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PDBsum entry 2b5d

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protein links
Hydrolase PDB id
2b5d
Jmol
Contents
Protein chain
518 a.a. *
Waters ×317
* Residue conservation analysis
PDB id:
2b5d
Name: Hydrolase
Title: Crystal structure of the novel alpha-amylase amyc from therm maritima
Structure: Alpha-amylase. Chain: x. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 243274. Strain: msb8. Gene: tm1438. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.20Å     R-factor:   0.221     R-free:   0.257
Authors: A.Dickmanns,M.Ballschmiter,W.Liebl,R.Ficner
Key ref:
A.Dickmanns et al. (2006). Structure of the novel alpha-amylase AmyC from Thermotoga maritima. Acta Crystallogr D Biol Crystallogr, 62, 262-270. PubMed id: 16510973 DOI: 10.1107/S0907444905041363
Date:
28-Sep-05     Release date:   07-Mar-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
No UniProt id for this chain
Struc: 518 a.a.
Key:    Secondary structure  CATH domain

 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     carbohydrate metabolic process   1 term 
  Biochemical function     catalytic activity     1 term  

 

 
DOI no: 10.1107/S0907444905041363 Acta Crystallogr D Biol Crystallogr 62:262-270 (2006)
PubMed id: 16510973  
 
 
Structure of the novel alpha-amylase AmyC from Thermotoga maritima.
A.Dickmanns, M.Ballschmiter, W.Liebl, R.Ficner.
 
  ABSTRACT  
 
alpha-Amylases are essential enzymes in alpha-glucan metabolism and catalyse the hydrolysis of long sugar polymers such as amylose and starch. The crystal structure of a previously unidentified amylase (AmyC) from the hyperthermophilic organism Thermotoga maritima was determined at 2.2 A resolution by means of MAD. AmyC lacks sequence similarity to canonical alpha-amylases, which belong to glycosyl hydrolase families 13, 70 and 77, but exhibits significant similarity to a group of as yet uncharacterized proteins in COG1543 and is related to glycerol hydrolase family 57 (GH-57). AmyC reveals features that are characteristic of alpha-amylases, such as a distorted TIM-barrel structure formed by seven beta-strands and alpha-helices (domain A), and two additional but less well conserved domains. The latter are domain B, which contains three helices inserted in the TIM-barrel after beta-sheet 2, and domain C, a five-helix region at the C-terminus. Interestingly, despite moderate sequence homology, structure comparison revealed significant similarities to a member of GH-57 with known three-dimensional structure, Thermococcus litoralis 4-glucanotransferase, and an even higher similarity to a structure of an enzyme of unknown function from Thermus thermophilus.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 AmyC shows the characteristics of a functional amylase. (a) A Lineweaver-Burk diagram showing the kinetics of the hydrolysis of starch by AmyC allows the calculation of a K[m] value of 1.1 mg ml-1 and a V[max] of 1.3 U mg-1. (b) AmyC activity is inhibited by the classical amylase inhibitor acarbose. The activity of Amy C is reduced to 25 or 20% using a 31-fold or 77-fold excess of acarbose, respectively.
 
  The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2006, 62, 262-270) copyright 2006.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21104698 C.R.Santos, C.C.Tonoli, D.M.Trindade, C.Betzel, H.Takata, T.Kuriki, T.Kanai, T.Imanaka, R.K.Arni, and M.T.Murakami (2011).
Structural basis for branching-enzyme activity of glycoside hydrolase family 57: structure and stability studies of a novel branching enzyme from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1.
  Proteins, 79, 547-557.
PDB codes: 3n8t 3n92 3n98
17064285 S.B.Conners, E.F.Mongodin, M.R.Johnson, C.I.Montero, K.E.Nelson, and R.M.Kelly (2006).
Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species.
  FEMS Microbiol Rev, 30, 872-905.  
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.