PDBsum entry 4mpy

Oxidoreductase

PDB id: 4mpy

Contents

Protein chains

(+ 2 more) 500 a.a.

Ligands

NAD ×8

Metals

_NA ×19

Waters ×4722

PDB id:

4mpy

Name:

Oxidoreductase

Title:

1.85 angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betb) from staphylococcus aureus (idp00699) in complex with NAD+

Structure:

Betaine aldehyde dehydrogenase. Chain: a, b, c, d, e, f, g, h. Engineered: yes

Source:

Staphylococcus aureus subsp. Aureus. Organism_taxid: 93062. Strain: col. Gene: betb, sacol2628. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.85Å R-factor: 0.127 R-free: 0.167

Authors:

A.S.Halavaty,G.Minasov,L.Shuvalova,J.Winsor,S.N.Peterson, W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid)

Key ref:

C.Chen et al. (2014). Structure-based mutational studies of substrate inhibition of betaine aldehyde dehydrogenase BetB from Staphylococcus aureus. Appl Environ Microbiol, 80, 3992-4002. PubMed id: 24747910 DOI: 10.1128/AEM.00215-14

Date:

14-Sep-13 Release date: 09-Oct-13

Supersedes:

3fg0

Protein chains

A0A0H2X0S3  (A0A0H2X0S3_STAAC) -  Betaine-aldehyde dehydrogenase from Staphylococcus aureus (strain COL)

Seq: 496 a.a.

Struc: 500 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.2.1.8 - betaine-aldehyde dehydrogenase.
• Reaction: betaine aldehyde + NAD⁺ + H2O = glycine betaine + NADH + 2 H⁺

betaine aldehyde + NAD(+) (Bound ligand (Het Group name = NAD) corresponds exactly) + H2O = glycine betaine + NADH + 2 × H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1128/AEM.00215-14

Appl Environ Microbiol 80:3992-4002 (2014)

PubMed id: 24747910

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

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

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 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.