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Hydrolase/hydrolase inhibitor PDB id
1bvn
Jmol
Contents
Protein chains
496 a.a. *
71 a.a. *
Metals
_CL
_CA
Waters ×161
* Residue conservation analysis
PDB id:
1bvn
Name: Hydrolase/hydrolase inhibitor
Title: Pig pancreatic alpha-amylase in complex with the proteinaceous inhibitor tendamistat
Structure: Protein (alpha-amylase). Chain: p. Synonym: 1,4-glucan-4-glucanohydrolase, glycosyltransferase. Protein (tendamistat). Chain: t
Source: Sus scrofa. Pig. Organism_taxid: 9823. Organ: pancreas. Streptomyces tendae. Organism_taxid: 1932. Strain: 4158
Resolution:
2.50Å     R-factor:   0.166     R-free:   0.260
Authors: M.Machius,G.Wiegand,O.Epp,R.Huber
Key ref: G.Wiegand et al. (1995). The crystal structure of porcine pancreatic alpha-amylase in complex with the microbial inhibitor Tendamistat. J Mol Biol, 247, 99. PubMed id: 7897663 DOI: 10.1006/jmbi.1994.0125
Date:
16-Sep-98     Release date:   23-Sep-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.*
Protein chain
Pfam   ArchSchema ?
P01092  (IAA_STRTE) -  Alpha-amylase inhibitor HOE-467A
Seq:
Struc: 		104 a.a.
71 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 12 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chain P: 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     9 terms  

 

 
DOI no: 10.1006/jmbi.1994.0125 J Mol Biol 247:99 (1995)
PubMed id: 7897663  
 
 
The crystal structure of porcine pancreatic alpha-amylase in complex with the microbial inhibitor Tendamistat.
G.Wiegand, O.Epp, R.Huber.
 
