1VAH

Crystal structure of the pig pancreatic-amylase complexed with r-nitrophenyl-a-D-maltoside

Summary for 1VAH

• Entry DOI: 10.2210/pdb1vah/pdb
• Related: 1JFH 1UA3
• Descriptor: Alpha-amylase, pancreatic, CHLORIDE ION, CALCIUM ION, ... (5 entities in total)
• Functional Keywords: beta-alpha-barrels, hydrolase
• Biological source: Sus scrofa (pig)
• Cellular location: Secreted, extracellular space: P00690
• Total number of polymer chains: 1
• Total formula weight: 55689.48

Authors

Zhuo, H.,Payan, F.,Qian, M. (deposition date: 2004-02-17, release date: 2005-04-26, Last modification date: 2024-11-20)

Primary citation

Zhuo, H.,Payan, F.,Qian, M.
Crystal structure of the pig pancreatic alpha-amylase complexed with rho-nitrophenyl-alpha-D-maltoside-flexibility in the active site
Protein J., 23:379-387, 2004

PubMed Abstract: The X-ray structure analysis of a crystal of pig pancreatic alpha-amylase soaked with a rho-nitrophenyl-alpha-D-maltoside (pNPG2) substrate showed a pattern of electron density corresponding to the binding of a rho-nitrophenol unit at subsite -2 of the active site. Binding of the product to subsite -2 after hydrolysis of the pNPG2 molecules, may explain the low catalytic efficiency of the hydrolysis of pNPG2 by PPA. Except a small movement of the segment from residues 304-305 the typical conformational changes of the "flexible loop" (303-309), that constitutes the surface edge of the substrate binding cleft, were not observed in the present complex structure. This result supports the hypothesis that significant movement of the loop may depend on aglycone site being filled (Payan and Qian, J. Protein Chen. 22: 275, 2003). Structural analyses have shown that pancreatic alpha-amylases undergo an induced conformational change of the catalytic residue Asp300 upon substrate binding; in the present complex the catalytic residue is observed in its unliganded orientation. The results suggest that the induced reorientation is likely due to the presence of a sugar unit at subsite -1 and not linked to the closure of the flexible surface loop. The crystal structure was refined at 2.4 A resolution to an R factor of 17.55% (Rfree factor of 23.32%).

PubMed: 15517985
DOI: 10.1023/B:JOPC.0000039552.94529.95

Experimental method

X-RAY DIFFRACTION (2.4 Å)