Summary: Cytochrome C biogenesis protein transmembrane region
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Disulfide oxidoreductase D Edit Wikipedia article
The Disufide Bond Oxidoreductase D (DsbD) Family (TC# 5.A.1) is a member of the Lysine Exporter (LysE) Superfamily. A representative list of proteins belonging to the DsbD family can be found in the Transporter Classification Base.
(1) several thiol-disufide exchange proteins
(7) components of sulfenic acid reductases.
Disulfide Bond Oxidoreductase D (DsbD)
The best characterized member of the DsbD family is DsbD ofÂ E. coli (TC# 5.A.1.1.1). The DsbD protein is membrane-embedded with a putative N-terminal transmembrane segment (TMS) plus 8 additionalTMSs. The smallest homologues (190 aas with 6 putative TMSs) are found in archaea, while the largest are found in both Gram-negative bacteria (758 aas with 9 putative TMSs) and Gram-positive bacteria (695 aas with 6 putative TMSs).
The overall vectorial electron transfer reaction catalyzed by DsbD is:
2 e-cytoplasmÂ â†’Â 2 e-periplasm
DsbB contains 4 essential cysteine residues, reversibly forming two disulfide bonds. Although DsbA displays no proofreading activity for repair of wrongly paired disulfides, DsbC, DsbE and DsbG have been found to demonstrate proofreading activity. Therefore, the two transmembrane pathways involving DsbD and DsbB together catalyze extracellular disulfide reduction (DsbD) and oxidation (DsbB) in a superficially reversible process that allows dithiol/disulfide exchange.
Some of these PDB structures include:â€‹, â€‹, â€‹, â€‹, â€‹, â€‹, â€‹, â€‹, â€‹
System Reduction Pathway
In theÂ E. coli DsbD system, electrons are transferred from NADPH in the cytoplasm to periplasmic dithiol/disulfide-containing proteins via an electron transfer chain that sequentially involves NADPH, thioredoxin reductase (TrxB; present in the cytoplasm), thioredoxin (TrxA; also in the cytoplasm), DsbD (the integral membrane constituent of the system), and the periplasmic electron acceptors (DsbC, DsbE (CcmG) and DsbG).
All of these last three proteins (DsbC, DsbE (CcmG) and DsbG) can donate electrons to oxidized disulfide-containing proteins in the periplasm of a Gram-negative bacterium or presumably in the external milieu of a Gram-positive bacterium or an archaeon.
Thus, the pathway is:
NADPH â†’Â TrxB â†’Â TrxA â†’Â DsbD â†’Â (DsbC, DsbE, or DsbG) â†’Â proteins.
DsbD contains three cysteine pairs that undergo reversible disulfide rearrangements. TrxA donates electrons to the transmembrane cysteines C163 (C3) and C285 (C5) in putative TMSs 1 and 4 in the DsbD model proposed by Katzen and Beckwith (2000). This dithiol then donates electrons to the periplasmic C-terminal thioredoxin motif (CXXC) of DsbD, thereby reducing C461 and C464 (C6 and C7, respectively). This dithiol pair attacks the periplasmic N-terminal disulfide bridge at C103 and C109 (C1 and C2, respectively) which transfers electrons to DsbC and other protein electron acceptors as noted above.
DsbD catalyses an essentially irreversible reaction due to the fact that electrons flow down their electrochemical gradient from inside the cell (negative inside) to outside the cell (positive outside). In order to reverse the reaction, electrons are transferred from dithiol proteins in the periplasm to an electron acceptor in the cytoplasm as follows:
reduced proteinperiplasmÂ â†’Â DsbAperiplasmÂ â†’Â DsbBmembraneÂ â†’Â quinonesmembraneÂ â†’Â reductasemembraneâ†’Â terminal electron acceptorcytoplasmÂ (e.g., O2, NO3-Â or fumarate).
- Bardischewsky, F.; Friedrich, C. G. (2001-01-01)."Identification of ccdA in Paracoccus pantotrophus GB17: disruption of ccdA causes complete deficiency in c-type cytochromes".Â Journal of BacteriologyÂ 183Â (1): 257â€“263.doi:10.1128/JB.183.1.257-263.2001.Â ISSNÂ 0021-9193.PMCÂ 94873.Â PMIDÂ 11114924.
- Cho, Seung-Hyun; Beckwith, Jon (2006-07-01)."Mutations of the membrane-bound disulfide reductase DsbD that block electron transfer steps from cytoplasm to periplasm in Escherichia coli".Â Journal of BacteriologyÂ 188(14): 5066â€“5076.Â doi:10.1128/JB.00368-06.Â ISSNÂ 0021-9193.Â PMCÂ 1539965.Â PMIDÂ 16816179.
- Collet, Jean-Francois; Bardwell, James C. A. (2002-04-01).Â "Oxidative protein folding in bacteria".Molecular MicrobiologyÂ 44Â (1): 1â€“8.Â ISSNÂ 0950-382X.PMIDÂ 11967064.
- Bardischewsky, F.; Friedrich, C. G. (2001-01-01). "Identification of ccdA in Paracoccus pantotrophus GB17: disruption of ccdA causes complete deficiency in c-type cytochromes". Journal of Bacteriology. 183 (1): 257â€“263. doi:10.1128/JB.183.1.257-263.2001. ISSNÂ 0021-9193. PMCÂ 94873. PMIDÂ 11114924.
- Le Brun, N. E.; Bengtsson, J.; Hederstedt, L. (2000-05-01). "Genes required for cytochrome c synthesis in Bacillus subtilis". Molecular Microbiology. 36 (3): 638â€“650. ISSNÂ 0950-382X. PMIDÂ 10844653.
- Chistoserdov, A. Y.; Boyd, J.; Mathews, F. S.; Lidstrom, M. E. (1992-05-15). "The genetic organization of the mau gene cluster of the facultative autotroph Paracoccus denitrificans". Biochemical and Biophysical Research Communications. 184 (3): 1181â€“1189. ISSNÂ 0006-291X. PMIDÂ 1590782.
- Van Spanning, R. J.; van der Palen, C. J.; Slotboom, D. J.; Reijnders, W. N.; Stouthamer, A. H.; Duine, J. A. (1994-11-15). "Expression of the mau genes involved in methylamine metabolism in Paracoccus denitrificans is under control of a LysR-type transcriptional activator". European journal of biochemistry / FEBS. 226 (1): 201â€“210. ISSNÂ 0014-2956. PMIDÂ 7957249.
- BrÃ¼nker, P.; Rother, D.; Sedlmeier, R.; Klein, J.; Mattes, R.; Altenbuchner, J. (1996-06-12). "Regulation of the operon responsible for broad-spectrum mercury resistance in Streptomyces lividans 1326". Molecular & general genetics: MGG. 251 (3): 307â€“315. ISSNÂ 0026-8925. PMIDÂ 8676873.
- Sedlmeier, R.; Altenbuchner, J. (1992-12-01). "Cloning and DNA sequence analysis of the mercury resistance genes of Streptomyces lividans". Molecular & general genetics: MGG. 236 (1): 76â€“85. ISSNÂ 0026-8925. PMIDÂ 1494353.
- Choudhury, P.; Kumar, R. (1996-07-01). "Association of metal tolerance with multiple antibiotic resistance of enteropathogenic organisms isolated from coastal region of deltaic Sunderbans". The Indian Journal of Medical Research. 104: 148â€“151. ISSNÂ 0971-5916. PMIDÂ 8783519.
- Gupta, S. D.; Wu, H. C.; Rick, P. D. (1997-08-01). "A Salmonella typhimurium genetic locus which confers copper tolerance on copper-sensitive mutants of Escherichia coli". Journal of Bacteriology. 179 (16): 4977â€“4984. ISSNÂ 0021-9193. PMCÂ 179352. PMIDÂ 9260936.
- Katzen, F.; Beckwith, J. (2000-11-22). "Transmembrane electron transfer by the membrane protein DsbD occurs via a disulfide bond cascade". Cell. 103 (5): 769â€“779. ISSNÂ 0092-8674. PMIDÂ 11114333.
- Krupp, R.; Chan, C.; Missiakas, D. (2001-02-02). "DsbD-catalyzed transport of electrons across the membrane of Escherichia coli". The Journal of Biological Chemistry. 276 (5): 3696â€“3701. doi:10.1074/jbc.M009500200. ISSNÂ 0021-9258. PMIDÂ 11085993.
- Williamson, Jessica A.; Cho, Seung-Hyun; Ye, Jiqing; Collet, Jean-Francois; Beckwith, Jonathan R.; Chou, James J. (2015-10-01). "Structure and multistate function of the transmembrane electron transporter CcdA". Nature Structural & Molecular Biology. 22 (10): 809â€“814. doi:10.1038/nsmb.3099. ISSNÂ 1545-9985. PMIDÂ 26389738.
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Cytochrome C biogenesis protein transmembrane region Provide feedback
This family consists of the transmembrane (i.e. non-catalytic) region of Cytochrome C biogenesis proteins also known as disulphide interchange proteins. These proteins posses a protein disulphide isomerase like domain that is not found within the aligned region of this family.
Crooke H, Cole J; , Mol Microbiol 1995;15:1139-1150.: The biogenesis of c-type cytochromes in Escherichia coli requires a membrane-bound protein, DipZ, with a protein disulphide isomerase-like domain. PUBMED:7623667 EPMC:7623667
Internal database links
|SCOOP:||DsbD_2 LysE NicO SfLAP|
|Similarity to PfamA using HHSearch:||DsbD_2|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR003834
This entry represents the transmembrane domain of Cytochrome C biogenesis proteins also known as disulphide interchange proteins, such as DsbD from E. coli and DipZ from Mycobacterium. These proteins posses a protein disulphide isomerase like domain that is not found within the aligned region of this family.
DsbA and DsbC, periplasmic proteins of E. coli, are two key players involved in disulphide bond formation. DsbD generates a reducing source in the periplasm, which is required for maintaining proper redox conditions [ PUBMED:7628442 ]. DipZ is essential for maintaining cytochrome c apoproteins in the correct conformations for the covalent attachment of haem groups to the appropriate pairs of cysteine residues [ PUBMED:7623667 ].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||membrane (GO:0016020)|
|Biological process||cytochrome complex assembly (GO:0017004)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
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This clan includes a diverse range of transporter families .
The clan contains the following 19 members:BacA Cad Colicin_V DsbD DsbD_2 DUF475 DUF6044 FTR1 HupE_UreJ HupE_UreJ_2 LysE MarC Mntp NicO OFeT_1 SfLAP TauE TerC UPF0016
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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|Author:||Bashton M , Bateman A , Eberhardt R|
|Number in seed:||7|
|Number in full:||10963|
|Average length of the domain:||203.3 aa|
|Average identity of full alignment:||24 %|
|Average coverage of the sequence by the domain:||51.31 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||18|
|Download:||download the raw HMM for this family|
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The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
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Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
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We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the DsbD domain has been found. There are 1 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.