SMTL ID : 4a0f.1

Structure of selenomethionine substituted bifunctional DAPA aminotransferase-dethiobiotin synthetase from Arabidopsis thaliana in its apo form.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.71 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 13 residues within 4Å: Chain A: N.450, G.451, S.452, Y.493, H.494, G.495, E.601, D.635, V.637, F.638, K.664 Chain B: H.699, S.700 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:E.601, A:V.637, A:F.638, A:K.664 Hydrogen bonds: A:G.451, A:S.452, A:S.452, B:S.700, B:S.700 Salt bridges: A:K.664, B:H.699 Water bridges: B:Y.701 PLP.4: 13 residues within 4Å: Chain A: H.699, S.700 Chain B: N.450, G.451, S.452, Y.493, H.494, G.495, E.601, D.635, V.637, F.638, K.664 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:E.601, B:V.637, B:F.638, B:K.664 Hydrogen bonds: B:G.451, B:S.452, B:S.452, A:S.700, A:S.700 Water bridges: B:Y.493 Salt bridges: B:K.664, A:H.699

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: T.44, K.48, K.75, E.208, G.211 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.44, A:E.208, A:G.211 Salt bridges: A:K.48, A:K.75 SO4.3: 9 residues within 4Å: Chain A: L.242, G.243, G.244, I.245, S.246, N.274 Chain B: S.163, S.215, P.216 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.243, A:G.244, A:I.245, A:S.246 SO4.5: 9 residues within 4Å: Chain B: T.44, S.45, K.48, K.75, D.86, T.209, A.210, G.211 Ligands: SO4.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.45, B:G.211 Salt bridges: B:K.48, B:K.75 SO4.6: 6 residues within 4Å: Chain B: S.45, L.46, G.47, K.48, T.49 Ligands: SO4.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.45, B:L.46, B:G.47, B:T.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cobessi, D. et al., Biochemical and Structural Characterization of the Arabidopsis Bifunctional Enzyme Dethiobiotin Synthetase-Diaminopelargonic Acid Aminotransferase: Evidence for Substrate Channeling in Biotin Synthesis. Plant Cell (2012)

Release Date

2012-06-13

Peptides

ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE