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TitleStructures of Proline Utilization A (PutA) Reveal the Fold and Functions of the Aldehyde Dehydrogenase Superfamily Domain of Unknown Function.
Journal, issue, pagesJ Biol Chem, Vol. 291, Issue 46, Page 24065-24075, Year 2016
Publish dateNov 11, 2016
AuthorsMin Luo / Thameesha T Gamage / Benjamin W Arentson / Katherine N Schlasner / Donald F Becker / John J Tanner /
PubMed AbstractAldehyde dehydrogenases (ALDHs) catalyze the NAD(P)-dependent oxidation of aldehydes to carboxylic acids and are important for metabolism and detoxification. Although the ALDH superfamily fold is ...Aldehyde dehydrogenases (ALDHs) catalyze the NAD(P)-dependent oxidation of aldehydes to carboxylic acids and are important for metabolism and detoxification. Although the ALDH superfamily fold is well established, some ALDHs contain an uncharacterized domain of unknown function (DUF) near the C terminus of the polypeptide chain. Herein, we report the first structure of a protein containing the ALDH superfamily DUF. Proline utilization A from Sinorhizobium meliloti (SmPutA) is a 1233-residue bifunctional enzyme that contains the DUF in addition to proline dehydrogenase and l-glutamate-γ-semialdehyde dehydrogenase catalytic modules. Structures of SmPutA with a proline analog bound to the proline dehydrogenase site and NAD bound to the ALDH site were determined in two space groups at 1.7-1.9 Å resolution. The DUF consists of a Rossmann dinucleotide-binding fold fused to a three-stranded β-flap. The Rossmann domain resembles the classic ALDH superfamily NAD-binding domain, whereas the flap is strikingly similar to the ALDH superfamily dimerization domain. Paradoxically, neither structural element performs its implied function. Electron density maps show that NAD does not bind to the DUF Rossmann fold, and small-angle X-ray scattering reveals a novel dimer that has never been seen in the ALDH superfamily. The structure suggests that the DUF is an adapter domain that stabilizes the aldehyde substrate binding loop and seals the substrate-channeling tunnel via tertiary structural interactions that mimic the quaternary structural interactions found in non-DUF PutAs. Kinetic data for SmPutA indicate a substrate-channeling mechanism, in agreement with previous studies of other PutAs.
External linksJ Biol Chem / PubMed:27679491 / PubMed Central
MethodsSAS (X-ray synchrotron) / X-ray diffraction
Resolution1.7 - 1.9 Å
Structure data

SASDDL2:
Sinorhizobium meliloti Proline Utilization A (PutA) lowest concentration, 1.00 mg/ml
Method: SAXS/SANS

SASDDM2:
Sinorhizobium meliloti Proline Utilization A (PutA) at 2.00 mg/ml
Method: SAXS/SANS

SASDDN2:
Sinorhizobium meliloti Proline Utilization A (PutA) at 3.00 mg/ml
Method: SAXS/SANS

SASDDP2:
Sinorhizobium meliloti Proline Utilization A (PutA) at high concentration, 4.00 mg/ml
Method: SAXS/SANS

PDB-5kf6:
Structure of proline utilization A from Sinorhizobium meliloti complexed with L-tetrahydrofuroic acid and NAD+ in space group P21
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-5kf7:
Structure of proline utilization A from Sinorhizobium meliloti complexed with L-tetrahydrofuroic acid and NAD+ in space group P3121
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

Chemicals

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

ChemComp-TFB:
TETRAHYDROFURAN-2-CARBOXYLIC ACID

ChemComp-MG:
Unknown entry

ChemComp-PGE:
TRIETHYLENE GLYCOL

ChemComp-PG4:
TETRAETHYLENE GLYCOL / precipitant*YM

ChemComp-HOH:
WATER

ChemComp-1PE:
PENTAETHYLENE GLYCOL / precipitant*YM

ChemComp-SO4:
SULFATE ION

Source
  • Sinorhizobium meliloti (bacteria)
  • sinorhizobium meliloti (strain sm11) (bacteria)
KeywordsOXIDOREDUCTASE / FLAVOENZYME / ROSSMANN FOLD / ALDEHYDE DEHYDROGENASE / PROLINE CATABOLISM / SUBSTRATE CHANNELING / BIFUNCTIONAL ENZYME

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