8Q9V

S-methylthiourocanate hydratase from Variovorax sp. RA8 in complex with NAD+ and imidazolone propionate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

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Literature

Structure and Substrate Specificity of S -Methyl Thiourocanate Hydratase.

Vasseur, C.M.Karunasegaram, D.Seebeck, F.P.

(2024) ACS Chem Biol 19: 718-724

  • DOI: https://doi.org/10.1021/acschembio.3c00745
  • Primary Citation of Related Structures:  
    8Q9U, 8Q9V

  • PubMed Abstract: 

    Nicotinamide adenine dinucleotide (NAD + ) is a common cofactor in enzyme-catalyzed reactions that involve hydride transfers. In contrast, urocanase and urocanase-like enzymes use NAD + for covalent electrophilic catalysis. Deciphering avenues by which this unusual catalytic strategy has diversified by evolution may point to approaches for the design of novel enzymes. In this report, we describe the S -methyl thiourocanate hydratase ( S -Me-TUC) from Variovorax sp. RA8 as a novel member of this small family of NAD + -dependent hydratases. This enzyme catalyzes the 1,4-addition of water to S -methyl thiourocanate as the second step in the catabolism of S -methyl ergothioneine. The crystal structure of this enzyme in complex with the cofactor and a product analogue identifies critical sequence motifs that explain the narrow and nonoverlapping substrate scopes of S -methyl thiourocanate-, urocanate-, thiourocanate-, and N τ-methyl urocanate-specific hydratases. The discovery of a S -methyl ergothioneine catabolic pathway also suggests that S -methylation or alkylation may be a significant activity in the biology of ergothioneine.


  • Organizational Affiliation

    Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, Basel 4002, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
urocanate hydratase549Variovorax sp. RA8Mutation(s): 0 
Gene Names: hutU_2
UniProt
Find proteins for A0A6P2DXK2 (Variovorax sp. RA8)
Explore A0A6P2DXK2 
Go to UniProtKB:  A0A6P2DXK2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6P2DXK2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
D [auth A]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
PG4 (Subject of Investigation/LOI)
Query on PG4

Download Ideal Coordinates CCD File 
B [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
O66 (Subject of Investigation/LOI)
Query on O66

Download Ideal Coordinates CCD File 
C [auth A]3-[(4~{R})-5-oxidanylidene-1,4-dihydroimidazol-4-yl]propanoic acid
C6 H8 N2 O3
HEXMLHKQVUFYME-SCSAIBSYSA-N
EDO (Subject of Investigation/LOI)
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACY (Subject of Investigation/LOI)
Query on ACY

Download Ideal Coordinates CCD File 
E [auth A]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: P 32 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.511α = 90
b = 96.511β = 90
c = 147.585γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland182023

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-06
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Database references