3VM5 | pdb_00003vm5

Recombinant medaka fish alpha-amylase expressed in yeast Pichia pastoris


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.248 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structural and functional characterization of recombinant medaka fish alpha-amylase expressed in yeast Pichia pastoris.

Mizutani, K.Toyoda, M.Otake, Y.Yoshioka, S.Takahashi, N.Mikami, B.

(2012) Biochim Biophys Acta 1824: 954-962

  • DOI: https://doi.org/10.1016/j.bbapap.2012.05.005
  • Primary Citation Related Structures: 
    3VM5

  • PubMed Abstract: 

    The medaka fish α-amylase was expressed and purified. The expression systems were constructed using methylotrophic yeast Pichia pastoris, and the recombinant proteins were secreted into the culture medium. Purified recombinant α-amylase exhibited starch hydrolysis activity. The optimal pH, denaturation temperature, and K(M) and V(max) values were determined; chloride ions were essential for enzyme activity. The purified protein was also crystallized and examined by X-ray crystallography. The structure has the (α/β)(8) barrel fold, as do other known α-amylases, and the overall structure is very similar to the structure of vertebrate (human and pig) α-amylases. A novel expression plasmid was developed. Using this plasmid, high-throughput construction of an expression system by homologous recombination in P. pastoris cells, previously reported for membrane proteins, was successfully applied to the secretory protein.


  • Organizational Affiliation
    • Graduate School of Agriculture, Kyoto University, Kyoto, Japan. kmizutani@kais.kyoto-u.ac.jp

Macromolecule Content 

  • Total Structure Weight: 56.79 kDa 
  • Atom Count: 3,987 
  • Modeled Residue Count: 499 
  • Deposited Residue Count: 505 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
alpha-amylase505Oryzias latipesMutation(s): 0 
EC: 3.2.1.1
UniProt
Find proteins for H2N0D4 (Oryzias latipes)
Explore H2N0D4 
Go to UniProtKB:  H2N0D4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH2N0D4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.248 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.045α = 90
b = 83.045β = 90
c = 174.228γ = 120
Software Package:
Software NamePurpose
Rayonixdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-06
    Type: Initial release
  • Version 1.1: 2013-06-26
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary