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PDBsum entry 1jd7

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protein metals links
Hydrolase PDB id
1jd7
Jmol
Contents
Protein chain
448 a.a. *
Metals
_CL ×2
_CA
Waters ×385
* Residue conservation analysis
PDB id:
1jd7
Name: Hydrolase
Title: Crystal structure analysis of the mutant k300r of pseudoalteromonas haloplanctis alpha-amylase
Structure: Alpha-amylase. Chain: a. Engineered: yes. Mutation: yes
Source: Pseudoalteromonas haloplanktis. Organism_taxid: 228. Strain: a23. Gene: amy. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.25Å     R-factor:   0.179     R-free:   0.215
Authors: N.Aghajari,R.Haser
Key ref:
N.Aghajari et al. (2002). Structural basis of alpha-amylase activation by chloride. Protein Sci, 11, 1435-1441. PubMed id: 12021442 DOI: 10.1110/ps.0202602
Date:
13-Jun-01     Release date:   18-Sep-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P29957  (AMY_PSEHA) -  Alpha-amylase
Seq:
Struc:
 
Seq:
Struc:
669 a.a.
448 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     carbohydrate metabolic process   1 term 
  Biochemical function     catalytic activity     2 terms  

 

 
DOI no: 10.1110/ps.0202602 Protein Sci 11:1435-1441 (2002)
PubMed id: 12021442  
 
 
Structural basis of alpha-amylase activation by chloride.
N.Aghajari, G.Feller, C.Gerday, R.Haser.
 
  ABSTRACT  
 
To further investigate the mechanism and function of allosteric activation by chloride in some alpha-amylases, the structure of the bacterial alpha-amylase from the psychrophilic micro-organism Pseudoalteromonas haloplanktis in complex with nitrate has been solved at 2.1 A degrees, as well as the structure of the mutants Lys300Gln (2.5 A degrees ) and Lys300Arg (2.25 A degrees ). Nitrate binds strongly to alpha-amylase but is a weak activator. Mutation of the critical chloride ligand Lys300 into Gln results in a chloride-independent enzyme, whereas the mutation into Arg mimics the binding site as is found in animal alpha-amylases with, however, a lower affinity for chloride. These structures reveal that the triangular conformation of the chloride ligands and the nearly equatorial coordination allow the perfect accommodation of planar trigonal monovalent anions such as NO3-, explaining their unusual strong binding. It is also shown that a localized negative charge such as that of Cl-, rather than a delocalized charge as in the case of nitrate, is essential for maximal activation. The chloride-free mutant Lys300Gln indicates that chloride is not mandatory for the catalytic mechanism but strongly increases the reactivity at the active site. Disappearance of the putative catalytic water molecule in this weakly active mutant supports the view that chloride helps to polarize the hydrolytic water molecule and enhances the rate of the second step in the catalytic reaction.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Schematic representation of the chloride binding site and of the interaction network with active site residues (adapted from Qian et al. 1994). The essential catalytic residues are in italics. Chloride ligands are Lys300(337), Arg172(195), Asn262(298), and H[2]O1003(525); active site residues are Glu200(233), Asp174(197), and Asp264(300) the putative catalytic water molecule H[2]O1004(cat) and His263(299). Numbers in parentheses refer to pig pancreas -amylase.
Figure 2.
Fig. 2. Superposition of the chloride binding site in P. haloplanktis -amylase (AHA), in green, complex AHA/nitrate in blue, mutant K300Q in yellow, and mutant K300R in pink.
 
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2002, 11, 1435-1441) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19329633 L.J.Gourlay, I.Santi, A.Pezzicoli, G.Grandi, M.Soriani, and M.Bolognesi (2009).
Group B streptococcus pullulanase crystal structures in the context of a novel strategy for vaccine development.
  J Bacteriol, 191, 3544-3552.
PDB codes: 3faw 3fax
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.  
18613721 S.Cheluvaraja, M.Mihailescu, and H.Meirovitch (2008).
Entropy and free energy of a mobile protein loop in explicit water.
  J Phys Chem B, 112, 9512-9522.  
17310272 S.Srimathi, G.Jayaraman, G.Feller, B.Danielsson, and P.R.Narayanan (2007).
Intrinsic halotolerance of the psychrophilic alpha-amylase from Pseudoalteromonas haloplanktis.
  Extremophiles, 11, 505-515.  
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
15216418 T.Kuroda, H.Bihler, E.Bashi, C.L.Slayman, and A.Rivetta (2004).
Chloride channel function in the yeast TRK-potassium transporters.
  J Membr Biol, 198, 177-192.  
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.