Crystal Structure and Functional Analysis of Glyceraldehyde-3-phosphate
Dehydrogenase from Oryza Sativa
Yueh-Chu Tien (田岳衢)1,2, Yi-Hung Lin (林易弘)2, Shou-Lin Chang (張壽麟)1,
and Chun-Jung Chen (陳俊榮)2
1
Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
2
National Synchrotron Radiation Research Center, Hsinchu, Taiwan
Cytoplasmic Oryza sativa GAPDH (OsGAPDH)is an enzyme belong to GAPDH family (E.C.
1.2.1.12) and essential in glycolysis pathway. This enzyme catalyzes phosphorylation of
glyceraldhyde-3-phosphate (G3P) to 1,3-biphosphoglycerate (BPG) only using the cofator NAD+ to
accept electrons from substrates. Another kind GAPDH belong to subfamily (E.C. 1.2.1.13) which
could use both NAD+ and NADP+ as cofactor transferring BPG to G3P. The OsGAPDH protein
structure is determeined by X-ray diffraction method. Three crystallizational conditons perform three
structures: NAD-free, NAD-bound and sulfate-soaked. Similar to the published GAPDH structure,
OsGAPDH shows homotetramer form and each subunit could be seperated to three domains:
NAD-binding domain, catalytic domain and S-loop domain. NAD+ bind to OsGAPDH by hydrogen
bonds directly and intermediated by water. Some residues form positive grooves to attract sulfate
molecules which are used to simulate phosphate groups of BPG. Some other features found in these
structures have not been reproted before. Phe37 is found forming a bottleneck which may improve
NAD+ binding, but this assumption should be proved advancely. Phe37 is also involved in
NAD-specific feature, together with Pro193 and Asp35 which have been reported as key residues in
NAD-specific feature.Align amino acid sequence with other organisms, reveal that Phe37 only exists
in higher organism, but lacks in lower organisms. In contrast, Pro193 and Asp35 exist in each
GAPDH belong to E.C.1.2.1.12. This phenomenon may be caused by evalution and results in
different biochemical performance between different organisms.