  ABSTRACT  
 
The crystal structure of the complex formed between the 498 amino acid residue porcine pancreatic alpha-amylase (PPA) and the 74 amino acid residue inhibitor Tendamistat secreted from Streptomyces tendae, has been determined by multiple isomorphous replacement in a crystal of space group P6(5)22 (a = b = 77.7 A, c = 359.5 A). The model has been refined to an R-factor of 0.194 by Powell minimization applying strong energy constraints based on 17,964 independent reflections in the 7 to 2.5 A resolution range, and obeys standard geometry within 0.011 A in bond lengths and 1.78 degrees in bond angles. The final model consists of all 496 amino acid residues of PPA, 71 amino acid residues of Tendamistat (without the three N-terminal residues), one calcium ion, one chloride ion and 167 water molecules. PPA exhibits the same topological fold in the complex as the uncomplexed PPA recently published by others. About 30% of the water-accessible surface of Tendamistat is in contact with PPA. Four segments of the polypeptide chain, with a total of 15 amino acid residues, are involved in the binding. One segment containing the staggered side-chains of the triplet Trp18, Arg19, Tyr20, typical for this class of inhibitors, binds into the catalytic site. The other segments fill out the groove in the PPA molecule, which also binds the carbohydrate inhibitor acarbose and is assumed to be the substrate-binding region. This extended interaction between Tendamistat and alpha-amylase explains the very high inhibition constant of about 9 x 10(-12) M.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21448869 K.Guitot, M.Larregola, T.K.Pradhan, J.L.Vasse, S.Lavielle, P.Bertus, J.Szymoniak, O.Lequin, and P.Karoyan (2011).
The combination of prolinoamino acids and cyclopropylamino acids leads to fully functionalized, stable β-turns in water.
  Chembiochem, 12, 1039-1042.  
20969427 A.M.Ruvinsky, and I.A.Vakser (2010).
Sequence composition and environment effects on residue fluctuations in protein structures.
  J Chem Phys, 133, 155101.  
19937896 C.Mothes, M.Larregola, J.Quancard, N.Goasdoué, S.Lavielle, G.Chassaing, O.Lequin, and P.Karoyan (2010).
Prolinoamino acids as tools to build bifunctionalized, stable beta-turns in water.
  Chembiochem, 11, 55-58.  
19067455 S.Rehm, S.Han, I.Hassani, A.Sokocevic, H.R.Jonker, J.W.Engels, and H.Schwalbe (2009).
The high resolution NMR structure of parvulustat (Z-2685) from Streptomyces parvulus FH-1641: comparison with tendamistat from Streptomyces tendae 4158.
  Chembiochem, 10, 119-127.
PDB code: 2ker
17724034 J.Fort, L.R.de la Ballina, H.E.Burghardt, C.Ferrer-Costa, J.Turnay, C.Ferrer-Orta, I.Usón, A.Zorzano, J.Fernández-Recio, M.Orozco, M.A.Lizarbe, I.Fita, and M.Palacín (2007).
The structure of human 4F2hc ectodomain provides a model for homodimerization and electrostatic interaction with plasma membrane.
  J Biol Chem, 282, 31444-31452.
PDB codes: 2dh2 2dh3
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.  
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.  
15722449 R.Maurus, A.Begum, H.H.Kuo, A.Racaza, S.Numao, C.Andersen, J.W.Tams, J.Vind, C.M.Overall, S.G.Withers, and G.D.Brayer (2005).
Structural and mechanistic studies of chloride induced activation of human pancreatic alpha-amylase.
  Protein Sci, 14, 743-755.
PDB codes: 1xgz 1xh0 1xh1 1xh2
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
15054893 K.Usui, T.Ojima, M.Takahashi, K.Nokihara, and H.Mihara (2004).
Peptide arrays with designed secondary structures for protein characterization using fluorescent fingerprint patterns.
  Biopolymers, 76, 129-139.  
  12573698 M.Takahashi, K.Nokihara, and H.Mihara (2003).
Construction of a protein-detection system using a loop peptide library with a fluorescence label.
  Chem Biol, 10, 53-60.  
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
11792867 J.G.Bann, J.Pinkner, S.J.Hultgren, and C.Frieden (2002).
Real-time and equilibrium (19)F-NMR studies reveal the role of domain-domain interactions in the folding of the chaperone PapD.
  Proc Natl Acad Sci U S A, 99, 709-714.  
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.  
11180535 D.J.Douglas, B.A.Collings, S.Numao, and V.J.Nesatyy (2001).
Detection of noncovalent complex between alpha-amylase and its microbial inhibitor tendamistat by electrospray ionization mass spectrometry.
