 - peptidase activity
GO:0016787 - hydrolase activity
GO:0046872 - metal ion binding
GO:0004175 - endopeptidase activity
GO:0004190 - aspartic-type endopeptidase activity
biological_process GO:0006464 - cellular protein modification process
GO:0006508 - proteolysis
GO:0016485 - protein processing
GO:0043085 - positive regulation of catalytic activity
Note(s): Note(s): ...[more].
Evidence: [APPH] Assay of protein purified to homogeneity
[HIFS] Human inference of function from sequence
[IMP] Inferred from mutant phenotype
Reference(s): [1] Ling MH., et al., 2014
[2] Menon NK., et al., 1994
[3] Pei J., et al., 2002
[4] Pinske C., et al., 2019
[5] Rossmann R., et al., 1995
[6] Senger M., et al., 2017
[7] Soboh B., et al., 2010
[8] Thomas C., et al., 2015
External database links:  
DIP:
DIP-9967N
ECOCYC:
EG11802-MONOMER
ECOLIWIKI:
b2993
INTERPRO:
IPR000671
INTERPRO:
IPR004419
INTERPRO:
IPR023430
MODBASE:
P37182
PANTHER:
PTHR30302
PDB:
1CFZ
PFAM:
PF01750
PRIDE:
P37182
PRINTS:
PR00446
PRODB:
PRO_000022950
REFSEQ:
NP_417467
SMR:
P37182
UNIPROT:
P37182


Operon      
Name: hybOABCDEFG         
Operon arrangement:
Transcription unit        Promoter
hybOABCDEFG


Transcriptional Regulation      
Display Regulation             
Repressed by: ArcA, NarL


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_3306 3141794 reverse nd [RS-EPT-CBR] [9]


Evidence    

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



Reference(s)    

 [1] Ling MH., Poh CL., 2014, A predictor for predicting Escherichia coli transcriptome and the effects of gene perturbations., BMC Bioinformatics 15:140

 [2] Menon NK., Chatelus CY., Dervartanian M., Wendt JC., Shanmugam KT., Peck HD., Przybyla AE., 1994, Cloning, sequencing, and mutational analysis of the hyb operon encoding Escherichia coli hydrogenase 2., J Bacteriol 176(14):4416-23

 [3] Pei J., Grishin NV., 2002, Breaking the singleton of germination protease., Protein Sci 11(3):691-7

 [4] Pinske C., Thomas C., Nutschan K., Sawers RG., 2019, Delimiting the Function of the C-Terminal Extension of the Escherichia coli [NiFe]-Hydrogenase 2 Large Subunit Precursor., Front Microbiol 10:2223

 [5] Rossmann R., Maier T., Lottspeich F., Bock A., 1995, Characterisation of a protease from Escherichia coli involved in hydrogenase maturation., Eur J Biochem 227(1-2):545-50

 [6] Senger M., Stripp ST., Soboh B., 2017, Proteolytic cleavage orchestrates cofactor insertion and protein assembly in [NiFe]-hydrogenase biosynthesis., J Biol Chem 292(28):11670-11681

 [7] Soboh B., Kruger S., Kuhns M., Pinske C., Lehmann A., Sawers RG., 2010, Development of a cell-free system reveals an oxygen-labile step in the maturation of [NiFe]-hydrogenase 2 of Escherichia coli., FEBS Lett 584(18):4109-14

 [8] Thomas C., Muhr E., Sawers RG., 2015, Coordination of Synthesis and Assembly of a Modular Membrane-Associated [NiFe]-Hydrogenase Is Determined by Cleavage of the C-Terminal Peptide., J Bacteriol 197(18):2989-98

 [9] 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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