3HGJ

Old Yellow Enzyme from Thermus scotoductus SA-01 complexed with p-hydroxy-benzaldehyde

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Crystal structure of a thermostable old yellow enzyme from Thermus scotoductus SA-01

Opperman, D.J., Sewell, B.T., Litthauer, D., Isupov, M.N., Littlechild, J.A., van Heerden, E.

(2010) Biochem.Biophys.Res.Commun. 393: 426-431

  • DOI: 10.1016/j.bbrc.2010.02.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Recent characterization of the chromate reductase (CrS) from the thermophile Thermus scotoductus SA-01 revealed this enzyme to be related to the Old Yellow Enzyme (OYE) family. Here, we report the structure of a thermostable OYE homolog in its holofo ...

    Recent characterization of the chromate reductase (CrS) from the thermophile Thermus scotoductus SA-01 revealed this enzyme to be related to the Old Yellow Enzyme (OYE) family. Here, we report the structure of a thermostable OYE homolog in its holoform at 2.2A as well as its complex with p-hydroxybenzaldehyde (pHBA). The enzyme crystallized as octamers with the monomers showing a classical TIM barrel fold which upon dimerization yields the biologically active form of the protein. A sulfate ion is bound above the si-side of the non-covalently bound FMN cofactor in the oxidized solved structure but is displaced upon pHBA binding. The active-site architecture is highly conserved as with other members of this enzyme family. The pHBA in the CrS complex is positioned by hydrogen bonding to the two conserved catalytic-site histidines. The most prominent structural difference between CrS and other OYE homologs is the size of the "capping domain". Thermostabilization of the enzyme is achieved in part through increased proline content within loops and turns as well as increased intersubunit interactions through hydrogen bonding and complex salt bridge networks. CrS is able to reduce the C=C bonds of alpha,beta-unsaturated carbonyl compounds with a preference towards cyclic substrates however no activity was observed towards beta-substituted substrates. Mutational studies have confirmed the role of Tyr177 as the proposed proton donor although reduction could still occur at a reduced rate when this residue was mutated to phenylalanine.

    Organizational Affiliation: 

    Department of Microbial, Biochemical and Food Biotechnology, BioPAD Metagenomics Platform, University of the Free State, Bloemfontein 9300, South Africa.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chromate reductase
A, B, C, D
349Thermus scotoductusMutation(s): 0 
Gene Names: chrR
Find proteins for B0JDW3 (Thermus scotoductus)
Go to UniProtKB:  B0JDW3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HBA
Query on HBA
Download SDF File 
Download CCD File 
A, B, C, D
P-HYDROXYBENZALDEHYDE
C7 H6 O2
RGHHSNMVTDWUBI-UHFFFAOYSA-N
 Ligand Interaction
FMN
Query on FMN
Download SDF File 
Download CCD File 
A, B, C, D
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.199 
  • Space Group: P 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 98.703α = 90.00
b = 101.169β = 114.32
c = 101.336γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing
REFMACrefinement
SCALAdata scaling
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-02-12
    Type: Database references