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PDBsum entry 1jae

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protein metals links
Glycosidase PDB id
1jae
Jmol
Contents
Protein chain
471 a.a. *
Metals
_CL
_CA
Waters ×261
* Residue conservation analysis
PDB id:
1jae
Name: Glycosidase
Title: Structure of tenebrio molitor larval alpha-amylase
Structure: Alpha-amylase. Chain: a. Fragment: residues 1 - 471. Ec: 3.2.1.1
Source: Tenebrio molitor. Yellow mealworm. Organism_taxid: 7067
Resolution:
1.65Å     R-factor:   0.177     R-free:   0.206
Authors: S.Strobl,K.Maskos,M.Betz,G.Wiegand,R.Huber,F.X.Gomis-Rueth, G.Frank,R.Glockshuber
Key ref:
S.Strobl et al. (1998). Crystal structure of yellow meal worm alpha-amylase at 1.64 A resolution. J Mol Biol, 278, 617-628. PubMed id: 9600843 DOI: 10.1006/jmbi.1998.1667
Date:
30-Sep-97     Release date:   04-Nov-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 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!
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
DOI no: 10.1006/jmbi.1998.1667 J Mol Biol 278:617-628 (1998)
PubMed id: 9600843  
 
 
Crystal structure of yellow meal worm alpha-amylase at 1.64 A resolution.
S.Strobl, K.Maskos, M.Betz, G.Wiegand, R.Huber, F.X.Gomis-Rüth, R.Glockshuber.
 
  ABSTRACT  
 
The three-dimensional structure of the alpha-amylase from Tenebrio molitor larvae (TMA) has been determined by molecular replacement techniques using diffraction data of a crystal of space group P212121 (a=51.24 A; b=93.46 A; c=96.95 A). The structure has been refined to a crystallographic R-factor of 17.7% for 58,219 independent reflections in the 7.0 to 1.64 A resolution range, with root-mean-square deviations of 0.008 A for bond lengths and 1.482 degrees for bond angles. The final model comprises all 471 residues of TMA, 261 water molecules, one calcium cation and one chloride anion. The electron density confirms that the N-terminal glutamine residue has undergone a post-transitional modification resulting in a stable 5-oxo-proline residue. The X-ray structure of TMA provides the first three-dimensional model of an insect alpha-amylase. The monomeric enzyme exhibits an elongated shape approximately 75 Ax46 Ax40 A and consists of three distinct domains, in line with models for alpha-amylases from microbial, plant and mammalian origin. However, the structure of TMA reflects in the substrate and inhibitor binding region a remarkable difference from mammalian alpha-amylases: the lack of a highly flexible, glycine-rich loop, which has been proposed to be involved in a "trap-release" mechanism of substrate hydrolysis by mammalian alpha-amylases. The structural differences between alpha-amylases of various origins might explain the specificity of inhibitors directed exclusively against insect alpha-amylases.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Superposition of the domain A/domain C interface of TMA (green) and barley α-amylase (BAA) (red). Only the trace of the TMA residues 251 to 326 and 359 to 471 and of the BAA residues 251 to 403 are shown. TMA residues 263 to 266, 304 to 315, 366 to 377, 390 to 406 and 460 to 467 were superimposed on BAA residues 262 to 265, 303 to 314, 333 to 344, 359 to 375 and 395 to 402.
Figure 5.
Figure 5. Coordination of the calcium ion in the TMA structure. The calcium ion is represented by a yellow sphere and water molecules by blue spheres. B domain residues are depicted in red and the A domain residue in green. Coordinating interactions are shown as blue lines.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 278, 617-628) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19756583 F.M.Reyes-Sosa, F.P.Molina-Heredia, and M.A.De la Rosa (2010).
A novel alpha-amylase from the cyanobacterium Nostoc sp. PCC 7119.
  Appl Microbiol Biotechnol, 86, 131-141.  
19476481 J.Pytelková, J.Hubert, M.Lepsík, J.Sobotník, R.Sindelka, I.Krízková, M.Horn, and M.Mares (2009).
Digestive alpha-amylases of the flour moth Ephestia kuehniella--adaptation to alkaline environment and plant inhibitors.
  FEBS J, 276, 3531-3546.  
17729287 J.C.Marx, J.Poncin, J.P.Simorre, P.W.Ramteke, and G.Feller (2008).
The noncatalytic triad of alpha-amylases: a novel structural motif involved in conformational stability.
  Proteins, 70, 320-328.  
18552192 J.Y.Damián-Almazo, A.Moreno, A.López-Munguía, X.Soberón, F.González-Muñoz, and G.Saab-Rincón (2008).
Enhancement of the alcoholytic activity of alpha-amylase AmyA from Thermotoga maritima MSB8 (DSM 3109) by site-directed mutagenesis.
  Appl Environ Microbiol, 74, 5168-5177.  
17359918 A.J.Plested, and M.L.Mayer (2007).
Structure and mechanism of kainate receptor modulation by anions.
  Neuron, 53, 829-841.
PDB code: 2ojt
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
17028947 F.Maczkowiak, and J.L.Da Lage (2006).
Origin and evolution of the Amyrel gene in the alpha-amylase multigene family of Diptera.
  Genetica, 128, 145-158.  
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.  
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
15356864 G.André, and V.Tran (2004).
Putative implication of alpha-amylase loop 7 in the mechanism of substrate binding and reaction products release.
  Biopolymers, 75, 95.  
12906828 X.Robert, R.Haser, T.E.Gottschalk, F.Ratajczak, H.Driguez, B.Svensson, and N.Aghajari (2003).
The structure of barley alpha-amylase isozyme 1 reveals a novel role of domain C in substrate recognition and binding: a pair of sugar tongs.
  Structure, 11, 973-984.
PDB codes: 1ht6 1p6w
12021442 N.Aghajari, G.Feller, C.Gerday, and R.Haser (2002).
Structural basis of alpha-amylase activation by chloride.
  Protein Sci, 11, 1435-1441.
PDB codes: 1jd7 1jd9 1l0p
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.  
11257505 E.A.MacGregor, S.Janecek, and B.Svensson (2001).
Relationship of sequence and structure to specificity in the alpha-amylase family of enzymes.
  Biochim Biophys Acta, 1546, 1.  
11737209 H.Mori, K.S.Bak-Jensen, T.E.Gottschalk, M.S.Motawia, I.Damager, B.L.Møller, and B.Svensson (2001).
Modulation of activity and substrate binding modes by mutation of single and double subsites +1/+2 and -5/-6 of barley alpha-amylase 1.
  Eur J Biochem, 268, 6545-6558.  
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
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.  
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.  
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
9862804 N.Aghajari, G.Feller, C.Gerday, and R.Haser (1998).
Structures of the psychrophilic Alteromonas haloplanctis alpha-amylase give insights into cold adaptation at a molecular level.
  Structure, 6, 1503-1516.
PDB code: 1b0i
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
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.