2YYY

Crystal structure of Glyceraldehyde-3-phosphate dehydrogenase

Summary for 2YYY

• Entry DOI: 10.2210/pdb2yyy/pdb
• Descriptor: Glyceraldehyde-3-phosphate dehydrogenase, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (3 entities in total)
• Functional Keywords: glyceraldehyde 3-phosphate binding, alpha and beta proteins (a/b) class, mj1146, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi, oxidoreductase
• Biological source: Methanocaldococcus jannaschii
• Cellular location: Cytoplasm (By similarity): Q58546
• Total number of polymer chains: 2
• Total formula weight: 77786.47

Authors

Malay, A.D.,Bessho, Y.,Padmanabhan, B.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2007-05-02, release date: 2007-11-06, Last modification date: 2023-10-25)

Primary citation

Malay, A.D.,Bessho, Y.,Ellis, M.J.,Antonyuk, S.V.,Strange, R.W.,Hasnain, S.S.,Shinkai, A.,Padmanabhan, B.,Yokoyama, S.
Structure of glyceraldehyde-3-phosphate dehydrogenase from the archaeal hyperthermophile Methanocaldococcus jannaschii.
Acta Crystallogr.,Sect.F, 65:1227-1233, 2009

PubMed Abstract: The X-ray crystal structure of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the hyperthermophilic archaeon Methanocaldococcus jannaschii (Mj-GAPDH) was determined to 1.81 A resolution. The crystal belonged to space group C222(1), with unit-cell parameters a = 83.4, b = 152.0, c = 118.6 A. The structure was solved by molecular replacement and was refined to a final R factor of 17.1% (R(free) = 19.8%). The final structure included the cofactor NADP(+) at the nucleotide-binding site and featured unoccupied inorganic and substrate phosphate-binding sites. A comparison with GAPDH structures from mesophilic sources suggested that Mj-GAPDH is stabilized by extensive electrostatic interactions between the C-terminal alpha-helices and various distal loop regions, which are likely to contribute to thermal stability. The key phosphate-binding residues in the active site of Mj-GAPDH are conserved in other archaeal GAPDH proteins. These residues undergo a conformational shift in response to occupancy of the inorganic phosphate site.

PubMed: 20054117
DOI: 10.1107/S1744309109047046

Experimental method

X-RAY DIFFRACTION (1.85 Å)