spacer
spacer

PDBsum entry 1dgd
Go to PDB code: 
protein ligands metals links
Lyase PDB id
1dgd

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chain
431 a.a. *
Ligands
PLP
MES
Metals
_NA
_LI
Waters ×99
* Residue conservation analysis
PDB id:
1dgd
Name: Lyase
Title: An alkali metal ion size-dependent switch in the active site structure of dialkylglycine decarboxylase
Structure: Dialkylglycine decarboxylase. Chain: a. Engineered: yes
Source: Burkholderia cepacia. Organism_taxid: 292
Biol. unit: Tetramer (from PQS)
Resolution:
2.80Å     R-factor:   0.178    
Authors: E.Hohenester,J.N.Jansonius
Key ref:
E.Hohenester et al. (1994). An alkali metal ion size-dependent switch in the active site structure of dialkylglycine decarboxylase. Biochemistry, 33, 13561-13570. PubMed id: 7947767 DOI: 10.1021/bi00250a008
Date:
29-Jun-94     Release date:   30-Sep-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
P16932  (DGDA_BURCE) -  2,2-dialkylglycine decarboxylase from Burkholderia cepacia
Seq:
Struc: 		433 a.a.
431 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.4.1.1.64  - 2,2-dialkylglycine decarboxylase (pyruvate).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2,2-dialkylglycine + pyruvate + H+ = dialkyl ketone + L-alanine + CO2
2,2-dialkylglycine
 + pyruvate
 + H(+)
 = dialkyl ketone
 + L-alanine
 + CO2
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Bound ligand (Het Group name = PLP) matches with 93.75% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1021/bi00250a008 Biochemistry 33:13561-13570 (1994)
PubMed id: 7947767  
 
 
An alkali metal ion size-dependent switch in the active site structure of dialkylglycine decarboxylase.
E.Hohenester, J.W.Keller, J.N.Jansonius.
 
