4MPY

1.85 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) from Staphylococcus aureus (IDP00699) in complex with NAD+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.126 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure-based mutational studies of substrate inhibition of betaine aldehyde dehydrogenase BetB from Staphylococcus aureus.

Chen, C.Joo, J.C.Brown, G.Stolnikova, E.Halavaty, A.S.Savchenko, A.Anderson, W.F.Yakunin, A.F.

(2014) Appl.Environ.Microbiol. 80: 3992-4002

  • DOI: 10.1128/AEM.00215-14
  • Primary Citation of Related Structures:  
  • Also Cited By: 5EZ4, 5EYU, 5DIB, 4ZXU

  • PubMed Abstract: 
  • Inhibition of enzyme activity by high concentrations of substrate and/or cofactor is a general phenomenon demonstrated in many enzymes, including aldehyde dehydrogenases. Here we show that the uncharacterized protein BetB (SA2613) from Staphylococcus ...

    Inhibition of enzyme activity by high concentrations of substrate and/or cofactor is a general phenomenon demonstrated in many enzymes, including aldehyde dehydrogenases. Here we show that the uncharacterized protein BetB (SA2613) from Staphylococcus aureus is a highly specific betaine aldehyde dehydrogenase, which exhibits substrate inhibition at concentrations of betaine aldehyde as low as 0.15 mM. In contrast, the aldehyde dehydrogenase YdcW from Escherichia coli, which is also active against betaine aldehyde, shows no inhibition by this substrate. Using the crystal structures of BetB and YdcW, we performed a structure-based mutational analysis of BetB and introduced the YdcW residues into the BetB active site. From a total of 32 mutations, those in five residues located in the substrate binding pocket (Val288, Ser290, His448, Tyr450, and Trp456) greatly reduced the substrate inhibition of BetB, whereas the double mutant protein H448F/Y450L demonstrated a complete loss of substrate inhibition. Substrate inhibition was also reduced by mutations of the semiconserved Gly234 (to Ser, Thr, or Ala) located in the BetB NAD(+) binding site, suggesting some cooperativity between the cofactor and substrate binding sites. Substrate docking analysis of the BetB and YdcW active sites revealed that the wild-type BetB can bind betaine aldehyde in both productive and nonproductive conformations, whereas only the productive binding mode can be modeled in the active sites of YdcW and the BetB mutant proteins with reduced substrate inhibition. Thus, our results suggest that the molecular mechanism of substrate inhibition of BetB is associated with the nonproductive binding of betaine aldehyde.


    Related Citations: 
    • Structural and functional analysis of betaine aldehyde dehydrogenase from Staphylococcus aureus
      Halavaty, A.S.,Rich, R.L.,Chen, C.,Joo, J.C.,Minasov, G.,Dubrovska, I.,Winsor, J.R.,Myszka, D.G.,Duban, M.,Shuvalova, L.,Yakunin, A.F.,Anderson, W.F.
      (2015) Acta Crystallogr.,Sect.D 71: 1159


    Organizational Affiliation

    Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Betaine aldehyde dehydrogenase
A, B, C, D, E, F, G, H
520Staphylococcus aureus (strain COL)Mutation(s): 0 
Gene Names: betB
EC: 1.2.1.8
Find proteins for A0A0H2X0S3 (Staphylococcus aureus (strain COL))
Go to UniProtKB:  A0A0H2X0S3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 99.866α = 90.00
b = 159.146β = 94.79
c = 122.993γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
REFMACrefinement
HKL-2000data scaling
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2015-04-01
    Type: Database references
  • Version 1.2: 2015-05-13
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description