Home LiteratureArticle Details
PMID: 19214188 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Dynamic nature of disulphide bond formation catalysts revealed by crystal structures of DsbB.

The EMBO journal ·Vol. 28 ·No. 6 ·2009-03-18 ·Pages 779-91

Inaba K, Murakami S, Nakagawa A, Iida H, Kinjo M, Ito K, Suzuki M

Abstract

In the Escherichia coli system catalysing oxidative protein folding, disulphide bonds are generated by the cooperation of DsbB and ubiquinone and transferred to substrate proteins through DsbA. The structures solved so far for different forms of DsbB lack the Cys104-Cys130 initial-state disulphide that is directly donated to DsbA. Here, we report the 3.4 A crystal structure of a DsbB-Fab complex, in which DsbB has this principal disulphide. Its comparison with the updated structure of the DsbB-DsbA complex as well as with the recently reported NMR structure of a DsbB variant having the rearranged Cys41-Cys130 disulphide illuminated conformational transitions of DsbB induced by the binding and release of DsbA. Mutational studies revealed that the membrane-parallel short alpha-helix of DsbB has a key function in physiological electron flow, presumably by controlling the positioning of the Cys130-containing loop. These findings demonstrate that DsbB has developed the elaborate conformational dynamism to oxidize DsbA for continuous protein disulphide bond formation in the cell.

MeSH Terms
Amino Acid Sequence Bacterial Proteins/chemistry,metabolism Biocatalysis Cell Membrane/enzymology Crystallization Crystallography, X-Ray Cysteine/metabolism Disulfides/metabolism Escherichia coli/enzymology Escherichia coli Proteins/chemistry,metabolism Immunoglobulin Fab Fragments/metabolism Membrane Proteins/chemistry,metabolism Molecular Sequence Data Oxidation-Reduction Protein Disulfide-Isomerases/chemistry,metabolism Protein Structure, Secondary Protein Transport Structure-Activity Relationship Ubiquinone/chemistry,metabolism
Chemicals
Bacterial Proteins Disulfides DsbB protein, Bacteria Escherichia coli Proteins Immunoglobulin Fab Fragments Membrane Proteins Ubiquinone Protein Disulfide-Isomerases dsbA protein, E coli Cysteine
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Inaba Kenji
Division of Protein Chemistry, Post-Genome Science Center, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan. inaba-k@bioreg.kyushu-u.ac.jp
Murakami Satoshi
Nakagawa Atsushi
Iida Hiroka
Kinjo Mai
Ito Koreaki
Suzuki Mamoru
References (31)
31 references, click to expand
  1. The CCP4 suite: programs for protein crystallography.
    Acta Crystallogr D Biol Crystallogr. 1994 Sep 1;50(Pt 5):760-3 PMID: 15299374
  2. Two cysteines in each periplasmic domain of the membrane protein DsbB are required for its function in protein disulfide bond formation.
    EMBO J. 1994 Nov 1;13(21):5121-7 PMID: 7957076
  3. Processing of X-ray diffraction data collected in oscillation mode.
    Methods Enzymol. 1997;276:307-26 PMID: 27754618
  4. Redox-active cysteines of a membrane electron transporter DsbD show dual compartment accessibility.
    EMBO J. 2007 Aug 8;26(15):3509-20 PMID: 17641688
  5. Critical role of a thiolate-quinone charge transfer complex and its adduct form in de novo disulfide bond generation by DsbB.
    Proc Natl Acad Sci U S A. 2006 Jan 10;103(2):287-92 PMID: 16384917
  6. Characterization of the menaquinone-dependent disulfide bond formation pathway of Escherichia coli.
    J Biol Chem. 2004 Nov 5;279(45):47057-65 PMID: 15347648
  7. A pathway for disulfide bond formation in vivo.
    Proc Natl Acad Sci U S A. 1993 Feb 1;90(3):1038-42 PMID: 8430071
  8. Respiratory chain is required to maintain oxidized states of the DsbA-DsbB disulfide bond formation system in aerobically growing Escherichia coli cells.
    Proc Natl Acad Sci U S A. 1997 Oct 28;94(22):11857-62 PMID: 9342327
  9. The disulfide bond formation (Dsb) system.
    Curr Opin Struct Biol. 2008 Aug;18(4):450-8 PMID: 18406599
  10. Formation and transfer of disulphide bonds in living cells.
    Nat Rev Mol Cell Biol. 2002 Nov;3(11):836-47 PMID: 12415301
  11. Role of the cytosolic loop of DsbB in catalytic turnover of the ubiquinone-DsbB complex.
    Antioxid Redox Signal. 2006 May-Jun;8(5-6):743-52 PMID: 16771666
  12. Protein disulfide bond formation in prokaryotes.
    Annu Rev Biochem. 2003;72:111-35 PMID: 12524212
  13. Preparation and structure of the charge-transfer intermediate of the transmembrane redox catalyst DsbB.
    FEBS Lett. 2008 Oct 15;582(23-24):3301-7 PMID: 18775700
  14. Mutants in DsbB that appear to redirect oxidation through the disulfide isomerization pathway.
    J Mol Biol. 2008 Apr 11;377(5):1433-42 PMID: 18325532
  15. Structure and mechanisms of the DsbB-DsbA disulfide bond generation machine.
    Biochim Biophys Acta. 2008 Apr;1783(4):520-9 PMID: 18082634
  16. DsbB elicits a red-shift of bound ubiquinone during the catalysis of DsbA oxidation.
    J Biol Chem. 2004 Feb 20;279(8):6761-8 PMID: 14634016
  17. Why is DsbA such an oxidizing disulfide catalyst?
    Cell. 1995 Dec 15;83(6):947-55 PMID: 8521518
  18. NMR solution structure of the integral membrane enzyme DsbB: functional insights into DsbB-catalyzed disulfide bond formation.
    Mol Cell. 2008 Sep 26;31(6):896-908 PMID: 18922471
  19. Conformational transition of Sec machinery inferred from bacterial SecYE structures.
    Nature. 2008 Oct 16;455(7215):988-91 PMID: 18923527
  20. Characterization of new DsbB-like thiol-oxidoreductases of Campylobacter jejuni and Helicobacter pylori and classification of the DsbB family based on phylogenomic, structural and functional criteria.
    Microbiology (Reading). 2005 Jan;151(Pt 1):219-231 PMID: 15632440
  21. Improved methods for building protein models in electron density maps and the location of errors in these models.
    Acta Crystallogr A. 1991 Mar 1;47 ( Pt 2):110-9 PMID: 2025413
  22. Environment of the active site region of RseP, an Escherichia coli regulated intramembrane proteolysis protease, assessed by site-directed cysteine alkylation.
    J Biol Chem. 2007 Feb 16;282(7):4553-4560 PMID: 17179147
  23. Crystal structure of the DsbB-DsbA complex reveals a mechanism of disulfide bond generation.
    Cell. 2006 Nov 17;127(4):789-801 PMID: 17110337
  24. Coot: model-building tools for molecular graphics.
    Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32 PMID: 15572765
  25. Disulfide bonds are generated by quinone reduction.
    J Biol Chem. 2000 Aug 25;275(34):26082-8 PMID: 10854438
  26. Partial (13)C and (15)N chemical-shift assignments of the disulfide-bond-forming enzyme DsbB by 3D magic-angle spinning NMR spectroscopy.
    Chembiochem. 2007 Mar 5;8(4):434-42 PMID: 17285659
  27. Respiratory chain strongly oxidizes the CXXC motif of DsbB in the Escherichia coli disulfide bond formation pathway.
    EMBO J. 1999 Mar 1;18(5):1192-8 PMID: 10064586
  28. Roles of a conserved arginine residue of DsbB in linking protein disulfide-bond-formation pathway to the respiratory chain of Escherichia coli.
    Proc Natl Acad Sci U S A. 2000 Sep 26;97(20):10884-9 PMID: 11005861
  29. Reactivities of quinone-free DsbB from Escherichia coli.
    J Biol Chem. 2005 Sep 23;280(38):33035-44 PMID: 16027117
  30. The name's bond......disulfide bond.
    Curr Opin Struct Biol. 2007 Dec;17(6):691-8 PMID: 17933514
  31. Four cysteines of the membrane protein DsbB act in concert to oxidize its substrate DsbA.
    EMBO J. 2002 May 15;21(10):2354-63 PMID: 12006488
Article Info
Journal
The EMBO journal
Abbr.
EMBO J
ISSN
1460-2075
Published
2009-03-18
Epub
2009-00-12
Pages
779-91
Language
English
Region
England
NLM ID
8208664
PMCID
PMC2666032
Subset
IM
Databases
PDB
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com