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PDBsum entry 1b9z

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protein ligands metals links
Hydrolase PDB id
1b9z
Jmol
Contents
Protein chain
516 a.a. *
Ligands
MAL ×4
ACT
SO4
Metals
_CA
Waters ×275
* Residue conservation analysis
PDB id:
1b9z
Name: Hydrolase
Title: Bacillus cereus beta-amylase complexed with maltose
Structure: Protein (beta-amylase). Chain: a. Engineered: yes
Source: Bacillus cereus. Organism_taxid: 1396. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.10Å     R-factor:   0.170     R-free:   0.220
Authors: B.Mikami,M.Adachi,T.Kage,E.Sarikaya,T.Nanmori,R.Shinke, S.Utsumi
Key ref:
B.Mikami et al. (1999). Structure of raw starch-digesting Bacillus cereus beta-amylase complexed with maltose. Biochemistry, 38, 7050-7061. PubMed id: 10353816 DOI: 10.1021/bi9829377
Date:
06-Mar-99     Release date:   15-Mar-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P36924  (AMYB_BACCE) -  Beta-amylase
Seq:
Struc:
 
Seq:
Struc:
546 a.a.
516 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   4 terms 
  Biochemical function     starch binding     5 terms  

 

 
DOI no: 10.1021/bi9829377 Biochemistry 38:7050-7061 (1999)
PubMed id: 10353816  
 
 
Structure of raw starch-digesting Bacillus cereus beta-amylase complexed with maltose.
B.Mikami, M.Adachi, T.Kage, E.Sarikaya, T.Nanmori, R.Shinke, S.Utsumi.
 
  ABSTRACT  
 
The crystals of beta-amylase from Bacillus cereus belong to space group P21 with the following cell dimensions: a = 57.70 A, b = 92.87 A, c = 65.93 A, and beta =101.95 degrees. The structures of free and maltose-bound beta-amylases were determined by X-ray crystallography at 2.1 and 2.5 A with R-factors of 0.170 and 0.164, respectively. The final model of the maltose-bound form comprises 516 amino acid residues, four maltose molecules, 275 water molecules, one Ca2+, one acetate, and one sulfate ion. The enzyme consists of a core (beta/alpha)8-barrel domain (residues 5-434) and a C-terminal starch-binding domain (residues 435-613). Besides the active site in the core where two maltose molecules are bound in tandem, two novel maltose-binding sites were found in the core L4 region and in the C-terminal domain. The structure of the core domain is similar to that of soybean beta-amylase except for the L4 maltose-binding site, whereas the C-terminal domain has the same secondary structure as domain E of cyclodextrin glucosyltransferase. These two maltose-binding sites are 32-36 A apart from the active site. These results indicate that the ability of B. cereus beta-amylase to digest raw starch can be attributed to the additional two maltose-binding sites.
 

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
21261814 S.Cuyvers, E.Dornez, M.N.Rezaei, A.Pollet, J.A.Delcour, and C.M.Courtin (2011).
Secondary substrate binding strongly affects activity and binding affinity of Bacillus subtilis and Aspergillus niger GH11 xylanases.
  FEBS J, 278, 1098-1111.  
19277485 H.Sun, P.Zhao, X.Ge, Y.Xia, Z.Hao, J.Liu, and M.Peng (2010).
Recent advances in microbial raw starch degrading enzymes.
  Appl Biochem Biotechnol, 160, 988.  
19682075 C.Christiansen, M.Abou Hachem, S.Janecek, A.Viksø-Nielsen, A.Blennow, and B.Svensson (2009).
The carbohydrate-binding module family 20--diversity, structure, and function.
  FEBS J, 276, 5006-5029.  
18981178 M.Kitamura, M.Okuyama, F.Tanzawa, H.Mori, Y.Kitago, N.Watanabe, A.Kimura, I.Tanaka, and M.Yao (2008).
Structural and functional analysis of a glycoside hydrolase family 97 enzyme from Bacteroides thetaiotaomicron.
  J Biol Chem, 283, 36328-36337.
PDB codes: 2d73 2zq0
16262690 M.Machovic, B.Svensson, E.A.MacGregor, and S.Janecek (2005).
A new clan of CBM families based on bioinformatics of starch-binding domains from families CBM20 and CBM21.
  FEBS J, 272, 5497-5513.  
15640201 R.Rodríguez-Sanoja, B.Ruiz, J.P.Guyot, and S.Sanchez (2005).
Starch-binding domain affects catalysis in two Lactobacillus alpha-amylases.
  Appl Environ Microbiol, 71, 297-302.  
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
12581203 S.Janecek, B.Svensson, and E.A.MacGregor (2003).
Relation between domain evolution, specificity, and taxonomy of the alpha-amylase family members containing a C-terminal starch-binding domain.
  Eur J Biochem, 270, 635-645.  
12486711 T.I.Zarembinski, Y.Kim, K.Peterson, D.Christendat, A.Dharamsi, C.H.Arrowsmith, A.M.Edwards, and A.Joachimiak (2003).
Deep trefoil knot implicated in RNA binding found in an archaebacterial protein.
  Proteins, 50, 177-183.
PDB code: 1k3r
11272837 Y.Mezaki, Y.Katsuya, M.Kubota, and Y.Matsuura (2001).
Crystallization and structural analysis of intact maltotetraose-forming exo-amylase from Pseudomonas stutzeri.
  Biosci Biotechnol Biochem, 65, 222-225.
PDB code: 1gcy
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
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.