6JPK

Crystal structure of S. pombe aspartate aminotransferase

Summary for 6JPK

• Entry DOI: 10.2210/pdb6jpk/pdb
• Descriptor: Aspartate aminotransferase, cytoplasmic, PHOSPHATE ION, GLYCEROL, ... (4 entities in total)
• Functional Keywords: amino acid, aspartate, aminotransferase, plp-dependent enzyme, pyridoxal 5'-phosphate dependent enzyme, vitamin b6 dependent enzyme, transferase
• Biological source: Schizosaccharomyces pombe 972h- (Fission yeast)
• Total number of polymer chains: 2
• Total formula weight: 94936.93

Authors

Jin, H.,Chang, J.H. (deposition date: 2019-03-27, release date: 2019-09-11, Last modification date: 2023-11-22)

Primary citation

Jeong, S.Y.,Jin, H.,Chang, J.H.
Crystal structure of L-aspartate aminotransferase from Schizosaccharomyces pombe.
Plos One, 14:e0221975-e0221975, 2019

PubMed Abstract: L-aspartate aminotransferase is a pyridoxal 5'-phosphate-dependent transaminase that catalyzes reversible transfer of an α-amino group from aspartate to α-ketoglutarate or from glutamate to oxaloacetate. L-aspartate aminotransferase not only mediates amino acid and carbohydrate metabolism but also regulates the cellular level of amino acids by catalyzing amino acid degradation and biosynthesis. To expand our structural information, we determined the crystal structure of L-aspartate aminotransferase from Schizosaccharomyces pombe at 2.1 Å resolution. A structural comparison between two yeast L-aspartate aminotransferases revealed conserved enzymatic mechanism mediated by the open-closed conformational change. Compared with higher eukaryotic species, L-aspartate aminotransferases showed distinguishable inter-subunit interaction between the N-terminal arm and a large domain of the opposite subunit. Interestingly, structural homology search showed varied conformation of the N-terminal arm among 71 structures of the family. Therefore, we classified pyridoxal 5'-phosphate-dependent enzymes into eight subclasses based on the structural feature of N-terminal arms. In addition, structure and sequence comparisons showed strong relationships among the eight subclasses. Our results may provide insights into structure-based evolutionary aspects of pyridoxal 5'-phosphate-dependent enzymes.

PubMed: 31465495
DOI: 10.1371/journal.pone.0221975

Experimental method

X-RAY DIFFRACTION (2.102 Å)