1QJ5

Crystal structure of 7,8-diaminopelargonic acid synthase

Summary for 1QJ5

• Entry DOI: 10.2210/pdb1qj5/pdb
• Related: 1QI3
• Descriptor: 7,8-DIAMINOPELARGONIC ACID SYNTHASE, POTASSIUM ION, PYRIDOXAL-5'-PHOSPHATE, ... (4 entities in total)
• Functional Keywords: aminotransferase, pyridoxal-5'-phosphate, biotin biosynthesis
• Biological source: ESCHERICHIA COLI BL21(DE3)
• Total number of polymer chains: 2
• Total formula weight: 95193.26

Authors

Kack, H.,Sandmark, J.,Gibson, K.J.,Lindqvist, Y.,Schneider, G. (deposition date: 1999-06-21, release date: 2000-06-22, Last modification date: 2025-04-09)

Primary citation

Kack, H.,Sandmark, J.,Gibson, K.J.,Schneider, G.,Lindqvist, Y.
Crystal Structure of Diaminopelargonic Acid Synthase; Evolutionary Relationships between Pyridoxal-5'-Phosphate Dependent Enzymes
J.Mol.Biol., 291:857-, 1999

PubMed Abstract: The three-dimensional structure of diaminopelargonic acid synthase, a vitamin B6-dependent enzyme in the pathway of the biosynthesis of biotin, has been determined to 1.8 A resolution by X-ray crystallography. The structure was solved by multi-wavelength anomalous diffraction techniques using a crystal derivatized with mercury ions. The protein model has been refined to a crystallographic R -value of 17.5% (R -free 22.6%). Each enzyme subunit consists of two domains, a large domain (residues 50-329) containing a seven-stranded predominantly parallel beta-sheet, surrounded by alpha-helices, and a small domain comprising residues 1-49 and 330-429. Two subunits, related by a non-crystallographic dyad in the crystals, form the homodimeric molecule, which contains two equal active sites. Pyridoxal-5'-phosphate is bound in a cleft formed by both domains of one subunit and the large domain of the second subunit. The cofactor is anchored to the enzyme by a covalent linkage to the side-chain of the invariant residue Lys274. The phosphate group interacts with main-chain nitrogen atoms and the side-chain of Ser113, located at the N terminus of an alpha-helix. The pyridine nitrogen forms a hydrogen bond to the side-chain of the invariant residue Asp245. Electron density corresponding to a metal ion, most likely Na(+), was found in a tight turn at the surface of the enzyme. Structure analysis reveals that diaminopelargonic acid synthase belongs to the family of vitamin B6-dependent aminotransferases with the same fold as originally observed in aspartate aminotransferase. A multiple structure alignment of enzymes in this family indicated that they form at least six different subclasses. Striking differences in the fold of the N-terminal part of the polypeptide chain are one of the hallmarks of these subclasses. Diaminopelargonic acid synthase is a member of the aminotransferase subclass III. From the structure of the non-productive complex of the holoenzyme with the substrate 7-keto-8-aminopelargonic acid the location of the active site and residues involved in substrate binding have been identified.

PubMed: 10452893
DOI: 10.1006/JMBI.1999.2997

Experimental method

X-RAY DIFFRACTION (1.8 Å)