  Rapid Commun Mass Spectrom, 15, 89-96.  
11284160 H.J.Gabius (2001).
Glycohistochemistry: the why and how of detection and localization of endogenous lectins.
  Anat Histol Embryol, 30, 3.  
11284678 N.Alam, S.Gourinath, S.Dey, A.Srinivasan, and T.P.Singh (2001).
Substrate-inhibitor interactions in the kinetics of alpha-amylase inhibition by ragi alpha-amylase/trypsin inhibitor (RATI) and its various N-terminal fragments.
  Biochemistry, 40, 4229-4233.  
11025543 J.Lehtiö, T.T.Teeri, and P.A.Nygren (2000).
Alpha-amylase inhibitors selected from a combinatorial library of a cellulose binding domain scaffold.
  Proteins, 41, 316-322.  
  16232845 J.Sumitani, Y.Tsujimoto, T.Kawaguchi, and M.Arai (2000).
Cloning and secretive expression of the gene encoding the proteinaceous alpha-amylase inhibitor paim from Streptomyces corchorusii.
  J Biosci Bioeng, 90, 214-216.  
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.  
10713515 S.Gourinath, N.Alam, A.Srinivasan, C.Betzel, and T.P.Singh (2000).
Structure of the bifunctional inhibitor of trypsin and alpha-amylase from ragi seeds at 2.2 A resolution.
  Acta Crystallogr D Biol Crystallogr, 56, 287-293.
PDB code: 1b1u
10336482 A.Eto, T.C.Saido, K.Fukushima, S.Tomioka, S.Imai, T.Nisizawa, and N.Hanada (1999).
Inhibitory effect of a self-derived peptide on glucosyltransferase of Streptococcus mutans. Possible novel anticaries measures.
  J Biol Chem, 274, 15797-15802.  
  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
10547530 G.André, A.Buléon, R.Haser, and V.Tran (1999).
Amylose chain behavior in an interacting context. III. Complete occupancy of the AMY2 barley alpha-amylase cleft and comparison with biochemical data.
  Biopolymers, 50, 751-762.  
  10508777 P.J.Pereira, V.Lozanov, A.Patthy, R.Huber, W.Bode, S.Pongor, and S.Strobl (1999).
Specific inhibition of insect alpha-amylases: yellow meal worm alpha-amylase in complex with the amaranth alpha-amylase inhibitor at 2.0 A resolution.
  Structure, 7, 1079-1088.
PDB code: 1clv
10089391 S.Gourinath, A.Srinivasan, and T.P.Singh (1999).
Structure of the bifunctional inhibitor of trypsin and alpha-amylase from ragi seeds at 2.9 A resolution.
  Acta Crystallogr D Biol Crystallogr, 55, 25-30.
PDB code: 1jfo
  9634702 F.Vallée, A.Kadziola, Y.Bourne, M.Juy, K.W.Rodenburg, B.Svensson, and R.Haser (1998).
Barley alpha-amylase bound to its endogenous protein inhibitor BASI: crystal structure of the complex at 1.9 A resolution.
  Structure, 6, 649-659.
PDB code: 1ava
9757571 S.Ono, T.Hirano, H.Yasutake, T.Matsumoto, I.Yamaura, T.Kato, H.Morita, T.Fujii, I.Yamazaki, C.Shimasaki, and T.Yoshimura (1998).
Biological and structural properties of cyclic peptides derived from the alpha-amylase inhibitor tendamistat.
  Biosci Biotechnol Biochem, 62, 1621-1623.  
  9687373 S.Strobl, K.Maskos, G.Wiegand, R.Huber, F.X.Gomis-Rüth, and R.Glockshuber (1998).
A novel strategy for inhibition of alpha-amylases: yellow meal worm alpha-amylase in complex with the Ragi bifunctional inhibitor at 2.5 A resolution.
  Structure, 6, 911-921.
PDB code: 1tmq
9134709 M.F.Grossi de Sa, and M.J.Chrispeels (1997).
Molecular cloning of bruchid (Zabrotes subfasciatus) alpha-amylase cDNA and interactions of the expressed enzyme with bean amylase inhibitors.
  Insect Biochem Mol Biol, 27, 271-281.  
8999834 M.Inohara-Ochiai, T.Nakayama, R.Goto, M.Nakao, T.Ueda, and Y.Shibano (1997).
Altering substrate specificity of Bacillus sp. SAM1606 alpha-glucosidase by comparative site-specific mutagenesis.
  J Biol Chem, 272, 1601-1607.  
  8994970 C.Bompard-Gilles, P.Rousseau, P.Rougé, and F.Payan (1996).
Substrate mimicry in the active center of a mammalian alpha-amylase: structural analysis of an enzyme-inhibitor complex.
  Structure, 4, 1441-1452.
PDB code: 1dhk
8681972 C.Gilles, J.P.Astier, G.Marchis-Mouren, C.Cambillau, and F.Payan (1996).
Crystal structure of pig pancreatic alpha-amylase isoenzyme II, in complex with the carbohydrate inhibitor acarbose.
  Eur J Biochem, 238, 561-569.
PDB code: 1ose
8721743 T.Suganuma, M.Ohnishi, K.Hiromi, and T.Nagahama (1996).
Elucidation of the subsite structure of bacterial saccharifying alpha-amylase and its mode of degradation of maltose.
  Carbohydr Res, 282, 171-180.  
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.