5VPS

Crystal structure of an SDR from Burkholderia ambifaria in complex with NADPH with a TCEP adduct


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Cautionary Tale of Using Tris(alkyl)phosphine Reducing Agents with NAD+-Dependent Enzymes.

Patel, S.M.Smith, T.G.Morton, M.Stiers, K.M.Seravalli, J.Mayclin, S.J.Edwards, T.E.Tanner, J.J.Becker, D.F.

(2020) Biochemistry 

  • DOI: https://doi.org/10.1021/acs.biochem.0c00490
  • Primary Citation of Related Structures:  
    5VPS

  • PubMed Abstract: 

    Protein biochemistry protocols typically include disulfide bond reducing agents to guard against unwanted thiol oxidation and protein aggregation. Commonly used disulfide bond reducing agents include dithiothreitol, β-mercaptoethanol, glutathione, and the tris(alkyl)phosphine compounds tris(2-carboxyethyl)phosphine (TCEP) and tris(3-hydroxypropyl)phosphine (THPP). While studying the catalytic activity of the NAD(P)H-dependent enzyme Δ 1 -pyrroline-5-carboxylate reductase, we unexpectedly observed a rapid non-enzymatic chemical reaction between NAD + and the reducing agents TCEP and THPP. The product of the reaction exhibits a maximum ultraviolet absorbance peak at 334 nm and forms with an apparent association rate constant of 231-491 M -1 s -1 . The reaction is reversible, and nuclear magnetic resonance characterization ( 1 H, 13 C, and 31 P) of the product revealed a covalent adduct between the phosphorus of the tris(alkyl)phosphine reducing agent and the C4 atom of the nicotinamide ring of NAD + . We also report a 1.45 Å resolution crystal structure of short-chain dehydrogenase/reductase with the NADP + -TCEP reaction product bound in the cofactor binding site, which shows that the adduct can potentially inhibit enzymes. These findings serve to caution researchers when using TCEP or THPP in experimental protocols with NAD(P) + . Because NAD(P) + -dependent oxidoreductases are widespread in nature, our results may be broadly relevant.


  • Organizational Affiliation

    Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Short-chain dehydrogenase/reductase SDR267Burkholderia ambifaria MC40-6Mutation(s): 0 
Gene Names: BamMC406_2208
UniProt
Find proteins for B1YU47 (Burkholderia ambifaria (strain MC40-6))
Explore B1YU47 
Go to UniProtKB:  B1YU47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1YU47
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9G1
Query on 9G1

Download Ideal Coordinates CCD File 
B [auth A][(4~{S})-3-aminocarbonyl-1-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]piperidin-4-yl]-tris(3-hydroxy-3-oxopropyl)phosphanium
C30 H48 N7 O23 P4
KCEMQRAWVXDPSM-NLJDEQFRSA-O
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.09α = 90
b = 64.09β = 90
c = 119.17γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
Cootmodel building
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2020-09-09
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description