RegulonDB RegulonDB 10.10: Gene Form
   

hdeA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

hdeD hdeA hdeB Lrp GadX GadW H-NS Lrp GadE Lrp GadX GadW Lrp Lrp TorR GadX GadW MarA PhoP TorR Lrp GadE FliZ anti-terminator terminator TSS_4124 (cluster) TSS_4124 (cluster) TSS_4123 (cluster) TSS_4123 (cluster) hdeDp hdeDp hdeAp hdeAp TSS_4120 TSS_4120 TSS_4119 TSS_4119 TSS_4118 TSS_4118 TSS_4117 TSS_4117 TSS_4116 TSS_4116 TSS_4115 TSS_4115 yhiDp1 yhiDp1 yhiDp8 yhiDp8

Gene      
Name: hdeA    Texpresso search in the literature
Synonym(s): ECK3494, EG11398, b3510, yhhC, yhiB
Genome position(nucleotides): 3656408 <-- 3656740 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
42.94
External database links:  
ASAP:
ABE-0011464
CGSC:
33734
ECHOBASE:
EB1370
ECOLIHUB:
hdeA
OU-MICROARRAY:
b3510
STRING:
511145.b3510
COLOMBOS: hdeA


Shine dalgarno      
Sequence: ctttatagttGAGGATattacGAT


Product      
Name: periplasmic acid stress chaperone HdeA
Synonym(s): HdeA, HdeA monomer, chaperone active form, YhhC, YhiB
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space
Molecular weight: 11.858
Isoelectric point: 4.825
Motif(s):
 
Type Positions Sequence
1 -> 21 MKKVLGVILGGLLLLPVVSNA
41 -> 41 D
56 -> 56 F
72 -> 72 D
13 -> 96 LLLPVVSNAADAQKAADNKKPVNSWTCEDFLAVDESFQPTAVGFAEALNNKDKPEDAVLDVQGIATVTPAIVQACTQDKQANFK

 

Classification:
Multifun Terms (GenProtEC)  
  5 - cell processes --> 5.10 - defense/survival
  5 - cell processes --> 5.5 - adaptations --> 5.5.4 - pH
Gene Ontology Terms (GO)  
cellular_component GO:0030288 - outer membrane-bounded periplasmic space
GO:0042597 - periplasmic space
molecular_function GO:0051082 - unfolded protein binding
GO:0042803 - protein homodimerization activity
biological_process GO:1990507 - ATP-independent chaperone mediated protein folding
GO:1990451 - cellular stress response to acidic pH
Note(s): Note(s): ...[more].
Reference(s): [1] Ahlstrom LS., et al., 2013
[2] Arnqvist A., et al., 1994
[3] Bordi C., et al., 2003
[4] Dudin O., et al., 2013
[5] Garrison MA., et al., 2014
[6] Holland RD., et al., 1999
[7] Liwo A., et al., 1999
[8] Masuda N., et al., 2003
[9] Spory A., et al., 2002
[10] Yang F., et al., 1998
[11] Yoshida T., et al., 1993
External database links:  
DIP:
DIP-47945N
ECOCYC:
EG11398-MONOMER
ECOLIWIKI:
b3510
INTERPRO:
IPR038303
INTERPRO:
IPR036831
INTERPRO:
IPR010486
INTERPRO:
IPR024972
MODBASE:
P0AES9
PDB:
1DJ8
PDB:
1BG8
PFAM:
PF06411
PRIDE:
P0AES9
PRODB:
PRO_000022868
REFSEQ:
NP_417967
SMR:
P0AES9
SWISSMODEL:
P0AES9
UNIPROT:
P0AES9


Operon      
Name: hdeAB-yhiD         
Operon arrangement:
Transcription unit        Promoter
hdeAB-yhiD
hdeAB-yhiD
yhiD


Transcriptional Regulation      
Display Regulation             
Activated by: GadX, PhoP, GadW, TorR, GadE, RcsB
Repressed by: FliZ, MarA, H-NS, GadX, Lrp, GadW


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 yhiDp8 3656039 reverse nd [ICWHO] [12]
  promoter yhiDp1 3656110 reverse nd [ICWHO] [12]
  promoter TSS_4115 3656259 reverse nd [RS-EPT-CBR] [13]
  promoter TSS_4116 3656277 reverse nd [RS-EPT-CBR] [13]
  promoter TSS_4117 3656279 reverse nd [RS-EPT-CBR] [13]
  promoter TSS_4118 3656618 reverse nd [RS-EPT-CBR] [13]
  promoter TSS_4119 3656719 reverse nd [RS-EPT-CBR] [13]
  promoter TSS_4120 3656761 reverse nd [RS-EPT-CBR] [13]
  promoter TSS_4123 (cluster) 3656977 forward nd [RS-EPT-CBR] [13]
  promoter TSS_4124 (cluster) 3657010 forward nd [RS-EPT-CBR] [13]


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] Ahlstrom LS., Dickson A., Brooks CL., 2013, Binding and folding of the small bacterial chaperone HdeA., J Phys Chem B 117(42):13219-25

 [2] Arnqvist A., Olsen A., Normark S., 1994, Sigma S-dependent growth-phase induction of the csgBA promoter in Escherichia coli can be achieved in vivo by sigma 70 in the absence of the nucleoid-associated protein H-NS., Mol Microbiol 13(6):1021-32

 [3] Bordi C., Theraulaz L., Mejean V., Jourlin-Castelli C., 2003, Anticipating an alkaline stress through the Tor phosphorelay system in Escherichia coli., Mol Microbiol 48(1):211-23

 [4] Dudin O., Lacour S., Geiselmann J., 2013, Expression dynamics of RpoS/Crl-dependent genes in Escherichia coli., Res Microbiol 164(8):838-47

 [5] Garrison MA., Crowhurst KA., 2014, NMR-monitored titration of acid-stress bacterial chaperone HdeA reveals that Asp and Glu charge neutralization produces a loosened dimer structure in preparation for protein unfolding and chaperone activation., Protein Sci 23(2):167-78

 [6] Holland RD., Duffy CR., Rafii F., Sutherland JB., Heinze TM., Holder CL., Voorhees KJ., Lay JO., 1999, Identification of bacterial proteins observed in MALDI TOF mass spectra from whole cells., Anal Chem 71(15):3226-30

 [7] Liwo A., Lee J., Ripoll DR., Pillardy J., Scheraga HA., 1999, Protein structure prediction by global optimization of a potential energy function., Proc Natl Acad Sci U S A 96(10):5482-5

 [8] Masuda N., Church GM., 2003, Regulatory network of acid resistance genes in Escherichia coli., Mol Microbiol 48(3):699-712

 [9] Spory A., Bosserhoff A., von Rhein C., Goebel W., Ludwig A., 2002, Differential regulation of multiple proteins of Escherichia coli and Salmonella enterica serovar Typhimurium by the transcriptional regulator SlyA., J Bacteriol 184(13):3549-59

 [10] Yang F., Gustafson KR., Boyd MR., Wlodawer A., 1998, Crystal structure of Escherichia coli HdeA., Nat Struct Biol 5(9):763-4

 [11] Yoshida T., Ueguchi C., Mizuno T., 1993, Physical map location of a set of Escherichia coli genes (hde) whose expression is affected by the nucleoid protein H-NS., J Bacteriol 175(23):7747-8

 [12] 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

 [13] 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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