RegulonDB RegulonDB 10.9: Gene Form
   

dsbD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

dsbD dcuA yjdC cutA anti-anti-terminator anti-terminator terminator TSS_4939 TSS_4939 TSS_4938 TSS_4938 TSS_4937 TSS_4937 TSS_4936 TSS_4936 TSS_4935 TSS_4935 TSS_4934 TSS_4934 cutAp cutAp TSS_4933 TSS_4933 TSS_4932 TSS_4932 yjdCp yjdCp

Gene      
Name: dsbD    Texpresso search in the literature
Synonym(s): ECK4130, EG12178, b4136, cutA2, cycZ, dipZ, htrI
Genome position(nucleotides): 4363345 <-- 4365042 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
54.42
Reference(s): [1] Stewart EJ., et al., 1999
External database links:  
ASAP:
ABE-0013539
CGSC:
34213
ECHOBASE:
EB2095
ECOLIHUB:
dipZ
OU-MICROARRAY:
b4136
STRING:
511145.b4136
COLOMBOS: dsbD


Product      
Name: thiol-disulfide exchange protein DsbD
Synonym(s): CycZ, DipZ, DsbD, HtrI, inner membrane copper tolerance protein, thiol:disulfide interchange protein DsbD
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 61.795
Isoelectric point: 7.22
Motif(s):
 
Type Positions Sequence
128 -> 128 C
182 -> 182 C
28 -> 138 SQFVPADQAFAFDFQQNQHDLNLTWQIKDGYYLYRKQIRITPEHAKIADVQLPQGVWHEDEFYGKSEIYRDRLTLPVTINQASAGATLTVTYQGCADAGFCYPPETKTVPL
243 -> 263 YVLIGLAIVFTLLAMSMFGLF
20 -> 565 GLFDAPGRSQFVPADQAFAFDFQQNQHDLNLTWQIKDGYYLYRKQIRITPEHAKIADVQLPQGVWHEDEFYGKSEIYRDRLTLPVTINQASAGATLTVTYQGCADAGFCYPPETKTVPLSEVVANNAAPQPVSVPQQEQPTAQLPFSALWALLIGIGIAFTPCVLPMYPLISGIVLGGKQRLSTARALLLTFIYVQGMALTYTALGLVVAAAGLQFQAALQHPYVLIGLAIVFTLLAMSMFGLFTLQLPSSLQTRLTLMSNRQQGGSPGGVFVMGAIAGLICSPCTTAPLSAILLYIAQSGNMWLGGGTLYLYALGMGLPLMLITVFGNRLLPKSGPWMEQVKTAFGFVILALPVFLLERVIGDVWGLRLWSALGVAFFGWAFITSLQAKRGWMRIVQIILLAAALVSVRPLQDWAFGATHTAQTQTHLNFTQIKTVDELNQALVEAKGKPVMLDLYADWCVACKEFEKYTFSDPQVQKALADTVLLQANVTANDAQDVALLKHLNVLGLPTILFFDGQGQEHPQARVTGFMDAETFSAHLRDRQP

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.6 - biosynthesis of macromolecules (cellular constituents) --> 1.6.15 - large molecule carriers --> 1.6.15.1 - cytochromes
  1 - metabolism --> 1.8 - metabolism of other compounds --> 1.8.2 - sulfur metabolism
  6 - cell structure --> 6.1 - membrane
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0005887 - integral component of plasma membrane
GO:0016021 - integral component of membrane
molecular_function GO:0005515 - protein binding
GO:0009055 - electron transfer activity
GO:0016491 - oxidoreductase activity
GO:0015035 - protein disulfide oxidoreductase activity
GO:0047134 - protein-disulfide reductase activity
biological_process GO:0017004 - cytochrome complex assembly
GO:0046688 - response to copper ion
GO:0045454 - cell redox homeostasis
GO:0022900 - electron transport chain
GO:0055114 - oxidation-reduction process
Note(s): Note(s): ...[more].
Reference(s): [2] Cho SH., et al., 2006
[3] Cho SH., et al., 2009
[4] Crooke H., et al., 1995
[5] Goldstone D., et al., 2001
[6] Goulding CW., et al., 2002
[7] Haebel PW., et al., 2002
[8] Haebel PW., et al., 2001
[9] Hemmis CW., et al., 2011
[10] Hiniker A., et al., 2006
[11] Katzen F., et al., 2002
[12] Kim JH., et al., 2003
[13] Krupp R., et al., 2001
[14] Mavridou DA., et al., 2011
[15] Mavridou DA., et al., 2014
[16] Mavridou DA., et al., 2012
[17] Mavridou DA., et al., 2007
[18] Rozhkova A., et al., 2007
[19] Rozhkova A., et al., 2008
[20] Rozhkova A., et al., 2004
[21] Sambongi Y., et al., 1994
[22] Stirnimann CU., et al., 2006
[23] Stirnimann CU., et al., 2005
External database links:  
BIGG:
dsbdrd
DIP:
DIP-9476N
ECOCYC:
DSBD-MONOMER
ECOLIWIKI:
b4136
INTERPRO:
IPR022910
INTERPRO:
IPR017937
INTERPRO:
IPR003834
INTERPRO:
IPR028250
INTERPRO:
IPR035671
INTERPRO:
IPR036249
INTERPRO:
IPR036929
INTERPRO:
IPR013766
MODBASE:
P36655
PANTHER:
PTHR32234:SF0
PDB:
5NHI
PDB:
4IP6
PDB:
4IP1
PDB:
3PFU
PDB:
2FWH
PDB:
2FWG
PDB:
2FWF
PDB:
2FWE
PDB:
1Z5Y
PDB:
1VRS
PDB:
1L6P
PDB:
1JZD
PDB:
1JPE
PFAM:
PF02683
PFAM:
PF13899
PFAM:
PF11412
PRIDE:
P36655
PRODB:
PRO_000022482
PROSITE:
PS00194
PROSITE:
PS51352
REFSEQ:
NP_418559
SMR:
P36655
UNIPROT:
P36655


Operon      
Name: dsbD-yjdC         
Operon arrangement:
Transcription unit        Promoter
yjdC
dsbD-yjdC


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_4932 4363473 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_4933 4364237 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_4934 4366101 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_4935 4366103 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_4936 4366114 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_4937 4366119 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_4938 4366313 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_4939 4366748 reverse nd [RS-EPT-CBR] [24]


Evidence    

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



Reference(s)    

 [1] Stewart EJ., Katzen F., Beckwith J., 1999, Six conserved cysteines of the membrane protein DsbD are required for the transfer of electrons from the cytoplasm to the periplasm of Escherichia coli., EMBO J 18(21):5963-71

 [2] Cho SH., Beckwith J., 2006, Mutations of the membrane-bound disulfide reductase DsbD that block electron transfer steps from cytoplasm to periplasm in Escherichia coli., J Bacteriol 188(14):5066-76

 [3] Cho SH., Beckwith J., 2009, Two snapshots of electron transport across the membrane: insights into the structure and function of DsbD., J Biol Chem 284(17):11416-24

 [4] Crooke H., Cole J., 1995, The biogenesis of c-type cytochromes in Escherichia coli requires a membrane-bound protein, DipZ, with a protein disulphide isomerase-like domain., Mol Microbiol 15(6):1139-50

 [5] Goldstone D., Haebel PW., Katzen F., Bader MW., Bardwell JC., Beckwith J., Metcalf P., 2001, DsbC activation by the N-terminal domain of DsbD., Proc Natl Acad Sci U S A 98(17):9551-6

 [6] Goulding CW., Sawaya MR., Parseghian A., Lim V., Eisenberg D., Missiakas D., 2002, Thiol-disulfide exchange in an immunoglobulin-like fold: structure of the N-terminal domain of DsbD., Biochemistry 41(22):6920-7

 [7] Haebel PW., Goldstone D., Katzen F., Beckwith J., Metcalf P., 2002, The disulfide bond isomerase DsbC is activated by an immunoglobulin-fold thiol oxidoreductase: crystal structure of the DsbC-DsbDalpha complex., EMBO J 21(18):4774-84

