6XJM

Biuret Hydrolase (BiuH) from Rhodococcus sp. Mel C169S bound with biuret


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.184 

wwPDB Validation   3D Report Full Report



Literature

Discovery of an ultra-specific triuret hydrolase (TrtA) establishes the triuret biodegradation pathway.

Tassoulas, L.J.Elias, M.H.Wackett, L.P.

(2020) J Biol Chem 

  • DOI: 10.1074/jbc.RA120.015631
  • Primary Citation of Related Structures:  
    6XJE, 6XIX, 6XJ4, 6XK1, 6XJM

  • PubMed Abstract: 
  • Triuret (carbonyldiurea) is an impurity found in industrial urea fertilizer (<0.1% w/w) that is applied, worldwide, around 300 million pounds each year on agricultural lands. In addition to anthropogenic sources, endogenous triuret has been identifie ...

    Triuret (carbonyldiurea) is an impurity found in industrial urea fertilizer (<0.1% w/w) that is applied, worldwide, around 300 million pounds each year on agricultural lands. In addition to anthropogenic sources, endogenous triuret has been identified in amoeba and human urine, the latter being diagnostic for hypokalemia. The present study is the first to describe the metabolic breakdown of triuret, which funnels into biuret metabolism. We identified the gene responsible for triuret decomposition ( trtA ) in bacterial genomes, clustered with biuH , that encodes biuret hydrolase and has close protein sequence homology. TrtA is a member of the isochorismatase-like hydrolase protein family (IHL), similarly to BiuH, and has a catalytic efficiency (k cat /K M ) of 6 x 10 5 (M -1 s -1 ), a K M for triuret of 20 μM, and exquisite substrate specificity. Indeed, TrtA has four orders of magnitude less activity with biuret. Crystal structures of TrtA in apo and holo form were solved and compared to the BiuH structure. The high substrate selectivity was found to be conveyed by second shell residues around each active site. Mutagenesis of residues conserved in TrtA to the alternate consensus found in BiuHs revealed residues critical to triuret hydrolase activity but no single mutant evolved more biuret activity and likely a combination of mutations is required to interconvert between TrtA, BiuH functions. TrtA-mediated triuret metabolism is relatively rare in recorded genomes (1-2%), but is largely found in plant-associated, nodulating and endophytic bacteria. This study suggests functions for triuret hydrolase in certain eukaryotic intermediary processes and prokaryotic intermediary or biodegradative metabolism.


    Organizational Affiliation

    Biochemistry, Molecular Biology, & Biophysics, University of Minnesota, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Biuret hydrolaseABCD244Rhodococcus sp. MelMutation(s): 1 
Find proteins for H8ZKV9 (Rhodococcus sp. Mel)
Explore H8ZKV9 
Go to UniProtKB:  H8ZKV9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C5J
Query on C5J

Download CCD File 
A, B, C, D
dicarbonimidic diamide
C2 H5 N3 O2
OHJMTUPIZMNBFR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.29α = 90
b = 103.34β = 90
c = 133.87γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United States Department of Agriculture (USDA)United States2019-67019-29403
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5T32GM008347-28

Revision History 

  • Version 1.0: 2020-11-18
    Type: Initial release