› 1wyt

X-ray diffraction
2.4Å resolution

Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in apo form

Released:
DOI: 10.2210/pdb1wyt/pdb
PDB entry 1wyt coloured by chain, front view.
PDB entry 1wyt coloured by chain, side view.
PDB entry 1wyt coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia.
Nakai T, Nakagawa N, Maoka N, Masui R, Kuramitsu S, Kamiya N
EMBO J 24 1523-36 (2005)
PMID: 15791207

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 domain:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-178118 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Probable glycine dehydrogenase (decarboxylating) subunit 1 Chains: A, C
Molecule details ›
Chains: A, C
Length: 438 amino acids
Theoretical weight: 47.17 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5SKW8 (Residues: 1-438; Coverage: 100%)
Gene names: TTHA0525, gcvPA
Sequence domains: Glycine cleavage system P-protein
Structure domains:
Probable glycine dehydrogenase (decarboxylating) subunit 2 Chains: B, D
Molecule details ›
Chains: B, D
Length: 474 amino acids
Theoretical weight: 52.78 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5SKW7 (Residues: 1-474; Coverage: 100%)
Gene names: TTHA0526, gcvPB
Sequence domains: Glycine dehydrogenase, C-terminal domain
Structure domains:

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL45XU
Spacegroup: P3221
Unit cell:
a: 89.554Å b: 89.554Å c: 371.052Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.18 0.177 0.237
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Glycine cleavage system: reaction mechanism, physiological significance, and hyperglycinemia.
Kikuchi et al. (2008)
3 more

6 mentions without citation

A Survey of Pyridoxal 5'-Phosphate-Dependent Proteins in the Gram-Positive Model Bacterium Bacillus subtilis.
Richts et al. (2019)
5 more