PDBsum entry 4lhc

Oxidoreductase

PDB id: 4lhc

Contents

Protein chains

942 a.a.

Ligands

GLY ×5

BCT ×3

PO4 ×6

EDO ×16

BCN

Waters ×1394

PDB id:

4lhc

Name:

Oxidoreductase

Title:

Crystal structure of synechocystis sp. Pcc 6803 glycine decarboxylase (p-protein), holo form with pyridoxal-5'-phosphate and glycine

Structure:

Glycine dehydrogenase [decarboxylating]. Chain: a, b. Synonym: glycine cleavage system p-protein, glycine decarboxylase. Engineered: yes

Source:

Synechocystis sp.. Organism_taxid: 1111708. Strain: pcc 6803 / kazusa. Gene: gcvp, slr0293. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.156 R-free: 0.186

Authors:

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

Key ref:

D.Hasse et al. (2013). Structure of the homodimeric glycine decarboxylase P-protein from Synechocystis sp. PCC 6803 suggests a mechanism for redox regulation. J Biol Chem, 288, 35333-35345. PubMed id: 24121504 DOI: 10.1074/jbc.M113.509976

Date:

01-Jul-13 Release date: 16-Oct-13

Protein chains

P74416  (GCSP_SYNY3) -  Glycine dehydrogenase (decarboxylating) from Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)

Seq: 983 a.a.

Struc: 942 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.4.4.2 - glycine dehydrogenase (aminomethyl-transferring).
• Pathway: Glycine Cleavage System
• Reaction: N₆-[(R)-lipoyl]-L-lysyl-[glycine-cleavage complex H protein] + glycine + H⁺ = N₆-[(R)-S(8)-aminomethyldihydrolipoyl]-L-lysyl-[glycine- cleavage complex H protein] + CO2

N(6)-[(R)-lipoyl]-L-lysyl-[glycine-cleavage complex H protein] + glycine (Bound ligand (Het Group name = GLY) corresponds exactly) + H(+) = N(6)-[(R)-S(8)-aminomethyldihydrolipoyl]-L-lysyl-[glycine- cleavage complex H protein] + CO2

• Cofactor: Pyridoxal 5'-phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M113.509976

J Biol Chem 288:35333-35345 (2013)

PubMed id: 24121504

Structure of the homodimeric glycine decarboxylase P-protein from Synechocystis sp. PCC 6803 suggests a mechanism for redox regulation.

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

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.