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PDBsum entry 1clv

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protein metals Protein-protein interface(s) links
Hydrolase PDB id
1clv
Jmol
Contents
Protein chains
471 a.a. *
32 a.a. *
Metals
_CL
_CA
Waters ×273
* Residue conservation analysis
PDB id:
1clv
Name: Hydrolase
Title: Yellow meal worm alpha-amylase in complex with the amaranth alpha-amylase inhibitor
Structure: Protein (alpha-amylase). Chain: a. Synonym: alpha-1,4-glucan-4-glucanohydrolase. Protein (alpha-amylase inhibitor). Chain: i. Engineered: yes
Source: Tenebrio molitor. Yellow mealworm. Organism_taxid: 7067. Synthetic: yes. Other_details: the protein was chemically synthesized. The sequence of this protein is naturally found in amaranthus hypochondriacus (prince's feather).
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.161     R-free:   0.190
Authors: P.J.B.Pereira,V.Lozanov,A.Patthy,R.Huber,W.Bode,S.Pongor, S.Strobl
Key ref:
P.J.Pereira et al. (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. PubMed id: 10508777 DOI: 10.1016/S0969-2126(99)80175-0
Date:
04-May-99     Release date:   03-May-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P56634  (AMY_TENMO) -  Alpha-amylase
Seq:
Struc:
471 a.a.
471 a.a.*
Protein chain
Pfam   ArchSchema ?
P80403  (IAAI_AMAHP) -  Alpha-amylase inhibitor AAI
Seq:
Struc:
32 a.a.
32 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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!
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     8 terms  

 

 
DOI no: 10.1016/S0969-2126(99)80175-0 Structure 7:1079-1088 (1999)
PubMed id: 10508777  
 
 
Specific inhibition of insect alpha-amylases: yellow meal worm alpha-amylase in complex with the amaranth alpha-amylase inhibitor at 2.0 A resolution.
P.J.Pereira, V.Lozanov, A.Patthy, R.Huber, W.Bode, S.Pongor, S.Strobl.
 
  ABSTRACT  
 
BACKGROUND: alpha-Amylases constitute a family of enzymes that catalyze the hydrolysis of alpha-D-(1,4)-glucan linkages in starch and related polysaccharides. The Amaranth alpha-amylase inhibitor (AAI) specifically inhibits alpha-amylases from insects, but not from mammalian sources. AAI is the smallest proteinaceous alpha-amylase inhibitor described so far and has no known homologs in the sequence databases. Its mode of inhibition of alpha-amylases was unknown until now. RESULTS: The crystal structure of yellow meal worm alpha-amylase (TMA) in complex with AAI was determined at 2.0 A resolution. The overall fold of AAI, its three-stranded twisted beta sheet and the topology of its disulfide bonds identify it as a knottin-like protein. The inhibitor binds into the active-site groove of TMA, blocking the central four sugar-binding subsites. Residues from two AAI segments target the active-site residues of TMA. A comparison of the TMA-AAI complex with a modeled complex between porcine pancreatic alpha-amylase (PPA) and AAI identified six hydrogen bonds that can be formed only in the TMA-AAI complex. CONCLUSIONS: The binding of AAI to TMA presents a new inhibition mode for alpha-amylases. Due to its unique specificity towards insect alpha-amylases, AAI might represent a valuable tool for protecting crop plants from predatory insects. The close structural homology between AAI and 'knottins' opens new perspectives for the engineering of various novel activities onto the small scaffold of this group of proteins.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Stereoview of the AAI model. The hydrophobic hemisphere of the inhibitor (residues 1-3 and 8-20) is shown in black, the hydrophilic hemisphere (residues 4-7 and 21-32) in red. Disulfide bonds are depicted in yellow. Cysteine residues and relevant sidechains are labeled. This figure was made with the program MOLMOL [46].
 
  The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 1079-1088) copyright 1999.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18498107 P.B.Pelegrini, F.T.Lay, A.M.Murad, M.A.Anderson, and O.L.Franco (2008).
Novel insights on the mechanism of action of alpha-amylase inhibitors from the plant defensin family.
  Proteins, 73, 719-729.  
18497884 Z.Zhi-Fei, N.Ting-Ting, X.Zu-Min, Z.Ge-Xin, and M.Yan-He (2008).
The crystal water affect in the interaction between the tenebrio molitor alpha-amylase and its inhibitor.
  Bioinorg Chem Appl, (), 469062.  
17444520 K.F.Lin, T.R.Lee, P.H.Tsai, M.P.Hsu, C.S.Chen, and P.C.Lyu (2007).
Structure-based protein engineering for alpha-amylase inhibitory activity of plant defensin.
  Proteins, 68, 530-540.
PDB code: 2gl1
16544327 Y.J.Liu, C.S.Cheng, S.M.Lai, M.P.Hsu, C.S.Chen, and P.C.Lyu (2006).
Solution structure of the plant defensin VrD1 from mung bean and its possible role in insecticidal activity against bruchids.
  Proteins, 63, 777-786.
PDB code: 1ti5
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
16003953 S.C.Dias, O.L.Franco, C.P.Magalhães, O.B.de Oliveira-Neto, R.A.Laumann, E.L.Figueira, F.R.Melo, and M.F.Grossi-De-Sá (2005).
Molecular cloning and expression of an alpha-amylase inhibitor from rye with potential for controlling insect pests.
  Protein J, 24, 113-123.  
14749333 M.Cemazar, S.Zahariev, S.Pongor, and P.J.Hore (2004).
Oxidative folding of Amaranthus alpha-amylase inhibitor: disulfide bond formation and conformational folding.
  J Biol Chem, 279, 16697-16705.  
12724517 M.Cemazar, S.Zahariev, J.J.Lopez, O.Carugo, J.A.Jones, P.J.Hore, and S.Pongor (2003).
Oxidative folding intermediates with nonnative disulfide bridges between adjacent cysteine residues.
  Proc Natl Acad Sci U S A, 100, 5754-5759.  
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.  
11298757 J.C.Martins, M.Enassar, R.Willem, J.M.Wieruzeski, G.Lippens, and S.J.Wodak (2001).
Solution structure of the main alpha-amylase inhibitor from amaranth seeds.
  Eur J Biochem, 268, 2379-2389.
PDB code: 1htx
11551471 R.C.Ladner, and A.C.Ley (2001).
Novel frameworks as a source of high-affinity ligands.
  Curr Opin Biotechnol, 12, 406-410.  
11137459 J.Iulek, O.L.Franco, M.Silva, C.T.Slivinski, C.Bloch, D.J.Rigden, and M.F.Grossi de Sá (2000).
Purification, biochemical characterisation and partial primary structure of a new alpha-amylase inhibitor from Secale cereale (rye).
  Int J Biochem Cell Biol, 32, 1195-1204.  
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.