 [8] Haebel PW., Wichman S., Goldstone D., Metcalf P., 2001, Crystallization and initial crystallographic analysis of the disulfide bond isomerase DsbC in complex with the alpha domain of the electron transporter DsbD., J Struct Biol 136(2):162-6

 [9] Hemmis CW., Berkmen M., Eser M., Schildbach JF., 2011, TrbB from conjugative plasmid F is a structurally distinct disulfide isomerase that requires DsbD for redox state maintenance., J Bacteriol 193(18):4588-97

 [10] Hiniker A., Vertommen D., Bardwell JC., Collet JF., 2006, Evidence for conformational changes within DsbD: possible role for membrane-embedded proline residues., J Bacteriol 188(20):7317-20

 [11] Katzen F., Deshmukh M., Daldal F., Beckwith J., 2002, Evolutionary domain fusion expanded the substrate specificity of the transmembrane electron transporter DsbD., EMBO J 21(15):3960-9

 [12] Kim JH., Kim SJ., Jeong DG., Son JH., Ryu SE., 2003, Crystal structure of DsbDgamma reveals the mechanism of redox potential shift and substrate specificity(1)., FEBS Lett 543(1-3):164-9

 [13] Krupp R., Chan C., Missiakas D., 2001, DsbD-catalyzed transport of electrons across the membrane of Escherichia coli., J Biol Chem 276(5):3696-701

 [14] Mavridou DA., Saridakis E., Kritsiligkou P., Goddard AD., Stevens JM., Ferguson SJ., Redfield C., 2011, Oxidation state-dependent protein-protein interactions in disulfide cascades., J Biol Chem 286(28):24943-56

 [15] Mavridou DA., Saridakis E., Kritsiligkou P., Mozley EC., Ferguson SJ., Redfield C., 2014, An extended active-site motif controls the reactivity of the thioredoxin fold., J Biol Chem 289(12):8681-96

 [16] Mavridou DA., Stelzl LS., Ferguson SJ., Redfield C., 2012, 1H, 13C and 15N resonance assignments for the oxidized and reduced states of the N-terminal domain of DsbD from Escherichia coli., Biomol NMR Assign 6(2):163-7

 [17] Mavridou DA., Stevens JM., Ferguson SJ., Redfield C., 2007, Active-site properties of the oxidized and reduced C-terminal domain of DsbD obtained by NMR spectroscopy., J Mol Biol 370(4):643-58

 [18] Rozhkova A., Glockshuber R., 2007, Kinetics of the intramolecular disulfide exchange between the periplasmic domains of DsbD., J Mol Biol 367(4):1162-70

 [19] Rozhkova A., Glockshuber R., 2008, Thermodynamic aspects of DsbD-mediated electron transport., J Mol Biol 380(5):783-8

 [20] Rozhkova A., Stirnimann CU., Frei P., Grauschopf U., Brunisholz R., Grutter MG., Capitani G., Glockshuber R., 2004, Structural basis and kinetics of inter- and intramolecular disulfide exchange in the redox catalyst DsbD., EMBO J 23(8):1709-19

 [21] Sambongi Y., Ferguson SJ., 1994, Specific thiol compounds complement deficiency in c-type cytochrome biogenesis in Escherichia coli carrying a mutation in a membrane-bound disulphide isomerase-like protein., FEBS Lett 353(3):235-8

 [22] Stirnimann CU., Rozhkova A., Grauschopf U., Bockmann RA., Glockshuber R., Capitani G., Grutter MG., 2006, High-resolution structures of Escherichia coli cDsbD in different redox states: A combined crystallographic, biochemical and computational study., J Mol Biol 358(3):829-45

 [23] Stirnimann CU., Rozhkova A., Grauschopf U., Grutter MG., Glockshuber R., Capitani G., 2005, Structural basis and kinetics of DsbD-dependent cytochrome c maturation., Structure 13(7):985-93

 [24] 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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