4D7L | pdb_00004d7l

Methionine sulfoxide reductase A of Corynebacterium diphtheriae

• PDB DOI: https://doi.org/10.2210/pdb4D7L/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Corynebacterium diphtheriae NCTC 13129
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-11-25 Released: 2015-03-18 
• Deposition Author(s): Van Molle, I., Tossounian, M.A., Pedre, B., Wahni, K., Vertommen, D., Messens, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.190 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

Corynebacterium Diphtheriae Methionine Sulfoxide Reductase a Exploits a Unique Mycothiol Redox Relay Mechanism.

Tossounian, M., Pedre, B., Wahni, K., Erdogan, H., Vertommen, D., Van Molle, I., Messens, J.

(2015) J Biological Chem 290: 11365

• PubMed: 25752606 
• DOI: https://doi.org/10.1074/jbc.M114.632596
• Primary Citation Related Structures: 
  4D7L


• PubMed Abstract: 
  

  Methionine sulfoxide reductases are conserved enzymes that reduce oxidized methionines in proteins and play a pivotal role in cellular redox signaling. We have unraveled the redox relay mechanisms of methionine sulfoxide reductase A of the pathogen Corynebacterium diphtheriae (Cd-MsrA) and shown that this enzyme is coupled to two independent redox relay pathways. Steady-state kinetics combined with mass spectrometry of Cd-MsrA mutants give a view of the essential cysteine residues for catalysis. Cd-MsrA combines a nucleophilic cysteine sulfenylation reaction with an intramolecular disulfide bond cascade linked to the thioredoxin pathway. Within this cascade, the oxidative equivalents are transferred to the surface of the protein while releasing the reduced substrate. Alternatively, MsrA catalyzes methionine sulfoxide reduction linked to the mycothiol/mycoredoxin-1 pathway. After the nucleophilic cysteine sulfenylation reaction, MsrA forms a mixed disulfide with mycothiol, which is transferred via a thiol disulfide relay mechanism to a second cysteine for reduction by mycoredoxin-1. With x-ray crystallography, we visualize two essential intermediates of the thioredoxin relay mechanism and a cacodylate molecule mimicking the substrate interactions in the active site. The interplay of both redox pathways in redox signaling regulation forms the basis for further research into the oxidative stress response of this pathogen.

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Organizational Affiliation: 
• From the Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, 1050 Brussels, Belgium, the Brussels Center for Redox Biology, 1050 Brussels, Belgium, Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium, and.
the de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium.
From the Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, 1050 Brussels, Belgium, the Brussels Center for Redox Biology, 1050 Brussels, Belgium, Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium, and [e-mail].
From the Structural Biology Research Center, Vlaams Instituut voor Biotechnologie, 1050 Brussels, Belgium, the Brussels Center for Redox Biology, 1050 Brussels, Belgium, Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium, and [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 82.08 kDa 
• Atom Count: 5,790 
• Modeled Residue Count: 638 
• Deposited Residue Count: 720 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDE METHIONINE SULFOXIDE REDUCTASE MSRA	A, B, C	240	Corynebacterium diphtheriae NCTC 13129	Mutation(s): 0  EC: 1.8.4.11
UniProt
Find proteins for Q6NEL2 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NEL2  Go to UniProtKB:  Q6NEL2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	AA [auth C], BA [auth C], CA [auth C], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
CAC	D [auth A], N [auth B], X [auth C]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
SO4	E [auth A], O [auth B], Y [auth C], Z [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.190 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.395	α = 90
b = 140.175	β = 90
c = 140.551	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-18 
Deposition Author(s): Van Molle, I., Tossounian, M.A., Pedre, B., Wahni, K., Vertommen, D., Messens, J.

Revision History  

• Version 1.0: 2015-03-18
  Type: Initial release
  
• Version 1.1: 2015-05-13
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary