8IXM

Pseudomoans Aerugiona Wildtype Ketopantoate Reductase ternary complex with NADP+ and alpha-Ketoisocaproic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Implication of Molecular Constraints Facilitating the Functional Evolution of Pseudomonas aeruginosa KPR2 into a Versatile alpha-Keto-Acid Reductase.

Basu Choudhury, G.Datta, S.

(2024) Biochemistry 63: 1808-1823

  • DOI: https://doi.org/10.1021/acs.biochem.4c00087
  • Primary Citation of Related Structures:  
    8IWG, 8IWQ, 8IX9, 8IXH, 8IXM

  • PubMed Abstract: 

    Theoretical concepts linking the structure, function, and evolution of a protein, while often intuitive, necessitate validation through investigations in real-world systems. Our study empirically explores the evolutionary implications of multiple gene copies in an organism by shedding light on the structure-function modulations observed in Pseudomonas aeruginosa 's second copy of ketopantoate reductase (PaKPR2). We demonstrated with two apo structures that the typical active site cleft of the protein transforms into a two-sided pocket where a molecular gate made up of two residues controls the substrate entry site, resulting in its inactivity toward the natural substrate ketopantoate. Strikingly, this structural modification made the protein active against several important α-keto-acid substrates with varied efficiency. Structural constraints at the binding site for this altered functional trait were analyzed with two binary complexes that show the conserved residue microenvironment faces restricted movements due to domain closure. Finally, its mechanistic highlights gathered from a ternary complex structure help in delineating the molecular perspectives behind its kinetic cooperativity toward these broad range of substrates. Detailed structural characteristics of the protein presented here also identified four key amino acid residues responsible for its versatile α-keto-acid reductase activity, which can be further modified to improve its functional properties through protein engineering.


  • Organizational Affiliation

    CSIR-Indian Institute of Chemical Biology, Raja S C Mullick Road, Jadavpur, Kolkata 700032, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-dehydropantoate 2-reductase
A, B
315Pseudomonas aeruginosaMutation(s): 0 
Gene Names: K3T18_18035
EC: 1.1.1.169
UniProt
Find proteins for Q9I2Y5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I2Y5 
Go to UniProtKB:  Q9I2Y5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I2Y5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
NHE
Query on NHE

Download Ideal Coordinates CCD File 
D [auth A]2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
COI (Subject of Investigation/LOI)
Query on COI

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B]
2-OXO-4-METHYLPENTANOIC ACID
C6 H10 O3
BKAJNAXTPSGJCU-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.587α = 90
b = 46.769β = 98.11
c = 95.775γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Council of Scientific & Industrial Research (CSIR)India--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-03
    Type: Initial release
  • Version 1.1: 2024-07-17
    Changes: Database references
  • Version 1.2: 2024-07-31
    Changes: Database references