1VAH

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of the pig pancreatic alpha-amylase complexed with rho-nitrophenyl-alpha-D-maltoside-flexibility in the active site

Zhuo, H.Payan, F.Qian, M.

(2004) Protein J 23: 379-387

  • DOI: 10.1023/b:jopc.0000039552.94529.95
  • Primary Citation of Related Structures:  
    1VAH

  • 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 ...

    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%).


    Related Citations: 
    • Structure of a pancreatic alpha-amylase bound to a substrate analogue at 2.03 A resolution
      Qian, M., Spinelli, S., Driguez, H., Payan, F.
      (1997) Protein Sci 6: 2285
    • Crystal structure of the pig pancreatic alpha-amylase complexed with malto-oligosaccharides
      Payan, F., Qian, M.
      (2003) J Protein Chem 22: 275

    Organizational Affiliation

    Department of Chemical Biology, Peking University, 100871, PR China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-amylase, pancreaticA496Sus scrofaMutation(s): 0 
Gene Names: AMY2
EC: 3.2.1.1
UniProt
Find proteins for P00690 (Sus scrofa)
Explore P00690 
Go to UniProtKB:  P00690
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NPO
Query on NPO

Download Ideal Coordinates CCD File 
D [auth A]P-NITROPHENOL
C6 H5 N O3
BTJIUGUIPKRLHP-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.3α = 90
b = 87.8β = 90
c = 103.4γ = 90
Software Package:
Software NamePurpose
MAR345data collection
XDSdata reduction
X-PLORmodel building
X-PLORrefinement
XDSdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-04-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description