6GHW | pdb_00006ghw

Substituting the prolines of 4-oxalocrotonate tautomerase with non-canonical analogue (2S)-3,4-dehydroproline

• PDB DOI: https://doi.org/10.2210/pdb6GHW/pdb

• Classification: ISOMERASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-05-09 Released: 2019-03-06 
• Deposition Author(s): Pavkov-Keller, T., Lukesch, M.S., Wiltschi, B., Gruber, K.
• Funding Organization(s): Austrian Science Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.320 (Depositor), 0.321 (DCC) 
• R-Value Work: 
  0.288 (Depositor), 0.289 (DCC) 
• R-Value Observed: 
  0.290 (Depositor) 

Starting Model: experimental

Literature

Substituting the catalytic proline of 4-oxalocrotonate tautomerase with non-canonical analogues reveals a finely tuned catalytic system.

Lukesch, M.S., Pavkov-Keller, T., Gruber, K., Zangger, K., Wiltschi, B.

(2019) Sci Rep 9: 2697-2697

• PubMed: 30804446 
• DOI: https://doi.org/10.1038/s41598-019-39484-9
• Primary Citation Related Structures: 
  6GHW


• PubMed Abstract: 
  

  The enzyme 4-oxalocrotonate tautomerase shows remarkable catalytic versatility due to the secondary amine of its N-terminal proline moiety. In this work, we incorporated a range of proline analogues into the enzyme and examined the effects on structure and activity. While the structure of the enzyme remained unperturbed, its promiscuous Michael-type activity was severely affected. This finding demonstrates how atomic changes in a biocatalytic system can abolish its activity. Our work provides a toolbox for successful generation of enzyme variants with non-canonical catalytic proline analogues.

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Organizational Affiliation: 
• Graz University of Technology, Institute of Molecular Biotechnology, Petersgasse 14, 8010, Graz, Austria.
Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50, 8010, Graz, Austria.
Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria.
Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria.
Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010, Graz, Austria. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 20.49 kDa 
• Atom Count: 1,368 
• Modeled Residue Count: 171 
• Deposited Residue Count: 186 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-hydroxymuconate tautomerase	A, B, C	62	Pseudomonas putida	Mutation(s): 0  Gene Names: xylH EC: 5.3.2.6
UniProt
Find proteins for Q01468 (Pseudomonas putida) Explore Q01468  Go to UniProtKB:  Q01468

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	D [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
8LJ	A, B, C	L-PEPTIDE LINKING	C5 H7 N O2		PRO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.320 (Depositor), 0.321 (DCC) 
• R-Value Work:  0.288 (Depositor), 0.289 (DCC) 
• R-Value Observed: 0.290 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.296	α = 90
b = 85.296	β = 90
c = 155.463	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-03-06 
Deposition Author(s): Pavkov-Keller, T., Lukesch, M.S., Wiltschi, B., Gruber, K.

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Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	901

Revision History  

• Version 1.0: 2019-03-06
  Type: Initial release
  
• Version 1.1: 2019-04-24
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description