1D7V

CRYSTAL STRUCTURE OF THE COMPLEX OF 2,2-DIALKYLGLYCINE DECARBOXYLASE WITH NMA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of dialkylglycine decarboxylase inhibitor complexes.

Malashkevich, V.N.Strop, P.Keller, J.W.Jansonius, J.N.Toney, M.D.

(1999) J.Mol.Biol. 294: 193-200

  • DOI: 10.1006/jmbi.1999.3254
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structures of four inhibitor complexes of dialkylglycine decarboxylase are reported. The enzyme does not undergo a domain closure, as does aspartate aminotransferase, upon inhibitor binding. Two active-site conformations have been observe ...

    The crystal structures of four inhibitor complexes of dialkylglycine decarboxylase are reported. The enzyme does not undergo a domain closure, as does aspartate aminotransferase, upon inhibitor binding. Two active-site conformations have been observed in previous structures that differ in alkali metal ion content, and two active-site conformations have been shown to coexist in solution when a single type of metal ion is present. There is no indication of coexisting conformers in the structures reported here or in the previously reported structures, and the observed conformation is that expected based on the presence of potassium in the enzyme. Thus, although two active-site conformations coexist in solution, a single conformation, corresponding to the more active enzyme, predominates in the crystal. The structure of 1-aminocyclopropane-1-carboxylate bound in the active site shows the aldimine double bond to the pyridoxal phosphate cofactor to be fully out of the plane of the coenzyme ring, whereas the Calpha-CO2(-) bond lies close to it. This provides an explanation for the observed lack of decarboxylation reactivity with this amino acid. The carboxylate groups of both 1-aminocyclopropane-1-carboxylate and 5'-phosphopyridoxyl-2-methylalanine interact with Ser215 and Arg406 as previously proposed. This demonstrates structurally that alternative binding modes, which constitute substrate inhibition, occur in the decarboxylation half-reaction. The structures of d and l-cycloserine bound to the active-site show that the l-isomer is deprotonated at C(alpha), presumably by Lys272, while the d-isomer is not. This difference explains the approximately 3000-fold greater potency of the l versus the d-isomer as a competitive inhibitor of dialkylglycine decarboxylase.


    Related Citations: 
    • 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
    • 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.,Vajdos, F.F.
      (1990) J.Biol.Chem. 265: 5531


    Organizational Affiliation

    Department of Structural Biology, Biozentrum University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland. malashkevich@wi.mit.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE))
A
433Burkholderia cepaciaMutation(s): 0 
Gene Names: dgdA
EC: 4.1.1.64
Find proteins for P16932 (Burkholderia cepacia)
Go to UniProtKB:  P16932
Small Molecules
Ligands 3 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
NMA
Query on NMA

Download SDF File 
Download CCD File 
A
N-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-2-METHYLALANINE
N-PYRIDOXYL-2-METHYLALANINE-5-PHOSPHATE
C12 H19 N2 O7 P
NHGDGJKONAZETF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Work: 0.185 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 153.200α = 90.00
b = 153.200β = 90.00
c = 86.900γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
CCP4data scaling
TNTrefinement
MOSFLMdata reduction
ROTAVATAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-11-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description