3FDD
The Crystal Structure of the Pseudomonas dacunhae Aspartate-Beta-Decarboxylase Reveals a Novel Oligomeric Assembly for a Pyridoxal-5-Phosphate Dependent Enzyme
Summary for 3FDD
| Entry DOI | 10.2210/pdb3fdd/pdb |
| Descriptor | L-aspartate-beta-decarboxylase, PYRIDOXAL-5'-PHOSPHATE, ACETATE ION, ... (5 entities in total) |
| Functional Keywords | l-aspartate-beta-decarboxylase, aspartate 4-decarboxylase, l-aspartate 4-carboxy-lyase, pyridoxal-5'-phosphate, plp, aspd, dodecamer, abdc, lyase |
| Biological source | Pseudomonas dacunhae ATCC 21192 |
| Total number of polymer chains | 1 |
| Total formula weight | 59923.31 |
| Authors | Lima, S.,Sundararaju, B.,Huang, C.,Khristoforov, R.,Momany, C.,Phillips, R.S. (deposition date: 2008-11-25, release date: 2009-03-17, Last modification date: 2023-12-27) |
| Primary citation | Lima, S.,Sundararaju, B.,Huang, C.,Khristoforov, R.,Momany, C.,Phillips, R.S. The crystal structure of the Pseudomonas dacunhae aspartate-beta-decarboxylase dodecamer reveals an unknown oligomeric assembly for a pyridoxal-5'-phosphate-dependent enzyme. J.Mol.Biol., 388:98-108, 2009 Cited by PubMed Abstract: The Pseudomonas dacunhael-aspartate-beta-decarboxylase (ABDC, aspartate 4-decarboxylase, aspartate 4-carboxylyase, E.C. 4.1.1.12) is a pyridoxal-5'-phosphate (PLP)-dependent enzyme that catalyzes the beta-decarboxylation of l-aspartate to produce l-alanine and CO(2). This catalytically versatile enzyme is known to form functional dodecamers at its optimal pH and is thought to work in conjunction with an l-Asp/l-Ala antiporter to establish a proton gradient across the membrane that can be used for ATP biosynthesis. We have solved the atomic structure of ABDC to 2.35 A resolution using single-wavelength anomalous dispersion phasing. The structure reveals that ABDC oligomerizes as a homododecamer in an unknown mode among PLP-dependent enzymes and has highest structural homology with members of the PLP-dependent aspartate aminotransferase subfamily. The structure shows that the ABDC active site is very similar to that of aspartate aminotransferase. However, an additional arginine side chain (Arg37) was observed flanking the re-side of the PLP ring in the ABDC active site. The mutagenesis results show that although Arg37 is not required for activity, it appears to be involved in the ABDC catalytic cycle. PubMed: 19265705DOI: 10.1016/j.jmb.2009.02.055 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.35 Å) |
Structure validation
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