Thiol:disulfide interchange protein DsbD precursor

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P36655 (DSBD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 145. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Thiol:disulfide interchange protein DsbD
EC=1.8.1.8

Alternative name(s):
C-type cytochrome biogenesis protein CycZ
Inner membrane copper tolerance protein
Protein-disulfide reductase
Short name=Disulfide reductase

Gene names

Name:	dsbD
Synonyms:	cutA2, cycZ, dipZ
Ordered Locus Names:	b4136, JW5734

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	565 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Required to facilitate the formation of correct disulfide bonds in some periplasmic proteins and for the assembly of the periplasmic c-type cytochromes. Acts by transferring electrons from cytoplasmic thioredoxin to the periplasm, thereby maintaining the active site of DsbC, DsbE and DsbG in a reduced state. This transfer involves a cascade of disulfide bond formation and reduction steps. HAMAP-Rule MF_00399
Catalytic activity	Protein dithiol + NAD(P)⁺ = protein disulfide + NAD(P)H. HAMAP-Rule MF_00399
Subcellular location	Cell inner membrane; Multi-pass membrane protein HAMAP-Rule MF_00399.
Miscellaneous	The consequences of replacement of the cysteines with alanines were found to depend on the conditions tested and on the reporter system used for the analysis, and then differ depending on the references. HAMAP-Rule MF_00399
Sequence similarities	Belongs to the thioredoxin family. DsbD subfamily. Contains 1 thioredoxin domain.
Sequence caution	The sequence CAA54781.1 differs from that shown. Reason: Erroneous initiation. The sequence CAA85375.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Biological process	Cytochrome c-type biogenesis Electron transport Transport
Cellular component	Cell inner membrane Cell membrane Membrane
Domain	Redox-active center Signal Transmembrane Transmembrane helix
Ligand	NAD
Molecular function	Oxidoreductase
PTM	Disulfide bond
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	cell redox homeostasis Inferred from mutant phenotype Ref.1. Source: EcoCyc cellular response to temperature stimulus Inferred from mutant phenotype Ref.1. Source: EcoliWiki cytochrome complex assembly Inferred from mutant phenotype Ref.10. Source: EcoliWiki electron transport chain Inferred from electronic annotation. Source: UniProtKB-KW response to drug Inferred from mutant phenotype Ref.1. Source: EcoliWiki response to stress Inferred from mutant phenotype Ref.1. Source: EcoliWiki
Cellular_component	integral to plasma membrane Inferred from direct assay PubMed 19258316. Source: EcoliWiki
Molecular_function	electron carrier activity Inferred from electronic annotation. Source: HAMAP protein disulfide oxidoreductase activity Inferred from mutant phenotype PubMed 8917542. Source: EcoCyc protein-disulfide reductase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 19

Ref.8

Chain

20 – 565

546

Thiol:disulfide interchange protein DsbD HAMAP-Rule MF_00399

PRO_0000007373

Regions

Topological domain

20 – 162

143

Periplasmic Potential

Transmembrane

163 – 183

Helical; Potential

Topological domain

184 – 207

Cytoplasmic Potential

Transmembrane

208 – 228

Helical; Potential

Topological domain

229 – 242

Periplasmic Potential

Transmembrane

243 – 263

Helical; Potential

Topological domain

264 – 295

Cytoplasmic Potential

Transmembrane

296 – 316

Helical; Potential

Topological domain

317 – 322

Periplasmic Potential

Transmembrane

323 – 343

Helical; Potential

Topological domain

344 – 356

Cytoplasmic Potential

Transmembrane

357 – 377

Helical; Potential

Topological domain

378 – 383

Periplasmic Potential

Transmembrane

384 – 404

Helical; Potential

Topological domain

405 – 417

Cytoplasmic Potential

Transmembrane

418 – 438

Helical; Potential

Topological domain

439 – 565

127

Periplasmic Potential

Domain

434 – 565

132

Thioredoxin

Amino acid modifications

Disulfide bond

122 ↔ 128

Redox-active Probable

Disulfide bond

182 ↔ 304

Redox-active Probable

Disulfide bond

480 ↔ 483

Redox-active Probable

Experimental info

Mutagenesis

C → A: No loss of activity. Ref.11

Mutagenesis

122

C → A: Loss of activity. Ref.7 Ref.8 Ref.11

Mutagenesis

128

C → A: Loss of activity. Ref.7 Ref.8 Ref.11

Mutagenesis

182

C → A: Loss of activity. Ref.7 Ref.8 Ref.11

Mutagenesis

301

C → A: No loss of activity. Ref.7 Ref.8 Ref.11

Mutagenesis

304

C → A: Loss of activity. Ref.7 Ref.8 Ref.11

Mutagenesis

480

C → A: Loss of activity; when associated with A-483. Ref.7 Ref.8 Ref.11

Mutagenesis

483

C → A: Loss of activity; when associated with A-480. Ref.7 Ref.8 Ref.11

Secondary structure

565

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P36655 [UniParc].

Last modified June 1, 2001. Version 4.
Checksum: 41EFAA1C9EAC6C5F
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FASTA

565

61,795

        10         20         30         40         50         60 
MAQRIFTLIL LLCSTSVFAG LFDAPGRSQF VPADQAFAFD FQQNQHDLNL TWQIKDGYYL 

        70         80         90        100        110        120 
YRKQIRITPE HAKIADVQLP QGVWHEDEFY GKSEIYRDRL TLPVTINQAS AGATLTVTYQ 

       130        140        150        160        170        180 
GCADAGFCYP PETKTVPLSE VVANNAAPQP VSVPQQEQPT AQLPFSALWA LLIGIGIAFT 

       190        200        210        220        230        240 
PCVLPMYPLI SGIVLGGKQR LSTARALLLT FIYVQGMALT YTALGLVVAA AGLQFQAALQ 

       250        260        270        280        290        300 
HPYVLIGLAI VFTLLAMSMF GLFTLQLPSS LQTRLTLMSN RQQGGSPGGV FVMGAIAGLI 

       310        320        330        340        350        360 
CSPCTTAPLS AILLYIAQSG NMWLGGGTLY LYALGMGLPL MLITVFGNRL LPKSGPWMEQ 

       370        380        390        400        410        420 
VKTAFGFVIL ALPVFLLERV IGDVWGLRLW SALGVAFFGW AFITSLQAKR GWMRIVQIIL 

       430        440        450        460        470        480 
LAAALVSVRP LQDWAFGATH TAQTQTHLNF TQIKTVDELN QALVEAKGKP VMLDLYADWC 

       490        500        510        520        530        540 
VACKEFEKYT FSDPQVQKAL ADTVLLQANV TANDAQDVAL LKHLNVLGLP TILFFDGQGQ 

       550        560 
EHPQARVTGF MDAETFSAHL RDRQP

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Identification and characterization of a new disulfide isomerase-like protein (DsbD) in Escherichia coli." Missiakas D., Schwager F., Raina S. EMBO J. 14:3415-3424(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHARACTERIZATION.
[2]	"Molecular genetics of a chromosomal locus involved in copper tolerance in Escherichia coli K-12." Fong S.-T., Camakaris J., Lee B.T.O. Mol. Microbiol. 15:1127-1137(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"The biogenesis of c-type cytochromes in Escherichia coli requires a membrane-bound protein, DipZ, with a protein disulphide isomerase-like domain." Crooke H.R., Cole J.A. Mol. Microbiol. 15:1139-1150(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[4]	"Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes." Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R. Nucleic Acids Res. 23:2105-2119(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[5]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[6]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[7]	"Escherichia coli DipZ: anatomy of a transmembrane protein disulphide reductase in which three pairs of cysteine residues, one in each of three domains, contribute differentially to function." Gordon E.H.J., Page M.D., Willis A.C., Ferguson S.J. Mol. Microbiol. 35:1360-1374(2000) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-8 AND 20-34, TOPOLOGY, MUTAGENESIS OF CYS-122; CYS-128; CYS-182; CYS-301; CYS-304; CYS-480 AND CYS-483.
[8]	"Transfer of electrons across the cytoplasmic membrane by DsbD, a membrane protein involved in thiol-disulphide exchange and protein folding in the bacterial periplasm." Chung J., Chen T., Missiakas D. Mol. Microbiol. 35:1099-1109(2000) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 20-27, TOPOLOGY, MUTAGENESIS OF CYS-122; CYS-128; CYS-182; CYS-301; CYS-304; CYS-480 AND CYS-483. Strain: BL21-DE3.
[9]	Missiakas D., Hughes G.J., Frutiger S., Paquet N., Raina S. Submitted (MAY-1995) to UniProtKB Cited for: PROTEIN SEQUENCE OF 78-82.
[10]	"Specific thiol compounds complement deficiency in c-type cytochrome biogenesis in Escherichia coli carrying a mutation in a membrane-bound disulphide isomerase-like protein." Sambongi Y., Ferguson S.J. FEBS Lett. 353:235-238(1994) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION.
[11]	"Six conserved cysteines of the membrane protein DsbD are required for the transfer of electrons from the cytoplasm to the periplasm of Escherichia coli." Stewart E.J., Katzen F., Beckwith J. EMBO J. 18:5963-5971(1999) [PubMed] [Europe PMC] [Abstract] Cited for: TOPOLOGY, MUTAGENESIS OF CYS-13; CYS-122; CYS-128; CYS-182; CYS-301; CYS-304; CYS-480 AND CYS-483. Strain: DHB4 and RI242.
[12]	"Transmembrane electron transfer by the membrane protein DsbD occurs via a disulfide bond cascade." Katzen F., Beckwith J. Cell 103:769-779(2000) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION.
[13]	"DsbD-catalyzed transport of electrons across the membrane of Escherichia coli." Krupp R., Chan C., Missiakas D. J. Biol. Chem. 276:3696-3701(2001) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION. Strain: K38.
[14]	"Global topology analysis of the Escherichia coli inner membrane proteome." Daley D.O., Rapp M., Granseth E., Melen K., Drew D., von Heijne G. Science 308:1321-1323(2005) [PubMed] [Europe PMC] [Abstract] Cited for: TOPOLOGY [LARGE SCALE ANALYSIS]. Strain: K12 / MG1655 / ATCC 47076.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Z36905 Genomic DNA. Translation: CAA85375.1. Different initiation.
X77707 Genomic DNA. Translation: CAA54781.1. Different initiation.
U14003 Genomic DNA. Translation: AAA97035.1.
U00096 Genomic DNA. Translation: AAC77096.1.
AP009048 Genomic DNA. Translation: BAE78138.1.

PIR

S56364.

RefSeq

NP_418559.1. NC_000913.2.
YP_492279.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1JPE	X-ray	1.90	A	20-151	[»]
1JZD	X-ray	2.30	C	20-151	[»]
1L6P	X-ray	1.65	A	20-144	[»]
1VRS	X-ray	2.85	A/B/C	20-162	[»]
			D/E/F	438-565	[»]
1Z5Y	X-ray	1.94	D	20-162	[»]
2FWE	X-ray	1.65	A	438-565	[»]
2FWF	X-ray	1.30	A	438-565	[»]
2FWG	X-ray	1.10	A	438-565	[»]
2FWH	X-ray	0.99	A	438-565	[»]
3PFU	X-ray	1.80	A	21-151	[»]

ProteinModelPortal

P36655.

SMR

P36655. Positions 23-143, 447-563.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-9476N.

STRING

511145.b4136.

Protein family/group databases

TCDB

5.A.1.1.1. disulfide bond oxidoreductase D (DsbD) family.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC77096; AAC77096; b4136.
BAE78138; BAE78138; BAE78138.

GeneID

12933697.
948649.

KEGG

ecj:Y75_p4023.
eco:b4136.

PATRIC

32123839. VBIEscCol129921_4267.

Organism-specific databases

EchoBASE

EB2095.

EcoGene

EG12178. dipZ.

Phylogenomic databases

eggNOG

COG4232.

HOGENOM

HOG000254981.

K04084.

OMA

LPKAGSW.

ProtClustDB

PRK00293.

Enzyme and pathway databases

BioCyc

EcoCyc:DSBD-MONOMER.
ECOL316407:JW5734-MONOMER.
MetaCyc:DSBD-MONOMER.

Gene expression databases

Genevestigator

P36655.

Family and domain databases

Gene3D

3.40.30.10. 1 hit.

HAMAP

MF_00399. DbsD.

InterPro

IPR003834. Cyt_c_assmbl_TM_dom.
IPR022910. Thiol_diS_interchange_DbsD.
IPR012336. Thioredoxin-like_fold.
IPR017937. Thioredoxin_CS.
[Graphical view]

PANTHER

PTHR32234:SF1. PTHR32234:SF1. 1 hit.

Pfam

PF02683. DsbD. 1 hit.
[Graphical view]

SUPFAM

SSF52833. Thiordxn-like_fd. 1 hit.

PROSITE

PS00194. THIOREDOXIN_1. 1 hit.
PS51352. THIOREDOXIN_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P36655.

Entry information

Entry name

DSBD_ECOLI

Accession

Primary (citable) accession number: P36655
Secondary accession number(s): P76796, Q2M6G8

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 1, 1994
Last sequence update:	June 1, 2001
Last modified:	May 1, 2013
This is version 145 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Amino acid modifications

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protein family/group databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents