6T87

Urocanate reductase in complex with urocanate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.114 
  • R-Value Observed: 0.115 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural characterization of the microbial enzyme urocanate reductase mediating imidazole propionate production.

Venskutonyte, R.Koh, A.Stenstrom, O.Khan, M.T.Lundqvist, A.Akke, M.Backhed, F.Lindkvist-Petersson, K.

(2021) Nat Commun 12: 1347-1347

  • DOI: 10.1038/s41467-021-21548-y
  • Primary Citation of Related Structures:  
    6T85, 6T87, 6T86, 6T88

  • PubMed Abstract: 
  • The human microbiome can produce metabolites that modulate insulin signaling. Type 2 diabetes patients have increased circulating concentrations of the microbially produced histidine metabolite, imidazole propionate (ImP) and administration of ImP in mice resulted in impaired glucose tolerance ...

    The human microbiome can produce metabolites that modulate insulin signaling. Type 2 diabetes patients have increased circulating concentrations of the microbially produced histidine metabolite, imidazole propionate (ImP) and administration of ImP in mice resulted in impaired glucose tolerance. Interestingly, the fecal microbiota of the patients had increased capacity to produce ImP, which is mediated by the bacterial enzyme urocanate reductase (UrdA). Here, we describe the X-ray structures of the ligand-binding domains of UrdA in four different states, representing the structural transitions along the catalytic reaction pathway of this unexplored enzyme linked to disease in humans. The structures in combination with functional data provide key insights into the mechanism of action of UrdA that open new possibilities for drug development strategies targeting type 2 diabetes.


    Organizational Affiliation

    LINXS - Lund Institute of Advanced Neutron and X-ray Science, Lund, Sweden. karin.lindkvist@med.lu.se.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Urocanate reductase A460Shewanella oneidensis MR-1Mutation(s): 0 
Gene Names: urdASO_4620
EC: 1.3.99.33
Find proteins for Q8CVD0 (Shewanella oneidensis (strain MR-1))
Explore Q8CVD0 
Go to UniProtKB:  Q8CVD0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
URO
Query on URO

Download Ideal Coordinates CCD File 
A
(2E)-3-(1H-IMIDAZOL-4-YL)ACRYLIC ACID
C6 H6 N2 O2
LOIYMIARKYCTBW-OWOJBTEDSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.114 
  • R-Value Observed: 0.115 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.705α = 90
b = 123.705β = 90
c = 66.3γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2016-01319
Swedish Research CouncilSweden2017-05816
European Research CouncilSweden780659

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release
  • Version 1.1: 2021-03-10
    Changes: Database references