SMTL ID : 4a0r.1

Structure of bifunctional DAPA aminotransferase-DTB synthetase from Arabidopsis thaliana bound to dethiobiotin (DTB).

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.68 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 14 residues within 4Å: Chain A: W.390, 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 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:E.601, A:V.637, 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 pi-Stacking: A:Y.493 PLP.4: 14 residues within 4Å: Chain A: H.699, S.700 Chain B: W.390, N.450, G.451, S.452, Y.493, H.494, G.495, E.601, D.635, V.637, F.638, K.664 13 PLIP interactions: 5 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:S.700, A:S.700, B:G.451, B:S.452, B:S.452 Water bridges: A:S.700, A:Y.701 Salt bridges: A:H.699, B:K.664 Hydrophobic interactions: B:E.601, B:V.637, B:K.664 pi-Stacking: B:Y.493

2 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.2: 13 residues within 4Å: Chain A: T.44, S.45, L.46, G.47, K.48, T.49, K.75, D.86, E.208, T.209, A.210, G.211 Ligands: DTB.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.45, A:L.46, A:G.47, A:K.48, A:K.48, A:T.49, A:T.49, A:K.75, A:D.86, A:G.211 Salt bridges: A:K.48, A:K.48, A:K.75 TLA.6: 13 residues within 4Å: Chain B: T.44, S.45, L.46, G.47, K.48, T.49, K.75, D.86, E.208, T.209, A.210, G.211 Ligands: DTB.5 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:T.44, B:S.45, B:L.46, B:G.47, B:K.48, B:K.48, B:T.49, B:D.86, B:G.211 Salt bridges: B:K.48, B:K.48, B:K.75

2 x DTB: 6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID(Non-covalent)

DTB.3: 14 residues within 4Å: Chain A: T.44, Q.78, T.79, I.162, S.163, P.164, G.211, S.215 Chain B: L.242, G.243, G.244, I.245, S.246 Ligands: TLA.2 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.78, A:T.79, A:T.79, A:S.215, B:G.243, B:I.245, B:S.246 DTB.5: 14 residues within 4Å: Chain A: L.242, G.243, G.244, I.245, S.246 Chain B: T.44, Q.78, T.79, I.162, S.163, G.211, S.215, P.216 Ligands: TLA.6 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.243, A:I.245, A:S.246, B:Q.78, B:T.79, B:T.79, B:S.215

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

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