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PDBsum entry 1byb

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Hydrolase(o-glycosyl) PDB id
1byb
Jmol
Contents
Protein chain
491 a.a. *
Ligands
GLC-GLC-GLC-GLC
SO4
Waters ×332
* Residue conservation analysis
PDB id:
1byb
Name: Hydrolase(o-glycosyl)
Title: Crystal structures of soybean beta-amylase reacted with beta-maltose and maltal: active site components and their apparent role in catalysis
Structure: Beta-amylase. Chain: a. Engineered: yes
Source: Glycine max. Soybean. Organism_taxid: 3847
Resolution:
1.90Å     R-factor:   0.149    
Authors: B.Mikami,M.Degano,E.J.Hehre,J.C.Sacchettini
Key ref:
B.Mikami et al. (1994). Crystal structures of soybean beta-amylase reacted with beta-maltose and maltal: active site components and their apparent roles in catalysis. Biochemistry, 33, 7779-7787. PubMed id: 8011643 DOI: 10.1021/bi00191a005
Date:
25-Jan-94     Release date:   31-Jul-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P10538  (AMYB_SOYBN) -  Beta-amylase
Seq:
Struc:
496 a.a.
491 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.2  - Beta-amylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of 1,4-alpha-glucosidic linkages in polysaccharides so as to remove successive maltose units from the non-reducing ends of the chains.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   3 terms 
  Biochemical function     hydrolase activity     3 terms  

 

 
DOI no: 10.1021/bi00191a005 Biochemistry 33:7779-7787 (1994)
PubMed id: 8011643  
 
 
Crystal structures of soybean beta-amylase reacted with beta-maltose and maltal: active site components and their apparent roles in catalysis.
B.Mikami, M.Degano, E.J.Hehre, J.C.Sacchettini.
 
