spacer
spacer
Go to PDB code: 
protein metals links
Hydrolase PDB id
1wza
Jmol
Contents
Protein chain
488 a.a. *
Metals
_CA ×2
Waters ×551
* Residue conservation analysis
PDB id:
1wza
Name: Hydrolase
Title: Crystal structure of alpha-amylase from h.Orenii
Structure: Alpha-amylase a. Chain: a. Fragment: residues 28-515. Engineered: yes. Other_details: halophilic and thermophilic
Source: Halothermothrix orenii. Organism_taxid: 31909. Gene: amya. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.60Å     R-factor:   0.186     R-free:   0.209
Authors: N.Sivakumar,K.Swaminathan,N.Li
Key ref:
N.Sivakumar et al. (2006). Crystal structure of AmyA lacks acidic surface and provide insights into protein stability at poly-extreme condition. FEBS Lett, 580, 2646-2652. PubMed id: 16647060 DOI: 10.1016/j.febslet.2006.04.017
Date:
03-Mar-05     Release date:   11-Apr-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q8GPL8  (Q8GPL8_9FIRM) -  Alpha-amylase A
Seq:
Struc: 		515 a.a.
488 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     catalytic activity     2 terms  

 

 
DOI no: 10.1016/j.febslet.2006.04.017 FEBS Lett 580:2646-2652 (2006)
PubMed id: 16647060  
 
 
Crystal structure of AmyA lacks acidic surface and provide insights into protein stability at poly-extreme condition.
N.Sivakumar, N.Li, J.W.Tang, B.K.Patel, K.Swaminathan.
 
  ABSTRACT  
 
Here we report the first crystal structure of a protein, AmyA, a secretory alpha-amylase isolated from Halothermothrix orenii, which is both halophilic and thermophilic. The crystal structure was determined at 1.6 A resolution. AmyA lacks the conserved acidic surface, which is considered essential for protein stability at high salinity. Sedimentation velocity and CD experiments on AmyA reveal the formation of unique reversible poly-dispersed oligomers that show unusually high thermal stability. These studies provide valuable insight into the structural elements that contribute to the stability of AmyA at both physical and chemical extremes and their functional implications.
 
  Selected figure(s)  
 
Figure 1.
 
  The above figure is reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (2006, 580, 2646-2652) copyright 2006.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21539921 F.Liu, J.Xiong, S.Kumar, C.Yang, S.Ge, S.Li, N.Xia, and K.Swaminathan (2011).
Structural and biophysical characterization of Mycobacterium tuberculosis dodecin Rv1498A.
  J Struct Biol, 175, 31-38.
PDB code: 3oqt
20871989 R.Yamaguchi, H.Tokunaga, M.Ishibashi, T.Arakawa, and M.Tokunaga (2011).
Salt-dependent thermo-reversible α-amylase: cloning and characterization of halophilic α-amylase from moderately halophilic bacterium, Kocuria varians.
  Appl Microbiol Biotechnol, 89, 673-684.  
20177823 M.Ghollasi, K.Khajeh, H.Naderi-Manesh, and A.Ghasemi (2010).
Engineering of a Bacillus alpha-amylase with improved thermostability and calcium independency.
  Appl Biochem Biotechnol, 162, 444-459.  
20159465 N.M.Koropatkin, and T.J.Smith (2010).
SusG: a unique cell-membrane-associated alpha-amylase from a prominent human gut symbiont targets complex starch molecules.
  Structure, 18, 200-215.
PDB codes: 3k8k 3k8l 3k8m
19698123 J.A.Winter, P.Christofi, S.Morroll, and K.A.Bunting (2009).
The crystal structure of Haloferax volcanii proliferating cell nuclear antigen reveals unique surface charge characteristics due to halophilic adaptation.
  BMC Struct Biol, 9, 55.
PDB code: 3ifv
19145256 K.Mavromatis, N.Ivanova, I.Anderson, A.Lykidis, S.D.Hooper, H.Sun, V.Kunin, A.Lapidus, P.Hugenholtz, B.Patel, and N.C.Kyrpides (2009).
Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii.
  PLoS ONE, 4, e4192.  
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.  
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.