1ZC9

The crystal structure of dialkylglycine decarboxylase complex with pyridoxamine 5-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Role of q52 in catalysis of decarboxylation and transamination in dialkylglycine decarboxylase.

Fogle, E.J.Liu, W.Woon, S.T.Keller, J.W.Toney, M.D.

(2005) Biochemistry 44: 16392-16404

  • DOI: 10.1021/bi051475b
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dialkylglycine decarboxylase (DGD) is a pyridoxal phosphate dependent enzyme that catalyzes both decarboxylation and transamination in its normal catalytic cycle. DGD uses stereoelectronic effects to control its unusual reaction specificity. X-ray cr ...

    Dialkylglycine decarboxylase (DGD) is a pyridoxal phosphate dependent enzyme that catalyzes both decarboxylation and transamination in its normal catalytic cycle. DGD uses stereoelectronic effects to control its unusual reaction specificity. X-ray crystallographic structures of DGD suggest that Q52 is important in maintaining the substrate carboxylate in a stereoelectronically activated position. Here, the X-ray structures of the Q52A mutant and the wild type (WT) DGD-PMP enzymes are presented, as is the analysis of steady-state and half-reaction kinetics of three Q52 mutants (Q52A, Q52I, and Q52E). As expected if stereoelectronic effects are important to catalysis, the steady-state rate of decarboxylation for all three mutants has decreased significantly compared to that of WT. Q52A exhibits an approximately 85-fold decrease in k(cat) relative to that of WT. The rate of the decarboxylation half-reaction decreases approximately 10(5)-fold in Q52I and approximately 10(4)-fold in Q52E compared to that of WT. Transamination half-reaction kinetics show that Q52A and Q52I have greatly reduced rates compared to that of WT and are seriously impaired in pyridoxamine phosphate (PMP) binding, with K(PMP) at least 50-100-fold greater than that of WT. The larger effect on the rate of l-alanine transamination than of pyruvate transamination in these mutants suggests that the rate decrease is the result of selective destabilization of the PMP form of the enzyme in these mutants. Q52E exhibits near-WT rates for transamination of both pyruvate and l-alanine. Substrate binding has been greatly weakened in Q52E with apparent dissociation constants at least 100-fold greater than that of WT. The rate of decarboxylation in Q52E allows the energetic contribution of stereoelectronic effects, DeltaG(stereoelectronic), to be estimated to be -7.3 kcal/mol for DGD.


    Organizational Affiliation

    Department of Chemistry, University of California, Davis, California 95616, UA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2,2-dialkylglycine decarboxylase
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

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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
PMP
Query on PMP

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Download CCD File 
A
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
PYRIDOXAMINE-5'-PHOSPHATE
C8 H13 N2 O5 P
ZMJGSOSNSPKHNH-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PMPKd: 600000 nM BINDINGMOAD
PMPKd: 600000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.199 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 151.652α = 90.00
b = 151.652β = 90.00
c = 85.044γ = 120.00
Software Package:
Software NamePurpose
PROTEUM PLUSdata reduction
CNSrefinement
PROTEUM PLUSdata collection
PROTEUM PLUSdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-03
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance