1MXG

Crystal Strucutre of a (Ca,Zn)-dependent alpha-amylase from the hyperthermophilic archaeon Pyrococcus woesei in complex with acarbose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Differential Regulation of a Hyperthermophilic alpha-Amylase with a Novel (Ca,Zn) Two-metal Center by Zinc

Linden, A.Mayans, O.Meyer-Klaucke, W.Antranikian, G.Wilmanns, M.

(2003) J.Biol.Chem. 278: 9875-9884

  • DOI: 10.1074/jbc.M211339200
  • Primary Citation of Related Structures:  1MWO, 1MXD

  • PubMed Abstract: 
  • The crystal structure of the alpha-amylase from the hyperthermophilic archaeon Pyrococcus woesei was solved in the presence of three inhibitors: acarbose, Tris, and zinc. In the absence of exogenous metals, this alpha-amylase bound 1 and 4 molar eq o ...

    The crystal structure of the alpha-amylase from the hyperthermophilic archaeon Pyrococcus woesei was solved in the presence of three inhibitors: acarbose, Tris, and zinc. In the absence of exogenous metals, this alpha-amylase bound 1 and 4 molar eq of zinc and calcium, respectively. The structure reveals a novel, activating, two-metal (Ca,Zn)-binding site and a second inhibitory zinc-binding site that is found in the -1 sugar-binding pocket within the active site. The data resolve the apparent paradox between the zinc requirement for catalytic activity and its strong inhibitory effect when added in molar excess. They provide a rationale as to why this alpha-amylase, in contrast to commercially available alpha-amylases, does not require the addition of metal ions for full catalytic activity, suggesting it as an ideal target to maximize the efficiency of industrial processes like liquefaction of starch.


    Organizational Affiliation

    European Molecular Biology Laboratory, Notkestrasse 85, D-22603 Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
alpha amylase
A
435Pyrococcus woeseiGene Names: amyA
EC: 3.2.1.1
Find proteins for Q7LYT7 (Pyrococcus woesei)
Go to UniProtKB:  Q7LYT7
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ETE
Query on ETE

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A
2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C9 H20 O5
ZNYRFEPBTVGZDN-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
ACR
Query on ACR

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A
ALPHA-ACARBOSE
1,4-DEOXY-4-((5-HYDROXYMETHYL-2,3,4-TRIHYDROXYCYCLOHEX-5,6-ENYL)AMINO)FRUCTOSE
C25 H43 N O18
XUFXOAAUWZOOIT-WVJZLWNXSA-N
 Ligand Interaction
TRS
Query on TRS

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Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
EOH
Query on EOH

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A
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.480α = 90.00
b = 76.507β = 90.00
c = 136.455γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-10
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance