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PDBsum entry 1dhk

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protein ligands metals Protein-protein interface(s) links
Complex (hydrolase/inhibitor) PDB id
1dhk
Jmol
Contents
Protein chains
496 a.a. *
195 a.a. *
Ligands
NAG-NAG ×2
NAG
Metals
_CL
_CA ×3
Waters ×966
* Residue conservation analysis
PDB id:
1dhk
Name: Complex (hydrolase/inhibitor)
Title: Structure of porcine pancreatic alpha-amylase
Structure: Porcine pancreatic alpha-amylase. Chain: a. Synonym: ppa. Bean lectin-like inhibitor. Chain: b
Source: Sus scrofa. Pig. Organism_taxid: 9823. Organ: pancreas. Phaseolus vulgaris. Organism_taxid: 3885. Organ: seed
Biol. unit: Tetramer (from PQS)
Resolution:
1.85Å     R-factor:   0.183     R-free:   0.220
Authors: C.Bompard-Gilles,F.Payan
Key ref:
C.Bompard-Gilles et al. (1996). Substrate mimicry in the active center of a mammalian alpha-amylase: structural analysis of an enzyme-inhibitor complex. Structure, 4, 1441-1452. PubMed id: 8994970 DOI: 10.1016/S0969-2126(96)00151-7
Date:
14-Oct-96     Release date:   24-Dec-97    
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.*
Protein chain
Pfam   ArchSchema ?
P02873  (LEA1_PHAVU) -  Alpha-amylase inhibitor 1
Seq:
Struc:
246 a.a.
195 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chain A: 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   4 terms 
  Biochemical function     catalytic activity     10 terms  

 

 
DOI no: 10.1016/S0969-2126(96)00151-7 Structure 4:1441-1452 (1996)
PubMed id: 8994970  
 
 
Substrate mimicry in the active center of a mammalian alpha-amylase: structural analysis of an enzyme-inhibitor complex.
C.Bompard-Gilles, P.Rousseau, P.Rougé, F.Payan.
 
  ABSTRACT  
 
BACKGROUND: alpha-Amylases catalyze the hydrolysis of glycosidic linkages in starch and other related polysaccharides. The alpha-amylase inhibitor (alpha-Al) from the bean Phaseolus vulgaris belongs to a family of plant defence proteins and is a potent inhibitor of mammalian alpha-amylases. The structure of pig pancreatic alpha-amylase (PPA) in complex with both a carbohydrate inhibitor (acarbose) and a proteinaceous inhibitor (Tendamistat) is known, but the catalytic mechanism is poorly understood. RESULTS: The crystal structure of pig pancreatic alpha-amylase complexed with alpha-Al was refined to 1.85 A resolution. It reveals that in complex with PPA, the inhibitor has the typical dimer structure common to legume lectins. Two hairpin loops extending out from the jellyroll fold of a monomer interact directly with the active site region of the enzyme molecule, with the inhibitor molecule filling the whole substrate-docking region of the PPA. The inhibitor makes substrate-mimetic interactions with binding subsites of the enzyme and targets catalytic residues in the active site. Binding of inhibitor induces structural changes at the active site of the enzyme. CONCLUSIONS: The present analysis reveals that there are extensive interactions between the inhibitor and residues that are highly conserved in the active site of alpha-amylases; alpha-Al1 inactivates PPA through elaborate blockage of substrate-binding sites. It provides a basis to design peptide analogue inhibitors. alpha-Amylase inhibition is of interest from several points of view, for example the treatment of diabetes and for crop protection.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Schematic representation of the network of interactions within the catalytic center. The enzyme chloride ion is shown in interaction with some of its ligands (Arg195, Asn298 and H[2]0). The calcium ion of the enzyme structure (liganded to Asn100 and His201) and the presumed calcium ion of the inhibitor structure are involved in the interaction. (Borders around inhibitor residues are thickened.)
 
  The above figure is reprinted by permission from Cell Press: Structure (1996, 4, 1441-1452) copyright 1996.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18566914 B.Nocek, L.Bigelow, J.Abdullah, and A.Joachimiak (2008).
Structure of SO2946 orphan from Shewanella oneidensis shows "jelly-roll" fold with carbohydrate-binding module.
  J Struct Funct Genomics, 9, 1-6.
PDB code: 2a5z
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.  
17881351 M.N.Dharmasena, D.A.Jewell, and R.K.Taylor (2007).
Development of peptide mimics of a protective epitope of Vibrio cholerae Ogawa O-antigen and investigation of the structural basis of peptide mimicry.
  J Biol Chem, 282, 33805-33816.  
17149640 Y.H.Kim, C.P.Woloshuk, E.H.Cho, J.M.Bae, Y.S.Song, and G.H.Huh (2007).
Cloning and functional expression of the gene encoding an inhibitor against Aspergillus flavus alpha-amylase, a novel seed lectin from Lablab purpureus (Dolichos lablab).
  Plant Cell Rep, 26, 395-405.  
16416448 P.B.Pelegrini, A.M.Murad, M.F.Grossi-de-Sá, L.V.Mello, L.A.Romeiro, E.F.Noronha, R.A.Caldas, and O.L.Franco (2006).
Structure and enzyme properties of Zabrotes subfasciatus alpha-amylase.
  Arch Insect Biochem Physiol, 61, 77-86.  
15657043 B.C.Bønsager, P.K.Nielsen, M.Abou Hachem, K.Fukuda, M.Praetorius-Ibba, and B.Svensson (2005).
Mutational analysis of target enzyme recognition of the beta-trefoil fold barley alpha-amylase/subtilisin inhibitor.
  J Biol Chem, 280, 14855-14864.  
15856483 F.Rodier, R.P.Bahadur, P.Chakrabarti, and J.Janin (2005).
Hydration of protein-protein interfaces.
  Proteins, 60, 36-45.  
16356852 L.Dolecková-Maresová, M.Pavlík, M.Horn, and M.Mares (2005).
De novo design of alpha-amylase inhibitor: a small linear mimetic of macromolecular proteinaceous ligands.
  Chem Biol, 12, 1349-1357.  
16356842 N.Pohl (2005).
Acyclic peptide inhibitors of amylases.
  Chem Biol, 12, 1257-1258.  
15849405 W.Hashimoto, K.Momma, Y.Maruyama, M.Yamasaki, B.Mikami, and K.Murata (2005).
Structure and function of bacterial super-biosystem responsible for import and depolymerization of macromolecules.
  Biosci Biotechnol Biochem, 69, 673-692.  
15388953 A.H.Parret, L.Wyns, R.De Mot, and R.Loris (2004).
Overexpression, purification and crystallization of bacteriocin LlpA from Pseudomonas sp. BW11M1.
  Acta Crystallogr D Biol Crystallogr, 60, 1922-1924.  
15181003 F.Payan, P.Leone, S.Porciero, C.Furniss, T.Tahir, G.Williamson, A.Durand, P.Manzanares, H.J.Gilbert, N.Juge, and A.Roussel (2004).
The dual nature of the wheat xylanase protein inhibitor XIP-I: structural basis for the inhibition of family 10 and family 11 xylanases.
  J Biol Chem, 279, 36029-36037.
PDB codes: 1ta3 1te1
15136569 M.Yamasaki, S.Moriwaki, O.Miyake, W.Hashimoto, K.Murata, and B.Mikami (2004).
Structure and function of a hypothetical Pseudomonas aeruginosa protein PA1167 classified into family PL-7: a novel alginate lyase with a beta-sandwich fold.
  J Biol Chem, 279, 31863-31872.
PDB code: 1vav
  16233728 W.Hashimoto, M.Yamasaki, T.Itoh, K.Momma, B.Mikami, and K.Murata (2004).
Super-channel in bacteria: structural and functional aspects of a novel biosystem for the import and depolymerization of macromolecules.
  J Biosci Bioeng, 98, 399-413.  
12784366 E.Ben-Zeev, A.Berchanski, A.Heifetz, B.Shapira, and M.Eisenstein (2003).
Prediction of the unknown: inspiring experience with the CAPRI experiment.
  Proteins, 52, 41-46.  
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
11960990 A.Desmyter, S.Spinelli, F.Payan, M.Lauwereys, L.Wyns, S.Muyldermans, and C.Cambillau (2002).
Three camelid VHH domains in complex with porcine pancreatic alpha-amylase. Inhibition and versatility of binding topology.
  J Biol Chem, 277, 23645-23650.
PDB codes: 1kxq 1kxt 1kxv
11841205 M.A.Johnson, A.Rotondo, and B.M.Pinto (2002).
NMR studies of the antibody-bound conformation of a carbohydrate-mimetic peptide.
  Biochemistry, 41, 2149-2157.  
11856298 O.L.Franco, D.J.Rigden, F.R.Melo, and M.F.Grossi-De-Sá (2002).
Plant alpha-amylase inhibitors and their interaction with insect alpha-amylases.
  Eur J Biochem, 269, 397-412.  
11948787 P.Chakrabarti, and J.Janin (2002).
Dissecting protein-protein recognition sites.
  Proteins, 47, 334-343.  
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.  
11864980 Y.Kaneda, R.F.Whittier, H.Yamanaka, E.Carredano, M.Gotoh, H.Sota, Y.Hasegawa, and Y.Shinohara (2002).
The high specificities of Phaseolus vulgaris erythro- and leukoagglutinating lectins for bisecting GlcNAc or beta 1-6-linked branch structures, respectively, are attributable to loop B.
  J Biol Chem, 277, 16928-16935.  
11497467 A.M.Fakhoury, and C.P.Woloshuk (2001).
Inhibition of growth of Aspergillus flavus and fungal alpha-amylases by a lectin-like protein from Lablab purpureus.
  Mol Plant Microbe Interact, 14, 955-961.  
11590016 C.Kleanthous, and D.Walker (2001).
Immunity proteins: enzyme inhibitors that avoid the active site.
  Trends Biochem Sci, 26, 624-631.  
11284160 H.J.Gabius (2001).
Glycohistochemistry: the why and how of detection and localization of endogenous lectins.
  Anat Histol Embryol, 30, 3.  
10821862 D.Jain, K.Kaur, B.Sundaravadivel, and D.M.Salunke (2000).
Structural and functional consequences of peptide-carbohydrate mimicry. Crystal structure of a carbohydrate-mimicking peptide bound to concanavalin A.
  J Biol Chem, 275, 16098-16102.
PDB code: 1jyi
10931189 E.J.Van Damme, C.H.Astoul, A.Barre, P.Rougé, and W.J.Peumans (2000).
Cloning and characterization of a monocot mannose-binding lectin from Crocus vernus (family Iridaceae).
  Eur J Biochem, 267, 5067-5077.  
10672010 K.W.Rodenburg, F.Vallée, N.Juge, N.Aghajari, X.Guo, R.Haser, and B.Svensson (2000).
Specific inhibition of barley alpha-amylase 2 by barley alpha-amylase/subtilisin inhibitor depends on charge interactions and can be conferred to isozyme 1 by mutation.
  Eur J Biochem, 267, 1019-1029.  
  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.  
10082956 S.Darnis, N.Juge, X.J.Guo, G.Marchis-Mouren, A.Puigserver, and J.C.Chaix (1999).
Molecular cloning and primary structure analysis of porcine pancreatic alpha-amylase.
  Biochim Biophys Acta, 1430, 281-289.  
10089450 V.Nahoum, F.Farisei, V.Le-Berre-Anton, M.P.Egloff, P.Rougé, E.Poerio, and F.Payan (1999).
A plant-seed inhibitor of two classes of alpha-amylases: X-ray analysis of Tenebrio molitor larvae alpha-amylase in complex with the bean Phaseolus vulgaris inhibitor.
  Acta Crystallogr D Biol Crystallogr, 55, 360-362.
PDB code: 1viw
9582323 L.Mourey, J.D.Pédelacq, C.Birck, C.Fabre, P.Rougé, and J.P.Samama (1998).
Crystal structure of the arcelin-1 dimer from Phaseolus vulgaris at 1.9-A resolution.
  J Biol Chem, 273, 12914-12922.
PDB code: 1avb
9761914 M.J.Cho, S.S.Cha, J.H.Park, H.J.Cha, H.S.Lee, K.H.Park, and B.H.Oh (1998).
Preliminary X-ray crystallographic analysis of a novel maltogenic amylase from Bacillus stearothermophilus ET1.
  Acta Crystallogr D Biol Crystallogr, 54, 416-418.  
9726420 T.R.Transue, E.De Genst, M.A.Ghahroudi, L.Wyns, and S.Muyldermans (1998).
Camel single-domain antibody inhibits enzyme by mimicking carbohydrate substrate.
  Proteins, 32, 515-522.  
9408941 L.Mourey, J.D.Pédelacq, C.Fabre, H.Causse, P.Rougé, and J.P.Samama (1997).
Small-angle X-ray scattering and crystallographic studies of arcelin-1: an insecticidal lectin-like glycoprotein from Phaseolus vulgaris L.
  Proteins, 29, 433-442.  
  9385631 M.Qian, S.Spinelli, H.Driguez, and F.Payan (1997).
Structure of a pancreatic alpha-amylase bound to a substrate analogue at 2.03 A resolution.
  Protein Sci, 6, 2285-2296.
PDB code: 1jfh
9428656 V.Le Berre-Anton, C.Bompard-Gilles, F.Payan, and P.Rougé (1997).
Characterization and functional properties of the alpha-amylase inhibitor (alpha-AI) from kidney bean (Phaseolus vulgaris) seeds.
  Biochim Biophys Acta, 1343, 31-40.  
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 code is shown on the right.