Motion in Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH) [gapdh]

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Classification Known Domain Motion, Shear Mechanism [D-s-2]

Structures
1GD1 Conformation 1 [ PartsList ]
2GD1 Conformation 2 [ PartsList ]

Description
Shear motion with XBAaba layering. GAPDH has 3 moving layers in one domain that shift relative to 3 rigid layers in the other domain. This distinctive layering pattern is of the form XBAabx, where abx are the 3 moving layers and XBA the rigid layers. The interface between the two middle layers is where the major shear motion occurs. One layer of helices from the mobile domain (a) slides over a layer of helices from the motionless domain (A). Helices in these two layers, which in a sense form gears upon which the domains slide, are often 'crossed'. Near to the a and A layer helices, the ligand binds in the interdomain cleft . Packed onto either side of the central layers of helices (a and A) are sheets (b and B) from the mobile and motionless domains, respectively. The mobile sheet (b) forms a second moving layer, which slides over the helices, and packed onto the other face of this sheet is a third layer (x) which moves with the sheet. Symmetrical to this third moving layer (x), a third motionless layer (X) is packed onto one side of the static sheet (B). In GAPDH layer x is made up of helices and layer X is a sheet from another subunit.

Particular values describing motion
Experimental Methods = x (Traditional x-ray)
Creation Date = 19970822
Modification Date = 19970822

References
T Skarzynski and A J Wonacott (1988). Coenzyme-induced Conformational Changes in Glyceraldehyde-3-phosphate Dehydrogenase from Bacillus stearothermophilus. J. Mol. Biol. 203: 1097-1118. [Medline info for 94157912]

Data and Graphics
Graphic-2 XABbax layering pattern (GAPDH on left) (copyright Biochemistry, 1994).
Graphic-1 The incremental quality of the overall motion.

GO terms associated with structures
Molecular functionglyceraldehyde-3-phosphate dehydrogenase activity, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) activity, NAD binding
Cellular componentcytoplasm
Biological processglycolysis, glucose metabolism

Morphs

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Best representative
Morph Morph name Structure #1 Structure #2 Residues
Glyceraldehyde 5-phosphate dehydrogenase 1gd1 [ O ] 2gd1 [ O ] 334

User-submitted morphs
Morph Morph name Structure #1 Structure #2 Residues
995224-29676 gapdh 1gd1 [ O ] 2gd1 [ O ] 334


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Copyright 1995-2005 M. Gerstein, W. Krebs, S. Flores, N. Echols, and others
Email: Mark.Gerstein _at_ yale.edu