› 4lhc

X-ray diffraction
1.9Å resolution

Crystal structure of Synechocystis sp. PCC 6803 glycine decarboxylase (P-protein), holo form with pyridoxal-5'-phosphate and glycine

Released:
DOI: 10.2210/pdb4lhc/pdb
PDB entry 4lhc coloured by chain, front view.
PDB entry 4lhc coloured by chain, side view.
PDB entry 4lhc coloured by chain, top view.
Source organism: Synechocystis sp. PCC 6803 substr. Kazusa
Primary publication:
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
J Biol Chem 288 35333-45 (2013)
PMID: 24121504

Function and Biology Details

Reaction catalysed: 
Glycine + [glycine-cleavage complex H protein]-N(6)-lipoyl-L-lysine = [glycine-cleavage complex H protein]-S-aminomethyl-N(6)-dihydrolipoyl-L-lysine + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159938 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glycine dehydrogenase (decarboxylating) Chains: A, B
Molecule details ›
Chains: A, B
Length: 983 amino acids
Theoretical weight: 107.65 KDa
Source organism: Synechocystis sp. PCC 6803 substr. Kazusa
Expression system: Escherichia coli
UniProt:
  • Canonical: P74416 (Residues: 1-983; Coverage: 100%)
Gene names: gcvP, slr0293
Sequence domains:

Ligands and Environments

5 bound ligands:
Ligand GLY 5 x GLY
Ligand BCT 3 x BCT
Ligand PO4 6 x PO4
Ligand EDO 16 x EDO
Ligand BCN 1 x BCN
1 modified residue:
Ligand LLP 2 x LLP

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P321
Unit cell:
a: 160.05Å b: 160.05Å c: 159.833Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.156 0.155 0.186
Expression system: Escherichia coli

Quick links

Citations

2 review citations

The redox control of photorespiration: from biochemical and physiological aspects to biotechnological considerations.
Keech et al. (2017)
1 more

5 mentions without citation

Biochemical and molecular predictors for prognosis in nonketotic hyperglycinemia.
Swanson et al. (2015)
4 more