+Open data
-Basic information
Entry | Database: PDB / ID: 6d97 | |||||||||
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Title | Structure of aldehyde dehydrogenase 12 (ALDH12) from Zea mays | |||||||||
Components | Aldehyde dehydrogenase 12 | |||||||||
Keywords | OXIDOREDUCTASE / ALDH12 / ROSSMANN FOLD / L-glutamate-gamma-semialdehyde dehydrogenase | |||||||||
Function / homology | Function and homology information cellular response to chemical stimulus / L-glutamate gamma-semialdehyde dehydrogenase / 1-pyrroline-5-carboxylate dehydrogenase activity / aldehyde dehydrogenase (NAD+) activity Similarity search - Function | |||||||||
Biological species | Zea mays (maize) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Tanner, J.J. / Korasick, D.A. / Kopecny, D. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J Mol Biol / Year: 2019 Title: Structural and Biochemical Characterization of Aldehyde Dehydrogenase 12, the Last Enzyme of Proline Catabolism in Plants. Authors: David A Korasick / Radka Končitíková / Martina Kopečná / Eva Hájková / Armelle Vigouroux / Solange Moréra / Donald F Becker / Marek Šebela / John J Tanner / David Kopečný / Abstract: Heterokonts, Alveolata protists, green algae from Charophyta and Chlorophyta divisions, and all Embryophyta plants possess an aldehyde dehydrogenase (ALDH) gene named ALDH12. Here, we provide a ...Heterokonts, Alveolata protists, green algae from Charophyta and Chlorophyta divisions, and all Embryophyta plants possess an aldehyde dehydrogenase (ALDH) gene named ALDH12. Here, we provide a biochemical characterization of two ALDH12 family members from the lower plant Physcomitrella patens and higher plant Zea mays. We show that ALDH12 encodes an NAD-dependent glutamate γ-semialdehyde dehydrogenase (GSALDH), which irreversibly converts glutamate γ-semialdehyde (GSAL), a mitochondrial intermediate of the proline and arginine catabolism, to glutamate. Sedimentation equilibrium and small-angle X-ray scattering analyses reveal that in solution both plant GSALDHs exist as equilibrium between a domain-swapped dimer and the dimer-of-dimers tetramer. Plant GSALDHs share very low-sequence identity with bacterial, fungal, and animal GSALDHs (classified as ALDH4), which are the closest related ALDH superfamily members. Nevertheless, the crystal structure of ZmALDH12 at 2.2-Å resolution shows that nearly all key residues involved in the recognition of GSAL are identical to those in ALDH4, indicating a close functional relationship with ALDH4. Phylogenetic analysis suggests that the transition from ALDH4 to ALDH12 occurred during the evolution of the endosymbiotic plant ancestor, prior to the evolution of green algae and land plants. Finally, ALDH12 expression in maize and moss is downregulated in response to salt and drought stresses, possibly to maintain proline levels. Taken together, these results provide molecular insight into the biological roles of the plant ALDH12 family. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d97.cif.gz | 804.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d97.ent.gz | 667.4 KB | Display | PDB format |
PDBx/mmJSON format | 6d97.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6d97_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6d97_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6d97_validation.xml.gz | 74.5 KB | Display | |
Data in CIF | 6d97_validation.cif.gz | 103 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/6d97 ftp://data.pdbj.org/pub/pdb/validation_reports/d9/6d97 | HTTPS FTP |
-Related structure data
Related structure data | 4mpyS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 60466.184 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Gene: ALDH12 / Production host: Escherichia coli (E. coli) References: UniProt: A0A2H4PMI3, L-glutamate gamma-semialdehyde dehydrogenase #2: Chemical | ChemComp-NAD / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.06 % |
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Crystal grow | Temperature: 293 K / Method: batch mode Details: 50% v/v of a precipitant mixture containing 25% v/v 2-methyl-2,4-pentanediol, 25% w/v polyethylene glycol 1000, and 25% w/v polyethylene glycol 3350; and 0.1 M Tris/bicine pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Nov 3, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→61.87 Å / Num. obs: 98196 / % possible obs: 99.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 32.5 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.057 / Rrim(I) all: 0.109 / Net I/σ(I): 11.6 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MPY Resolution: 2.2→46.68 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.19
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.78 Å2 / Biso mean: 36.7229 Å2 / Biso min: 15.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→46.68 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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