› 1wyu

X-ray diffraction
2.1Å resolution

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

Released:
DOI: 10.2210/pdb1wyu/pdb
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PDB entry 1wyu coloured by chain, front view.
PDB entry 1wyu coloured by chain, side view.
PDB entry 1wyu 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, E, G
Molecule details ›
Chains: A, C, E, G
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, F, H
Molecule details ›
Chains: B, D, F, H
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


Cofactor: Ligand PLP 4 x PLP
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL45XU
Spacegroup: P212121
Unit cell:
a: 134.874Å b: 166.673Å c: 189.007Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.191 0.189 0.229
Expression system: Escherichia coli

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Citations

4 review citations

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

2 mentions without citation

Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia.
Nakai et al. (2005)
1 more

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