spacer
spacer

PDBsum entry 1l6p

Go to PDB code: 
protein links
Electron transport PDB id
1l6p
Jmol
Contents
Protein chain
121 a.a. *
Waters ×245
* Residue conservation analysis
PDB id:
1l6p
Name: Electron transport
Title: N-terminal of dsbd (residues 20-144) from e. Coli.
Structure: Thiol:disulfide interchange protein dsbd. Chain: a. Fragment: residues 20-143. Synonym: c-type cytochrome biogenesis protein cycz, inner membrane copper tolerance protein. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli k12. Expression_system_taxid: 83333. Expression_system_cell_line: dh5alpha cells.
Biol. unit: Dimer (from PQS)
Resolution:
1.65Å     R-factor:   0.141     R-free:   0.226
Authors: C.W.Goulding,M.R.Sawaya,A.Parseghian
Key ref:
C.W.Goulding et al. (2002). Thiol-disulfide exchange in an immunoglobulin-like fold: structure of the N-terminal domain of DsbD. Biochemistry, 41, 6920-6927. PubMed id: 12033924 DOI: 10.1021/bi016038l
Date:
12-Mar-02     Release date:   12-Jun-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P36655  (DSBD_ECOLI) -  Thiol:disulfide interchange protein DsbD
Seq:
Struc:
 
Seq:
Struc:
565 a.a.
121 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.8.1.8  - Protein-disulfide reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Protein dithiol + NAD(P)(+) = protein disulfide + NAD(P)H
Protein dithiol
+ NAD(P)(+)
= protein disulfide
+ NAD(P)H
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     protein-disulfide reductase activity     1 term  

 

 
    reference    
 
 
DOI no: 10.1021/bi016038l Biochemistry 41:6920-6927 (2002)
PubMed id: 12033924  
 
 
Thiol-disulfide exchange in an immunoglobulin-like fold: structure of the N-terminal domain of DsbD.
C.W.Goulding, M.R.Sawaya, A.Parseghian, V.Lim, D.Eisenberg, D.Missiakas.
 
  ABSTRACT  
 
Escherichia coli DsbD transports electrons across the plasma membrane, a pathway that leads to the reduction of protein disulfide bonds. Three secreted thioredoxin-like factors, DsbC, DsbE, and DsbG, reduce protein disulfide bonds whereby an active site C-X-X-C motif is oxidized to generate a disulfide bond. DsbD catalyzes the reduction of the disulfide of DsbC, DsbE, and DsbG but not of the thioredoxin-like oxidant DsbA. The reduction of DsbC, DsbE, and DsbG occurs by transport of electrons from cytoplasmic thioredoxin to the C-terminal thioredoxin-like domain of DsbD (DsbD(C)). The N-terminal domain of DsbD, DsbD(N), acts as a versatile adaptor in electron transport and is capable of forming disulfides with oxidized DsbC, DsbE, or DsbG as well as with reduced DsbD(C). Isolated DsbD(N) is functional in electron transport in vitro. Crystallized DsbD(N) assumes an immunoglobulin-like fold that encompasses two active site cysteines, C103 and C109, forming a disulfide bond between beta-strands. The disulfide of DsbD(N) is shielded from the environment and capped by a phenylalanine (F70). A model is discussed whereby the immunoglobulin fold of DsbD(N) may provide for the discriminating interaction with thioredoxin-like factors, thereby triggering movement of the phenylalanine cap followed by disulfide rearrangement.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21058397 S.Indu, V.Kochat, S.Thakurela, C.Ramakrishnan, and R.Varadarajan (2011).
Conformational analysis and design of cross-strand disulfides in antiparallel β-sheets.
  Proteins, 79, 244-260.  
19634988 M.A.Wouters, S.W.Fan, and N.L.Haworth (2010).
Disulfides as redox switches: from molecular mechanisms to functional significance.
  Antioxid Redox Signal, 12, 53-91.  
19004826 D.A.Mavridou, J.M.Stevens, A.D.Goddard, A.C.Willis, S.J.Ferguson, and C.Redfield (2009).
Control of Periplasmic Interdomain Thiol:Disulfide Exchange in the Transmembrane Oxidoreductase DsbD.
  J Biol Chem, 284, 3219-3226.  
19604482 M.Quinternet, P.Tsan, L.Selme-Roussel, C.Jacob, S.Boschi-Muller, G.Branlant, and M.T.Cung (2009).
Formation of the complex between DsbD and PilB N-terminal domains from Neisseria meningitidis necessitates an adaptability of nDsbD.
  Structure, 17, 1024-1033.
PDB code: 2k9f
19258316 S.H.Cho, and J.Beckwith (2009).
Two Snapshots of Electron Transport across the Membrane: INSIGHTS INTO THE STRUCTURE AND FUNCTION OF DsbD.
  J Biol Chem, 284, 11416-11424.  
17641688 S.H.Cho, A.Porat, J.Ye, and J.Beckwith (2007).
Redox-active cysteines of a membrane electron transporter DsbD show dual compartment accessibility.
  EMBO J, 26, 3509-3520.  
16815710 C.W.Gruber, M.Cemazar, B.Heras, J.L.Martin, and D.J.Craik (2006).
Protein disulfide isomerase: the structure of oxidative folding.
  Trends Biochem Sci, 31, 455-464.  
17008712 J.L.Pan, and J.C.Bardwell (2006).
The origami of thioredoxin-like folds.
  Protein Sci, 15, 2217-2227.  
16446111 J.Messens, and J.F.Collet (2006).
Pathways of disulfide bond formation in Escherichia coli.
  Int J Biochem Cell Biol, 38, 1050-1062.  
16926157 N.Brot, J.F.Collet, L.C.Johnson, T.J.Jönsson, H.Weissbach, and W.T.Lowther (2006).
The thioredoxin domain of Neisseria gonorrhoeae PilB can use electrons from DsbD to reduce downstream methionine sulfoxide reductases.
  J Biol Chem, 281, 32668-32675.
PDB code: 2h30
17019698 N.Ouyang, Y.G.Gao, H.Y.Hu, and Z.X.Xia (2006).
Crystal structures of E. coli CcmG and its mutants reveal key roles of the N-terminal beta-sheet and the fingerprint region.
  Proteins, 65, 1021-1031.
PDB codes: 2b1k 2b1l 2g0f
  16511006 D.Goldstone, E.N.Baker, and P.Metcalf (2005).
Crystallization and preliminary diffraction studies of the C-terminal domain of the DipZ homologue from Mycobacterium tuberculosis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 243-245.  
15057279 A.Rozhkova, C.U.Stirnimann, P.Frei, U.Grauschopf, R.Brunisholz, M.G.Grütter, G.Capitani, and R.Glockshuber (2004).
Structural basis and kinetics of inter- and intramolecular disulfide exchange in the redox catalyst DsbD.
  EMBO J, 23, 1709-1719.
PDB codes: 1se1 1vrs
13678527 D.E.Fomenko, and V.N.Gladyshev (2003).
Genomics perspective on disulfide bond formation.
  Antioxid Redox Signal, 5, 397-402.  
12925743 F.Katzen, and J.Beckwith (2003).
Role and location of the unusual redox-active cysteines in the hydrophobic domain of the transmembrane electron transporter DsbD.
  Proc Natl Acad Sci U S A, 100, 10471-10476.  
12524212 H.Kadokura, F.Katzen, and J.Beckwith (2003).
Protein disulfide bond formation in prokaryotes.
  Annu Rev Biochem, 72, 111-135.  
13678528 R.Ortenberg, and J.Beckwith (2003).
Functions of thiol-disulfide oxidoreductases in E. coli: redox myths, realities, and practicalities.
  Antioxid Redox Signal, 5, 403-411.  
12415301 C.S.Sevier, and C.A.Kaiser (2002).
Formation and transfer of disulphide bonds in living cells.
  Nat Rev Mol Cell Biol, 3, 836-847.  
12234918 P.W.Haebel, D.Goldstone, F.Katzen, J.Beckwith, and P.Metcalf (2002).
The disulfide bond isomerase DsbC is activated by an immunoglobulin-fold thiol oxidoreductase: crystal structure of the DsbC-DsbDalpha complex.
  EMBO J, 21, 4774-4784.
PDB codes: 1jpe 1jzd 1jzo
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.