Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Biophysical investigation of type A PutAs reveals a conserved core oligomeric structure.
Journal, issue, pages	FEBS J, Vol. 284, Issue 18, Page 3029-3049, Year 2017
Publish date	Aug 1, 2017
Authors	David A Korasick / Harkewal Singh / Travis A Pemberton / Min Luo / Richa Dhatwalia / John J Tanner /
PubMed Abstract	Many enzymes form homooligomers, yet the functional significance of self-association is seldom obvious. Herein, we examine the connection between oligomerization and catalytic function for proline ...Many enzymes form homooligomers, yet the functional significance of self-association is seldom obvious. Herein, we examine the connection between oligomerization and catalytic function for proline utilization A (PutA) enzymes. PutAs are bifunctional enzymes that catalyze both reactions of proline catabolism. Type A PutAs are the smallest members of the family, possessing a minimal domain architecture consisting of N-terminal proline dehydrogenase and C-terminal l-glutamate-γ-semialdehyde dehydrogenase modules. Type A PutAs form domain-swapped dimers, and in one case (Bradyrhizobium japonicum PutA), two of the dimers assemble into a ring-shaped tetramer. Whereas the dimer has a clear role in substrate channeling, the functional significance of the tetramer is unknown. To address this question, we performed structural studies of four-type A PutAs from two clades of the PutA tree. The crystal structure of Bdellovibrio bacteriovorus PutA covalently inactivated by N-propargylglycine revealed a fold and substrate-channeling tunnel similar to other PutAs. Small-angle X-ray scattering (SAXS) and analytical ultracentrifugation indicated that Bdellovibrio PutA is dimeric in solution, in contrast to the prediction from crystal packing of a stable tetrameric assembly. SAXS studies of two other type A PutAs from separate clades also suggested that the dimer predominates in solution. To assess whether the tetramer of B. japonicum PutA is necessary for catalytic function, a hot spot disruption mutant that cleanly produces dimeric protein was generated. The dimeric variant exhibited kinetic parameters similar to the wild-type enzyme. These results implicate the domain-swapped dimer as the core structural and functional unit of type A PutAs. ENZYMES: Proline dehydrogenase (EC 1.5.5.2); l-glutamate-γ-semialdehyde dehydrogenase (EC 1.2.1.88). DATABASES: The atomic coordinates and structure factor amplitudes have been deposited in the Protein Data Bank under accession number 5UR2. The SAXS data have been deposited in the SASBDB under the following accession codes: SASDCP3 (BbPutA), SASDCQ3 (DvPutA 1.5 mg·mL ), SASDCX3 (DvPutA 3.0 mg·mL ), SASDCY3 (DvPutA 4.5 mg·mL ), SASDCR3 (LpPutA 3.0 mg·mL ), SASDCV3 (LpPutA 5.0 mg·mL ), SASDCW3 (LpPutA 8.0 mg·mL ), SASDCS3 (BjPutA 2.3 mg·mL ), SASDCT3 (BjPutA 4.7 mg·mL ), SASDCU3 (BjPutA 7.0 mg·mL ), SASDCZ3 (R51E 2.3 mg·mL ), SASDC24 (R51E 4.7 mg·mL ), SASDC34 (R51E 7.0 mg·mL ).
External links	FEBS J / PubMed:28710792 / PubMed Central
Methods	SAS (X-ray synchrotron) / X-ray diffraction
Resolution	2.23 Å
Structure data	SASDC24: Proline utilization A from Bradyrhizobium diazoefficiens (formerly Bradyrhizobium japonicum) R51E mutant 4.7 mg/mL Method: SAXS/SANS SASDC34: Proline utilization A from Bradyrhizobium diazoefficiens (formerly Bradyrhizobium japonicum) R51E mutant 7.0 mg/mL Method: SAXS/SANS SASDCP3: Proline utilization A from Bdellovibrio bacteriovorus Method: SAXS/SANS SASDCQ3: Proline utilization A from Desulfovibrio vulgaris 1.5 mg/mL Method: SAXS/SANS SASDCR3: Proline utilization A from Legionella pneumophila 3 mg/mL Method: SAXS/SANS SASDCS3: Proline utilization A from Bradyrhizobium diazoefficiens (formerly Bradyrhizobium japonicum) 2.3 mg/mL Method: SAXS/SANS SASDCT3: Proline utilization A from Bradyrhizobium diazoefficiens (formerly Bradyrhizobium japonicum) 4.7 mg/mL Method: SAXS/SANS SASDCU3: Proline utilization A from Bradyrhizobium diazoefficiens (formerly Bradyrhizobium japonicum) 7.0 mg/mL Method: SAXS/SANS SASDCV3: Proline utilization A from Legionella pneumophila 5 mg/mL Method: SAXS/SANS SASDCW3: Proline utilization A from Legionella pneumophila 8 mg/mL Method: SAXS/SANS SASDCX3: Proline utilization A from Desulfovibrio vulgaris 3.0 mg/mL Method: SAXS/SANS SASDCY3: Proline utilization A from Desulfovibrio vulgaris 4.5 mg/mL Method: SAXS/SANS SASDCZ3: Proline utilization A from Bradyrhizobium diazoefficiens (formerly Bradyrhizobium japonicum) R51E mutant 2.3 mg/mL Method: SAXS/SANS PDB-5ur2: Crystal structure of proline utilization A (PutA) from Bdellovibrio bacteriovorus inactivated by N-propargylglycine Method: X-RAY DIFFRACTION / Resolution: 2.23 Å
Chemicals	ChemComp-P5F: N-propargylglycine-modified flavin adenine dinucleotide ChemComp-HOH: WATER
Source	Bradyrhizobium diazoefficiens (strain jcm 10833 / iam 13628 / nbrc 14792 / usda 110) (bacteria) bdellovibrio bacteriovorus (strain atcc 15356 / dsm 50701 / ncib 9529 / hd100) (bacteria) Desulfovibrio vulgaris (strain rch1) (bacteria) Legionella pneumophila subsp. pneumophila (strain philadelphia 1 / atcc 33152 / dsm 7513) (bacteria)
Keywords	OXIDOREDUCTASE / FLAVOENZYME / ROSSMANN FOLD / ALDEHYDE DEHYDROGENASE / FLAVIN ADENINE DINUCLEOTIDE / NICOTINAMIDE ADENINE DINUCLEOTIDE / PROLINE CATABOLISM / SUBSTRATE CHANNELING / BIFUNCTIONAL ENZYME / MECHANISM-BASED INACTIVATION