  ABSTRACT  
 
The crystal structures of catalytically competent soybean beta-amylase, unliganded and bathed with small substrates (beta-maltose, maltal), were determined at 1.9-2.2-A resolution. Two molecules of beta-maltose substrate bind to the protein in tandem, with some maltotetraose enzymic condensation product sharing the same binding sites. The beta-amylase soaked with maltal shows a similar arrangement of two bound molecules of 2-deoxymaltose, the enzymic hydration product. In each case the nonreducing ends of the saccharide ligands are oriented toward the base of the protein's active site pocket. The catalytic center, located between the bound disaccharides and found deeper in the pocket than where the inhibitor alpha-cyclodextrin binds, is characterized by the presence of oppositely disposed carboxyl groups of two conserved glutamic acid residues. The OE2 carboxyl of Glu 186 is below the plane of the penultimate glucose residue (Glc 2) of bound maltotetraose, 2.6 A from the oxygen atom of that ligand's penultimate alpha-1,4-glucosidic linkage. The OE2 carboxyl of Glu 380 lies above the plane of Glc 2, 2.8 A from the O-1 atom of the more deeply bound beta-maltose. Saccharide binding does not alter the spatial coordinates of these two carboxyl groups or the overall conformation of the 57-kDa protein. However, the saccharide complexes of the active enzyme are associated with a significant (10 A) local conformational change in a peptide segment of a loop (L3) that borders the active site pocket.(ABSTRACT TRUNCATED AT 250 WORDS)
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21085740 M.Rejzek, C.E.Stevenson, A.M.Southard, D.Stanley, K.Denyer, A.M.Smith, M.J.Naldrett, D.M.Lawson, and R.A.Field (2011).
Chemical genetics and cereal starch metabolism: structural basis of the non-covalent and covalent inhibition of barley β-amylase.
  Mol Biosyst, 7, 718-730.
PDB codes: 2xff 2xfr 2xfy 2xg9 2xgb 2xgi
15701681 A.T.Laurie, and R.M.Jackson (2005).
Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites.
  Bioinformatics, 21, 1908-1916.  
14638688 A.Hirata, M.Adachi, A.Sekine, Y.N.Kang, S.Utsumi, and B.Mikami (2004).
Structural and enzymatic analysis of soybean beta-amylase mutants with increased pH optimum.
  J Biol Chem, 279, 7287-7295.
PDB codes: 1q6c 1q6d 1q6e 1q6f 1q6g
12738774 T.Bravman, V.Belakhov, D.Solomon, G.Shoham, B.Henrissat, T.Baasov, and Y.Shoham (2003).
Identification of the catalytic residues in family 52 glycoside hydrolase, a beta-xylosidase from Geobacillus stearothermophilus T-6.
  J Biol Chem, 278, 26742-26749.  
12221104 D.Shallom, V.Belakhov, D.Solomon, G.Shoham, T.Baasov, and Y.Shoham (2002).
Detailed kinetic analysis and identification of the nucleophile in alpha-L-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycoside hydrolase.
  J Biol Chem, 277, 43667-43673.  
11733023 E.J.Van Damme, J.Hu, A.Barre, B.Hause, G.Baggerman, P.Rougé, and W.J.Peumans (2001).
Purification, characterization, immunolocalization and structural analysis of the abundant cytoplasmic beta-amylase from Calystegia sepium (hedge bindweed) rhizomes.
  Eur J Biochem, 268, 6263-6273.  
11468361 G.Pujadas, and J.Palau (2001).
Molecular mimicry of substrate oxygen atoms by water molecules in the beta-amylase active site.
  Protein Sci, 10, 1645-1657.  
11358519 G.Zaide, D.Shallom, S.Shulami, G.Zolotnitsky, G.Golan, T.Baasov, G.Shoham, and Y.Shoham (2001).
Biochemical characterization and identification of catalytic residues in alpha-glucuronidase from Bacillus stearothermophilus T-6.
  Eur J Biochem, 268, 3006-3016.  
10842343 W.M.Rockey, A.Laederach, and P.J.Reilly (2000).
Automated docking of alpha-(1-->4)- and alpha-(1-->6)-linked glucosyl trisaccharides and maltopentaose into the soybean beta-amylase active site.
  Proteins, 40, 299-309.  
11080624 Z.Marković-Housley, G.Miglierini, L.Soldatova, P.J.Rizkallah, U.Müller, and T.Schirmer (2000).
Crystal structure of hyaluronidase, a major allergen of bee venom.
  Structure, 8, 1025-1035.
PDB codes: 1fcq 1fcu 1fcv
10584063 A.Laederach, M.K.Dowd, P.M.Coutinho, and P.J.Reilly (1999).
Automated docking of maltose, 2-deoxymaltose, and maltotetraose into the soybean beta-amylase active site.
  Proteins, 37, 166-175.  
  10210191 D.H.Juers, R.E.Huber, and B.W.Matthews (1999).
Structural comparisons of TIM barrel proteins suggest functional and evolutionary relationships between beta-galactosidase and other glycohydrolases.
  Protein Sci, 8, 122-136.  
10089328 T.Yamane, H.Tasaki, F.Matsumoto, A.Suzuki, N.Uozumi, and T.Ashida (1999).
Crystallization and preliminary x-ray analysis of beta-amylase from Bacillus polymyxa.
  Acta Crystallogr D Biol Crystallogr, 55, 898-900.  
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.  
9345621 B.Henrissat, and G.Davies (1997).
Structural and sequence-based classification of glycoside hydrolases.
  Curr Opin Struct Biol, 7, 637-644.  
9309217 F.A.Quiocho, J.C.Spurlino, and L.E.Rodseth (1997).
Extensive features of tight oligosaccharide binding revealed in high-resolution structures of the maltodextrin transport/chemosensory receptor.
  Structure, 5, 997.
PDB codes: 1anf 3mbp 4mbp
  9385643 G.Pujadas, and J.Palau (1997).
Anatomy of a conformational transition of beta-strand 6 in soybean beta-amylase caused by substrate (or inhibitor) binding to the catalytical site.
  Protein Sci, 6, 2409-2417.  
10904554 H.Nakatani (1997).
Monte Carlo simulation of multiple attack mechanism of beta-amylase-catalyzed reaction.
  Biopolymers, 42, 831-836.  
18576090 M.E.Himmel, P.A.Karplus, J.Sakon, W.S.Adney, J.O.Baker, and S.R.Thomas (1997).
Polysaccharide hydrolase folds diversity of structure and convergence of function.
  Appl Biochem Biotechnol, 63, 315-325.  
9145112 M.O'Reilly, K.A.Watson, R.Schinzel, D.Palm, and L.N.Johnson (1997).
Oligosaccharide substrate binding in Escherichia coli maltodextrin phosphorylase.
  Nat Struct Biol, 4, 405-412.
PDB code: 1ahp
8856067 A.Totsuka, and C.Fukazawa (1996).
Functional analysis of Glu380 and Leu383 of soybean beta-amylase. A proposed action mechanism.
  Eur J Biochem, 240, 655-659.  
7777485 C.G.Cheong, S.H.Eom, C.Chang, D.H.Shin, H.K.Song, K.Min, J.H.Moon, K.K.Kim, K.Y.Hwang, and S.W.Suh (1995).
Crystallization, molecular replacement solution, and refinement of tetrameric beta-amylase from sweet potato.
  Proteins, 21, 105-117.
PDB code: 1fa2
  8528065 G.Kreil (1995).
Hyaluronidases--a group of neglected enzymes.
  Protein Sci, 4, 1666-1669.  
8574693 R.J.Woods (1995).
Three-dimensional structures of oligosaccharides.
  Curr Opin Struct Biol, 5, 591-598.  
7712292 J.D.McCarter, and S.G.Withers (1994).
Mechanisms of enzymatic glycoside hydrolysis.
  Curr Opin Struct Biol, 4, 885-892.  
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.