Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 215.46 kDa 
• Atom Count: 15465 
• Residue Count: 1878 
• Unique protein chains: 1

4LGL

Crystal Structure of Glycine Decarboxylase P-protein from Synechocystis sp. PCC 6803, apo form

• DOI: 10.2210/pdb4LGL/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Synechocystis sp. PCC 6803 substr. Kazusa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-06-28 Released: 2013-10-16 
• Deposition Author(s): Hasse, D., Andersson, E., Carlsson, G., Masloboy, A., Hagemann, M., Bauwe, H., Andersson, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.192 
• R-Value Work: 0.161 
• R-Value Observed: 0.162 

Literature

Structure of the Homodimeric Glycine Decarboxylase P-protein from Synechocystis sp. PCC 6803 Suggests a Mechanism for Redox Regulation.

Hasse, D., Andersson, E., Carlsson, G., Masloboy, A., Hagemann, M., Bauwe, H., Andersson, I.

(2013) J Biol Chem 288: 35333-35345

• PubMed: 24121504 
• DOI: 10.1074/jbc.M113.509976
• Primary Citation of Related Structures:  
  4LGL, 4LHC, 4LHD


• PubMed Abstract: 
  

Glycine decarboxylase, or P-protein, is a pyridoxal 5'-phosphate (PLP)-dependent enzyme in one-carbon metabolism of all organisms, in the glycine and serine catabolism of vertebrates, and in the photorespiratory pathway of oxygenic phototrophs. P-protein from the cyanobacterium Synechocystis sp. PCC 6803 is an α2 homodimer with high homology to eukaryotic P-proteins. The crystal structure of the apoenzyme shows the C terminus locked in a closed conformation by a disulfide bond between Cys(972) in the C terminus and Cys(353) located in the active site. The presence of the disulfide bridge isolates the active site from solvent and hinders the binding of PLP and glycine in the active site. Variants produced by substitution of Cys(972) and Cys(353) by Ser using site-directed mutagenesis have distinctly lower specific activities, supporting the crucial role of these highly conserved redox-sensitive amino acid residues for P-protein activity. Reduction of the 353-972 disulfide releases the C terminus and allows access to the active site. PLP and the substrate glycine bind in the active site of this reduced enzyme and appear to cause further conformational changes involving a flexible surface loop. The observation of the disulfide bond that acts to stabilize the closed form suggests a molecular mechanism for the redox-dependent activation of glycine decarboxylase observed earlier.

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Related Citations: 

• Crystallization and preliminary X-ray diffraction analyses of the homodimeric glycine decarboxylase (P-protein) from the cyanobacterium Synechocystis sp. PCC 6803.
  Hasse, D., Hagemann, M., Andersson, I., Bauwe, H.
  (2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 187

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Organizational Affiliation: 

From the Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine dehydrogenase [decarboxylating]	A, B	983	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0  Gene Names: gcvP, slr0293 EC: 1.4.4.2
Find proteins for P74416 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore P74416  Go to UniProtKB:  P74416

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	A, B	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
CL	A, B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A,B	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.192 
• R-Value Work: 0.161 
• R-Value Observed: 0.162 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.299	α = 90
b = 135.814	β = 90
c = 179.08	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-06-28 
• Released Date: 2013-10-16 
Deposition Author(s): Hasse, D., Andersson, E., Carlsson, G., Masloboy, A., Hagemann, M., Bauwe, H., Andersson, I.

Revision History 

• Version 1.0: 2013-10-16
  Type: Initial release
  
• Version 1.1: 2013-10-30
  Changes: Database references
• Version 1.2: 2013-12-25
  Changes: Database references