| Literature DB >> 33325526 |
Kaleena Zhang1, Josephine S Lee1, Regina Liu1, Zita T Chan1, Trenton J Dawson1, Elisa S De Togni1, Chris T Edwards1, Isabel K Eng1, Ashley R Gao1, Luis A Goicouria1, Erin M Hall1, Kelly A Hu1, Katherine Huang1, Alexander Kizhner1, Kelsie C Kodama1, Andrew Z Lin1, Jennifer Y Liu1, Alan Y Lu1, Owen W Peng1, Erica P Ryu1, Sophia Shi1, Maria L Sorkin1, Patricia L Walker1, Grace J Wang1, Mark C Xu1, Rebecca S Yang1, Barrie Cascella1, Wilhelm Cruz1, Cynthia K Holland1,2, Sheri A McClerkin1,3, Barbara N Kunkel1, Soon Goo Lee1,4, Joseph M Jez1.
Abstract
Aldehyde dehydrogenases (ALDHs) catalyze the conversion of various aliphatic and aromatic aldehydes into corresponding carboxylic acids. Traditionally considered as housekeeping enzymes, new biochemical roles are being identified for members of ALDH family. Recent work showed that AldA from the plant pathogen Pseudomonas syringae strain PtoDC3000 (PtoDC3000) functions as an indole-3-acetaldehyde dehydrogenase for the synthesis of indole-3-acetic acid (IAA). IAA produced by AldA allows the pathogen to suppress salicylic acid-mediated defenses in the model plant Arabidopsis thaliana. Here we present a biochemical and structural analysis of the AldA indole-3-acetaldehyde dehydrogenase from PtoDC3000. Site-directed mutants targeting the catalytic residues Cys302 and Glu267 resulted in a loss of enzymatic activity. The X-ray crystal structure of the catalytically inactive AldA C302A mutant in complex with IAA and NAD+ showed the cofactor adopting a conformation that differs from the previously reported structure of AldA. These structures suggest that NAD+ undergoes a conformational change during the AldA reaction mechanism similar to that reported for human ALDH. Site-directed mutagenesis of the IAA binding site indicates that changes in the active site surface reduces AldA activity; however, substitution of Phe169 with a tryptophan altered the substrate selectivity of the mutant to prefer octanal. The present study highlights the inherent biochemical versatility of members of the ALDH enzyme superfamily in P. syringae.Entities:
Keywords: NAD; Pseudomonas syringae; aldehyde dehydrogenase; auxin; crystal structure; reaction mechanism
Mesh:
Substances:
Year: 2020 PMID: 33325526 PMCID: PMC7745063 DOI: 10.1042/BSR20202959
Source DB: PubMed Journal: Biosci Rep ISSN: 0144-8463 Impact factor: 3.840
Figure 1AldA indole-3-acetaldehyde dehydrogenase reaction and sequence comparison
(A) Proposed mechanism for IAA synthesis catalyzed by AldA. The general reaction for conversion of an aldehyde into a carboxylic acid applies to other substrates of AldA, including octanal. (B) Sequence comparison of AldA (AAO53646.1) and AldC (AAO57114.1) from P. syringae strain PtoDC3000 and human ALDH (P05091.2). Residues corresponding to the catalytic, NAD(H) binding, and substrate binding sites of AldA are highlighted in orange, blue, and red, respectively. Invariant residues are highlighted in yellow.
Summary of crystallographic data collection and refinement statistics
| Crystal | AldA (C302A)•IAA•NAD+ |
|---|---|
| Space group | C2 |
| Cell dimensions | |
| Wavelength | 0.979 Å |
| Resolution range (highest shell) | 47.9–2.85 Å (2.92–2.85 Å) |
| Reflections (total/unique) | 555535/103193 |
| Completeness (highest shell) | 98.3% (99.8%) |
| <I/σ> (highest shell) | 13.9 (5.4) |
| Rsym (highest shell) | 9.2% (24.1%) |
| Rcryst/Rfree | 21.6%/25.4% |
| Number of protein atoms | 29536 |
| Number of ligand atoms | 456 |
| R.m.s. deviation, bond lengths | 0.010 Å |
| R.m.s. deviation, bond angles | 1.18° |
| Avg. B-factor: protein, ligand | 35.9, 69.4 Å2 |
| Stereochemistry: favored, allowed, outliers | 95.8, 4.2, 0% |
Steady-state kinetic parameters of wild-type and mutant AldA proteins
| Protein | Indole-3-acetaldehyde | Octanal | ||||
|---|---|---|---|---|---|---|
| WT | 240 ± 9 | 0.18 ± 0.02 | 22,040 | 96 ± 6 | 2.7 ± 0.6 | 593 |
| G123L | 202 ± 7 | 0.26 ± 0.04 | 12,950 | 71 ±4 | 2.5 ± 0.5 | 473 |
| F169A | 88 ± 12 | 4.7 ± 0.6 | 312 | 50 ± 4 | >10 | 83 |
| F169W | 41 ± 4 | 1.6 ± 0.4 | 427 | 108 +13 | 0.69 ±0.10 | 2609 |
| M172A | 220 ± 23 | 0.92 ± 0.11 | 3986 | 92 ± 4 | 2.7 ± 2.5 | 567 |
| M173A | 184 ± 23 | 1.5 ± 0.4 | 2044 | 63 ± 9 | >10 | 105 |
| W176A | 10 ± 2 | 8.8 ± 2.5 | 19 | - | - | - |
| F296A | 18 ± 1 | 7.0 ± 2.1 | 43 | 8 | >10 | 13 |
| V301A | 81 ± 10 | 7.2 ± 0.9 | 190 | 32 ± 9 | >10 | 54 |
| D459K | 72 ± 14 | 0.86 ± 0.23 | 1395 | – | – | – |
| G461W | 160 ± 14 | 0.29 ± 0.05 | 9195 | 98 ± 5 | 4.1 ± 0.8 | 398 |
The protein and location of the mutation are indicated.
Enzyme assays were performed as described in the ‘Materials and methods’ section.
Average values ± S.D. (n=3) are shown.
Estimated Km greater than 10 mM solubility of substrate tested.
Figure 2Overall three-dimensional structure of the AldA(C302A)•NAD+•IAA complex
(A) Tetrameric assembly of the AldA C302 mutant. Each monomer is colored individually with the locations of bound NAD+ and IAA indicated. The N-terminus of each monomer is also noted. (B) Domain organization of an AldA monomer. The view is slightly rotated from that in (A). The N-terminal Rossmann-fold (blue), C-terminal α/β domain (gold), oligomerization β-sheet (rose), and domain linker (green) are indicated and labeled with ligand positions indicated.
Figure 3NAD+ isomerization in AldA
(A) NAD+ binding in the AldA C302A X-ray crystal structure. The nicotinamide half of the ligand adopts a conformation that positions the nicotinamde ring away from the catalytic site (i.e., C302A in gold), which is ideal for the hydrolysis step of the reaction. The side-chain of Glu267 (blue; in) is positioned into the active site. (B) NAD+ binding in the AldA wild-type X-ray crystal structure. As previously reported [18], the nicotinamide half of the ligand adopts a conformation that positions the nicotinamde ring into the catalytic site (i.e., C302 in gold), which is ideal for the hydride transfer step of the reaction. The side-chain of Glu267 (blue; out) is positioned away from the active site.
Figure 4AldA C302A mutant substrate binding site
(A) IAA binding in the AldA C302A mutant X-ray crystal structure. Residues in the substrate binding site are shown. Two glycine residues in the site are represented by the rose colored secondary structure. (B) Surface stereo-view of the AldA substrate binding site. The surface corresponding to Phe169 is highlighted in gold.