4LWL

Crystal structure of methionine sulfoxide reductase U16C/E55A from clostridium oremlandii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Structural analysis of 1-Cys type selenoprotein methionine sulfoxide reductase A

Lee, E.H.Kwak, G.H.Kim, M.J.Kim, H.Y.Hwang, K.Y.

(2014) Arch.Biochem.Biophys. 545: 1-8

  • DOI: 10.1016/j.abb.2013.12.024
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Methionine sulfoxide reductase A (MsrA) reduces free and protein-based methionine-S-sulfoxide to methionine. Structures of 1-Cys MsrAs lacking a resolving Cys, which interacts with catalytic Cys, are unknown. In addition, no structural information on ...

    Methionine sulfoxide reductase A (MsrA) reduces free and protein-based methionine-S-sulfoxide to methionine. Structures of 1-Cys MsrAs lacking a resolving Cys, which interacts with catalytic Cys, are unknown. In addition, no structural information on selenocysteine (Sec)-containing MsrA enzymes has been reported. In this work, we determined the crystal structures of 1-Cys type selenoprotein MsrA from Clostridium oremlandii at 1.6-1.8Å, including the reduced, oxidized (sulfenic acid), and substrate-bound forms. The overall structure of Clostridium MsrA, consisting of ten α-helices and six β-strands, folds into a catalytic domain and a novel helical domain absent from other known MsrA structures. The helical domain, containing five helices, tightly interacts with the catalytic domain, and is likely critical for catalytic activity due to its association with organizing the active site. This helical domain is also conserved in several selenoprotein MsrAs. Our structural analysis reveals that the side chain length of Glu55 is critical for the proton donor function of this residue. Our structures also provide insights into the architecture of the 1-Cys MsrA active site and the roles of active site residues in substrate recognition and catalysis.


    Organizational Affiliation

    Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Republic of Korea. Electronic address: chahong@korea.ac.kr.,Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu 705-717, Republic of Korea.,Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu 705-717, Republic of Korea. Electronic address: hykim@ynu.ac.kr.,Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptide methionine sulfoxide reductase MsrA
A
217Alkaliphilus oremlandii (strain OhILAs)Mutation(s): 2 
Gene Names: msrA
EC: 1.8.4.11
Find proteins for A8MI53 (Alkaliphilus oremlandii (strain OhILAs))
Go to UniProtKB:  A8MI53
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.197 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 81.240α = 90.00
b = 81.240β = 90.00
c = 66.923γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-07-27 
  • Released Date: 2014-06-11 
  • Deposition Author(s): Hwang, K.Y., Lee, E.H.

Revision History 

  • Version 1.0: 2014-06-11
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description
  • Version 2.0: 2019-08-07
    Type: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary