4MN7

Structural and biochemical analysis of type II free methionine-R-sulfoxide reductase from Thermoplasma acidophilum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and biochemical analysis of a type II free methionine-R-sulfoxide reductase from Thermoplasma acidophilum

Kim, H.S.Kwak, G.H.Lee, K.Jo, C.H.Hwang, K.Y.Kim, H.Y.

(2014) Arch Biochem Biophys 560: 10-19

  • DOI: 10.1016/j.abb.2014.07.009
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Free methionine-R-sulfoxide reductase (fRMsr) enzymes only reduce the free form of methionine-R-sulfoxide and can be grouped into two types with respect to the number of conserved Cys residues in the active sites. In this work, the crystal structures ...

    Free methionine-R-sulfoxide reductase (fRMsr) enzymes only reduce the free form of methionine-R-sulfoxide and can be grouped into two types with respect to the number of conserved Cys residues in the active sites. In this work, the crystal structures of type II fRMsr from Thermoplasma acidophilum (TafRMsr), which contains two conserved Cys, have been determined in native form and in a complex with the substrate. The overall structure of TafRMsr consists of a central β-sheet encompassed by a two-α-helix bundle flanking on one side and one small α-helix on the other side. Based on biochemical and growth complementation assays, Cys(84) is demonstrated to be the catalytic Cys. The data also show that TafRMsr functions as an antioxidant protein. Structural analyses reveal insights into substrate recognition and orientation, conformational changes in the active site during substrate binding, and the role of active site residues in substrate binding. A model for the catalytic mechanism of type II TafRMsr is suggested, in which intramolecular disulfide bond formation is not involved. In addition, the biochemical, enzymatic, and structural properties of type II TafRMsr are compared with those of type I enzymes.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu 705-717, Republic of Korea. Electronic address: hykim@ynu.ac.kr.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative uncharacterized protein Ta0848A, B149Thermoplasma acidophilum DSM 1728Mutation(s): 1 
Gene Names: Ta0848
Find proteins for Q9HJW5 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165))
Explore Q9HJW5 
Go to UniProtKB:  Q9HJW5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SME
Query on SME

Download CCD File 
B
METHIONINE SULFOXIDE
C5 H11 N O3 S
QEFRNWWLZKMPFJ-ZXPFJRLXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.08α = 90
b = 120.08β = 90
c = 66.911γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-06
    Type: Initial release
  • Version 1.1: 2014-12-17
    Changes: Database references