SMTL ID : 4a0h.1

Structure of bifunctional DAPA aminotransferase-DTB synthetase from Arabidopsis thaliana bound to 7-keto 8-amino pelargonic acid (KAPA)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 15 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 Ligands: KAP.2 13 PLIP interactions: 10 interactions with chain A, 3 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, A:K.664, B:S.700, B:S.700 Salt bridges: A:K.664, B:H.699 pi-Stacking: A:Y.493 PLP.5: 15 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 Ligands: KAP.6 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 Salt bridges: B:K.664, A:H.699 pi-Stacking: B:Y.493

4 x KAP: 7-KETO-8-AMINOPELARGONIC ACID(Non-covalent)

KAP.2: 14 residues within 4Å: Chain A: F.346, W.389, W.390, Y.493, Y.509, A.607, K.664, R.795, P.796, L.797 Chain B: G.698, H.699, S.700 Ligands: PLP.1 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.346, A:F.346, A:W.389, A:W.389, A:W.390, A:A.607, A:L.797 Hydrogen bonds: A:W.389, B:G.698 Salt bridges: A:R.795 KAP.3: 10 residues within 4Å: Chain A: L.242, G.243, G.244, I.245, S.246 Chain B: T.44, T.79, S.163, S.215 Ligands: TLA.8 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.242 Hydrogen bonds: A:G.243, A:G.244, A:I.245, A:S.246, B:T.44, B:T.79 KAP.6: 12 residues within 4Å: Chain A: G.698 Chain B: F.346, W.389, W.390, Y.493, Y.509, A.607, K.664, R.795, P.796, L.797 Ligands: PLP.5 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.346, B:F.346, B:F.346, B:W.389, B:W.390, B:A.607, B:L.797 Hydrogen bonds: B:W.389, B:Y.493, A:G.698 Salt bridges: B:R.795 KAP.7: 13 residues within 4Å: Chain A: T.44, T.79, A.161, I.162, S.163, P.164, S.215 Chain B: L.242, G.243, G.244, I.245, S.246 Ligands: TLA.4 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.242 Hydrogen bonds: B:G.243, B:G.244, B:I.245, B:S.246, A:S.215

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

TLA.4: 11 residues within 4Å: Chain A: N.43, T.44, S.45, K.48, K.75, D.86, E.208, T.209, A.210, G.211 Ligands: KAP.7 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.44, A:T.44, A:S.45, A:K.48, A:D.86, A:E.208, A:G.211 Salt bridges: A:K.48, A:K.48, A:K.75 TLA.8: 11 residues within 4Å: Chain B: N.43, T.44, S.45, K.48, T.49, K.75, D.86, E.208, A.210, G.211 Ligands: KAP.3 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.45, B:K.48, B:T.49, B:G.211 Salt bridges: B:K.48, B:K.48, B:K.75

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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