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PDBsum entry 1jfh

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protein ligands metals links
Hydrolase PDB id
1jfh
Jmol
Contents
Protein chain
496 a.a. *
Ligands
MA2-MA3
GLC-MA1 ×2
Metals
_CA
_CL
_HG
Waters ×383
* Residue conservation analysis
PDB id:
1jfh
Name: Hydrolase
Title: Structure of a pancreatic alpha-amylase bound to a substrate analogue at 2.03 angstrom resolution
Structure: Alpha-amylase. Chain: a. Synonym: ppa. Other_details: complexed with methyl 4,4'-dithio-alpha- maltotrioside
Source: Sus scrofa. Pig. Organism_taxid: 9823. Organ: pancreas
Resolution:
2.03Å     R-factor:   0.160     R-free:   0.185
Authors: M.Qian,F.Payan
Key ref: M.Qian et al. (1997). Structure of a pancreatic alpha-amylase bound to a substrate analogue at 2.03 A resolution. Protein Sci, 6, 2285-2296. PubMed id: 9385631 DOI: 10.1002/pro.5560061102
Date:
19-Sep-97     Release date:   02-Dec-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00690  (AMYP_PIG) -  Pancreatic alpha-amylase
Seq:
Struc:
511 a.a.
496 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 10 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.1  - Alpha-amylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endohydrolysis of 1,4-alpha-glucosidic linkages in oligosaccharides and polysaccharides.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   2 terms 
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     8 terms  

 

 
DOI no: 10.1002/pro.5560061102 Protein Sci 6:2285-2296 (1997)
PubMed id: 9385631  
 
 
Structure of a pancreatic alpha-amylase bound to a substrate analogue at 2.03 A resolution.
M.Qian, S.Spinelli, H.Driguez, F.Payan.
 
  ABSTRACT  
 
The structure of pig pancreatic alpha-amylase in complex with carbohydrate inhibitor and proteinaceous inhibitors is known but the successive events occurring at the catalytic center still remain to be elucidated. The X-ray structure analysis of a crystal of pig pancreatic alpha-amylase (PPA, EC 3.2.1.1.) soaked with an enzyme-resistant substrate analogue, methyl 4,4'-dithio-alpha-maltotrioside, showed electron density corresponding to the binding of substrate analogue molecules at the active site and at the "second binding site." The electron density observed at the active site was interpreted in terms of overlapping networks of oligosaccharides, which show binding of substrate analogue molecules at subsites prior to and subsequent to the cleavage site. A weaker patch of density observed at subsite -1 (using a nomenclature where the site of hydrolysis is taken to be between subsites -1 and +1) was modeled with water molecules. Conformational changes take place upon substrate analogue binding and the "flexible loop" that constitutes the surface edge of the active site is observed in a specific conformation. This confirms that this loop plays an important role in the recognition and binding of the ligand. The crystal structure was refined at 2.03 A resolution, to an R-factor of 16.0 (Rfree, 18.5).
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20222716 S.B.Larson, J.S.Day, and A.McPherson (2010).
X-ray crystallographic analyses of pig pancreatic alpha-amylase with limit dextrin, oligosaccharide, and alpha-cyclodextrin.
  Biochemistry, 49, 3101-3115.
PDB codes: 3l2l 3l2m
18951906 C.Ragunath, S.G.Manuel, V.Venkataraman, H.B.Sait, C.Kasinathan, and N.Ramasubbu (2008).
Probing the role of aromatic residues at the secondary saccharide-binding sites of human salivary alpha-amylase in substrate hydrolysis and bacterial binding.
  J Mol Biol, 384, 1232-1248.  
18331662 W.C.Obiro, T.Zhang, and B.Jiang (2008).
The nutraceutical role of the Phaseolus vulgaris alpha-amylase inhibitor.
  Br J Nutr, 100, 1.  
16196067 J.R.Rich, W.W.Wakarchuk, and D.R.Bundle (2006).
Chemical and chemoenzymatic synthesis of S-linked ganglioside analogues and their protein conjugates for use as immunogens.
  Chemistry, 12, 845-858.  
16358009 S.Jacques, J.R.Rich, C.C.Ling, and D.R.Bundle (2006).
Chemoenzymatic synthesis of GM3 and GM2 gangliosides containing a truncated ceramide functionalized for glycoconjugate synthesis and solid phase applications.
  Org Biomol Chem, 4, 142-154.  
12649437 H.Baumann, S.Ohrman, Y.Shinohara, O.Ersoy, D.Choudhury, A.Axén, U.Tedebark, and E.Carredano (2003).
Rational design, synthesis, and verification of affinity ligands to a protein surface cleft.
  Protein Sci, 12, 784-793.  
14732931 M.Westerfors, U.Tedebark, H.O.Andersson, S.Ohrman, D.Choudhury, O.Ersoy, Y.Shinohara, A.Axén, E.Carredano, and H.Baumann (2003).
Structure-based discovery of a new affinity ligand to pancreatic alpha-amylase.
  J Mol Recognit, 16, 396-405.  
14501112 V.König, L.Vértesy, and T.R.Schneider (2003).
Structure of the alpha-amylase inhibitor tendamistat at 0.93 A.
  Acta Crystallogr D Biol Crystallogr, 59, 1737-1743.
PDB code: 1ok0
12392547 G.Gyémánt, G.Hovánszki, and L.Kandra (2002).
Subsite mapping of the binding region of alpha-amylases with a computer program.
  Eur J Biochem, 269, 5157-5162.  
11807243 T.R.Schneider (2002).
A genetic algorithm for the identification of conformationally invariant regions in protein molecules.
  Acta Crystallogr D Biol Crystallogr, 58, 195-208.  
11180561 A.P.Demchenko (2001).
Recognition between flexible protein molecules: induced and assisted folding.
  J Mol Recognit, 14, 42-61.  
11168426 R.Koukiekolo, V.Desseaux, Y.Moreau, G.Marchis-Mouren, and M.Santimone (2001).
Mechanism of porcine pancreatic alpha-amylase. Inhibition of amylose and maltopentaose hydrolysis by alpha-, beta- and gamma-cyclodextrins.
  Eur J Biochem, 268, 841-848.  
  10091666 E.H.Rydberg, G.Sidhu, H.C.Vo, J.Hewitt, H.C.Côte, Y.Wang, S.Numao, R.T.MacGillivray, C.M.Overall, G.D.Brayer, and S.G.Withers (1999).
Cloning, mutagenesis, and structural analysis of human pancreatic alpha-amylase expressed in Pichia pastoris.
  Protein Sci, 8, 635-643.
PDB code: 1bsi
10491154 R.Koukiekolo, V.Le Berre-Anton, V.Desseaux, Y.Moreau, P.Rougé, G.Marchis-Mouren, and M.Santimone (1999).
Mechanism of porcine pancreatic alpha-amylase inhibition of amylose and maltopentaose hydrolysis by kidney bean (Phaseolus vulgaris) inhibitor and comparison with that by acarbose.
  Eur J Biochem, 265, 20-26.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.