2K74 | pdb_00002k74

Solution NMR structure of DsbB-ubiquinone complex

• PDB DOI: https://doi.org/10.2210/pdb2K74/pdb

• Classification: MEMBRANE PROTEIN, OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2008-08-01 Released: 2008-10-07 
• Deposition Author(s): Zhou, Y., Cierpicki, T., Flores Jimenez, R.H., Lukasik, S.M., Ellena, J.F., Cafiso, D.S., Kadokura, H., Beckwith, J., Bushweller, J.H.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 195 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

NMR solution structure of the integral membrane enzyme DsbB: functional insights into DsbB-catalyzed disulfide bond formation.

Zhou, Y., Cierpicki, T., Jimenez, R.H., Lukasik, S.M., Ellena, J.F., Cafiso, D.S., Kadokura, H., Beckwith, J., Bushweller, J.H.

(2008) Mol Cell 31: 896-908

• PubMed: 18922471 
• DOI: https://doi.org/10.1016/j.molcel.2008.08.028
• Primary Citation Related Structures: 
  2K73, 2K74


• PubMed Abstract: 
  

  We describe the NMR structure of DsbB, a polytopic helical membrane protein. DsbB, a bacterial cytoplasmic membrane protein, plays a key role in disulfide bond formation. It reoxidizes DsbA, the periplasmic protein disulfide oxidant, using the oxidizing power of membrane-embedded quinones. We determined the structure of an interloop disulfide bond form of DsbB, an intermediate in catalysis. Analysis of the structure and interactions with substrates DsbA and quinone reveals functionally relevant changes induced by these substrates. Analysis of the structure, dynamics measurements, and NMR chemical shifts around the interloop disulfide bond suggest how electron movement from DsbA to quinone through DsbB is regulated and facilitated. Our results demonstrate the extraordinary utility of NMR for functional characterization of polytopic integral membrane proteins and provide insights into the mechanism of DsbB catalysis.

---

Organizational Affiliation: 
• Department of Molecular Physiology and Biological Physics, University of Virginia Health Sciences, Charlottesville, VA 22908, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.27 kDa 
• Atom Count: 1,505 
• Modeled Residue Count: 183 
• Deposited Residue Count: 183 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disulfide bond formation protein B	A	183	Escherichia coli K-12	Mutation(s): 4  Gene Names: dsbB, roxB, ycgA Membrane Entity: Yes
UniProt
Find proteins for P0A6M2 (Escherichia coli (strain K12)) Explore P0A6M2  Go to UniProtKB:  P0A6M2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UQ2	B [auth A]	UBIQUINONE-2 C19 H26 O4 SQQWBSBBCSFQGC-JLHYYAGUSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 195 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-07 
Deposition Author(s): Zhou, Y., Cierpicki, T., Flores Jimenez, R.H., Lukasik, S.M., Ellena, J.F., Cafiso, D.S., Kadokura, H., Beckwith, J., Bushweller, J.H.

Revision History  

• Version 1.0: 2008-10-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2011-12-07
  Changes: Database references
• Version 1.3: 2021-10-20
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-11-27
  Changes: Data collection, Structure summary