  ABSTRACT  
 
The pyridoxal 5'-phosphate-dependent enzyme dialkylglycine decarboxylase (DGD) is activated by K+ and Rb+ ions, whereas Li+ and Na+ ions are inhibitory. A binding site for alkali metal ions close to the active site (site 1) was discovered in the crystal structure of DGD, and an exchange of K+ for Na+ at this site was shown to affect the conformation of two active site residues [Toney, M. D., Hohenester, E., Cowan, S. W., & Jansonius, J. N. (1993) Science 261, 756-759]. We have investigated the effects of alkali metal ions on DGD activity and have determined the crystal structures at 2.8 A resolution of DGD with Li+ and Rb+ bound at site 1. Due to the weak scattering of the Li+ ion, its position had to be modeled using information from small molecule structures. A comparison of the DGD structures with Li+, Na+, K+, and Rb+ bound at site 1 reveals a striking correlation between active site structure and enzymatic activity. The small, inhibitory ions Li+ and Na+ are accommodated by replacing two protein-derived ligands of the larger, activating ions K+ and Rb+ by a single water molecule. This actuates a two-state structural switch between active and inactive enzyme that involves a concerted reorientation of the active site residues Ser80 and Tyr301 and a small change in the quaternary structure of the DGD tetramer. An important role of the essential K+ ion in both cofactor binding and the organization of a catalytically competent active site structure is proposed. In the structure of DGD with Rb+ bound at site 1, a second Rb+ ion has partially replaced the structural Na+ ion at metal binding site 2 on the surface of the DGD molecule, without significantly altering the protein structure. In contrast to Na+, the Rb+ ion is bound with unfavorable geometry, and it is proposed that the rigid site 2 structure results in a pronounced selectivity for Na+ ions.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
15162493 A.Berchanski, B.Shapira, and M.Eisenstein (2004).
Hydrophobic complementarity in protein-protein docking.
  Proteins, 56, 130-142.  
15498941 A.Paiardini, F.Bossa, and S.Pascarella (2004).
Evolutionarily conserved regions and hydrophobic contacts at the superfamily level: The case of the fold-type I, pyridoxal-5'-phosphate-dependent enzymes.
  Protein Sci, 13, 2992-3005.  
14635124 A.Berchanski, and M.Eisenstein (2003).
Construction of molecular assemblies via docking: modeling of tetramers with D2 symmetry.
  Proteins, 53, 817-829.  
12682056 N.Lah, J.Lah, I.Zegers, L.Wyns, and J.Messens (2003).
Specific potassium binding stabilizes pI258 arsenate reductase from Staphylococcus aureus.
  J Biol Chem, 278, 24673-24679.  
12842041 W.K.Wang, V.Tereshko, P.Boccuni, D.MacGrogan, S.D.Nimer, and D.J.Patel (2003).
Malignant brain tumor repeats: a three-leaved propeller architecture with ligand/peptide binding pockets.
  Structure, 11, 775-789.
PDB codes: 1oyx 1oz2 1oz3
12119022 C.G.Cheong, J.C.Escalante-Semerena, and I.Rayment (2002).
Structural studies of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica: the apo, substrate, and product-aldimine complexes.
  Biochemistry, 41, 9079-9089.
PDB codes: 1l4n 1l5f 1l5k 1l5l 1l5m 1l5n 1lc5 1lc7 1lc8
12169596 J.Jin, A.A.Guffanti, D.H.Bechhofer, and T.A.Krulwich (2002).
Tet(L) and tet(K) tetracycline-divalent metal/H+ antiporters: characterization of multiple catalytic modes and a mutagenesis approach to differences in their efflux substrate and coupling ion preferences.
  J Bacteriol, 184, 4722-4732.  
11329261 A.Ahmad, M.S.Akhtar, and V.Bhakuni (2001).
Monovalent cation-induced conformational change in glucose oxidase leading to stabilization of the enzyme.
  Biochemistry, 40, 1945-1955.  
11170465 M.D.Toney (2001).
Computational studies on nonenzymatic and enzymatic pyridoxal phosphate catalyzed decarboxylations of 2-aminoisobutyrate.
  Biochemistry, 40, 1378-1384.  
11170464 X.Zhou, X.Jin, R.Medhekar, X.Chen, T.Dieckmann, and M.D.Toney (2001).
Rapid kinetic and isotopic studies on dialkylglycine decarboxylase.
  Biochemistry, 40, 1367-1377.  
10679990 L.C.Ngoka, and M.L.Gross (2000).
Location of alkali metal binding sites in endothelin A selective receptor antagonists, cyclo(D-Trp-D-Asp-Pro-D-Val-Leu) and cyclo(D-Trp-D-Asp-Pro-D-Ile-Leu), from multistep collisionally activated decompositions.
  J Mass Spectrom, 35, 265-276.  
10878101 X.W.Niu, and R.W.Meech (2000).
Potassium inhibition of sodium-activated potassium (K(Na)) channels in guinea-pig ventricular myocytes.
  J Physiol, 526, 81-90.  
10584065 A.Poupon, F.Jebai, G.Labesse, F.Gros, J.Thibault, J.P.Mornon, and M.Krieger (1999).
Structure modelling and site-directed mutagenesis of the rat aromatic L-amino acid pyridoxal 5'-phosphate-dependent decarboxylase: a functional study.
  Proteins, 37, 191-203.  
9890912 X.Zhou, and M.D.Toney (1999).
pH studies on the mechanism of the pyridoxal phosphate-dependent dialkylglycine decarboxylase.
  Biochemistry, 38, 311-320.  
9914259 J.N.Jansonius (1998).
Structure, evolution and action of vitamin B6-dependent enzymes.
  Curr Opin Struct Biol, 8, 759-769.  
9837895 K.D.Schnackerz, and A.Mozzarelli (1998).
Plasticity of the tryptophan synthase active site probed by 31P NMR spectroscopy.
  J Biol Chem, 273, 33247-33253.  
9548963 X.Zhou, S.Kay, and M.D.Toney (1998).
Coexisting kinetically distinguishable forms of dialkylglycine decarboxylase engendered by alkali metal ions.
  Biochemistry, 37, 5761-5769.  
8999910 B.A.Hirayama, D.D.Loo, and E.M.Wright (1997).
Cation effects on protein conformation and transport in the Na+/glucose cotransporter.
  J Biol Chem, 272, 2110-2115.  
9230051 G.Kaim, F.Wehrle, U.Gerike, and P.Dimroth (1997).
Molecular basis for the coupling ion selectivity of F1F0 ATP synthases: probing the liganding groups for Na+ and Li+ in the c subunit of the ATP synthase from Propionigenium modestum.
  Biochemistry, 36, 9185-9194.  
9428713 L.Ramírez-Silva, J.Oria, A.Gómez-Puyou, and M.Tuena de Gómez-Puyou (1997).
The contribution of water to the selectivity of pyruvate kinase for Na+ and K+.
  Eur J Biochem, 250, 583-589.  
9360597 R.MacKinnon, and D.A.Doyle (1997).
Prokaryotes offer hope for potassium channel structural studies.
  Nat Struct Biol, 4, 877-879.  
8576135 B.Xiang, J.C.Taylor, and G.D.Markham (1996).
Monovalent cation activation and kinetic mechanism of inosine 5'-monophosphate dehydrogenase.
  J Biol Chem, 271, 1435-1440.  
8688415 E.R.Guinto, and E.Di Cera (1996).
Large heat capacity change in a protein-monovalent cation interaction.
  Biochemistry, 35, 8800-8804.  
8968582 I.Favre, E.Moczydlowski, and L.Schild (1996).
On the structural basis for ionic selectivity among Na+, K+, and Ca2+ in the voltage-gated sodium channel.
  Biophys J, 71, 3110-3125.  
8672457 S.Rhee, K.D.Parris, S.A.Ahmed, E.W.Miles, and D.R.Davies (1996).
Exchange of K+ or Cs+ for Na+ induces local and long-range changes in the three-dimensional structure of the tryptophan synthase alpha2beta2 complex.
  Biochemistry, 35, 4211-4221.
PDB codes: 1bks 1ttp 1ttq
7756539 E.Di Cera (1995).
Preferential interactions: it's as simple as 1, 2, 3.
  Biophys J, 68, 727-728.  
7538310 R.MacKinnon (1995).
Pore loops: an emerging theme in ion channel structure.
  Neuron, 14, 889-892.  
7615535 S.B.Ruvinov, S.A.Ahmed, P.McPhie, and E.W.Miles (1995).
Monovalent cations partially repair a conformational defect in a mutant tryptophan synthase alpha 2 beta 2 complex (beta-E109A).
  J Biol Chem, 270, 17333-17338.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

spacer
spacer