1DKA

DIALKYLGLYCINE DECARBOXYLASE STRUCTURE: BIFUNCTIONAL ACTIVE SITE AND ALKALI METAL BINDING SITES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Dialkylglycine decarboxylase structure: bifunctional active site and alkali metal sites.

Toney, M.D.Hohenester, E.Cowan, S.W.Jansonius, J.N.

(1993) Science 261: 756-759

  • Primary Citation of Related Structures:  2DKB

  • PubMed Abstract: 
  • The structure of the bifunctional, pyridoxal phosphate-dependent enzyme dialkylglycine decarboxylase was determined to 2.1-angstrom resolution. Model building suggests that a single cleavage site catalyzes both decarboxylation and transamination by m ...

    The structure of the bifunctional, pyridoxal phosphate-dependent enzyme dialkylglycine decarboxylase was determined to 2.1-angstrom resolution. Model building suggests that a single cleavage site catalyzes both decarboxylation and transamination by maximizing stereoelectronic advantages and providing electrostatic and general base catalysis. The enzyme contains two binding sites for alkali metal ions. One is located near the active site and accounts for the dependence of activity on potassium ions. The other is located at the carboxyl terminus of an alpha helix. These sites help show how proteins can specifically bind alkali metals and how these ions can exert functional effects.


    Related Citations: 
    • Pseudomonas Cepacia 2,2-Dialkylglycine Decarboxylase: Sequence and Expression in Escherichia Coli of Structural and Repressor Genes
      Keller, J.W.,Baurick, K.B.,Rutt, G.C.,O'Malley, M.V.,Sonafrank, N.L.,Reynolds, R.A.,Ebbesson, L.O.E.,Vajdos, F.F.
      (1990) J.Biol.Chem. 265: 5531
    • Crystallization and Preliminary X-Ray Diffraction Studies of Dialkylglycine Decarboxylase, a Decarboxylating Transaminase
      Toney, M.D.,Keller, J.W.,Pauptit, R.A.,Jaeger, J.,Wise, M.K.,Sauder, U.,Jansonius, J.N.
      (1991) J.Mol.Biol. 222: 873


    Organizational Affiliation

    Department of Structural Biology, University of Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE)
A
433Burkholderia cepaciaGene Names: dgdA
EC: 4.1.1.64
Find proteins for P16932 (Burkholderia cepacia)
Go to UniProtKB:  P16932
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
PLP
Query on PLP

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Download CCD File 
A
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

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Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 152.700α = 90.00
b = 152.700β = 90.00
c = 86.600γ = 120.00
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-10-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other