SMTL ID : 3fdd.1

The Crystal Structure of the Pseudomonas dacunhae Aspartate-Beta-Decarboxylase Reveals a Novel Oligomeric Assembly for a Pyridoxal-5-Phosphate Dependent Enzyme

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-12-mer

Ligands

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

PLP.1: 16 residues within 4Å: Chain A: R.37, G.173, G.174, T.175, F.204, Y.207, V.252, N.256, D.286, V.288, Y.289, S.312, S.314, K.315, R.323 Chain B: Y.134 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:R.37, A:F.204, A:V.252, A:V.288, A:K.315 Hydrogen bonds: A:R.37, A:G.174, A:T.175, A:N.256, A:Y.289, A:S.312, A:S.312, A:S.314, B:Y.134 Salt bridges: A:R.37, A:R.323 pi-Cation interactions: A:R.37 PLP.4: 16 residues within 4Å: Chain A: Y.134 Chain B: R.37, G.173, G.174, T.175, F.204, Y.207, V.252, N.256, D.286, V.288, Y.289, S.312, S.314, K.315, R.323 17 PLIP interactions: 1 interactions with chain A, 16 interactions with chain B Hydrogen bonds: A:Y.134, B:R.37, B:G.174, B:T.175, B:N.256, B:Y.289, B:S.312, B:S.312, B:S.314 Hydrophobic interactions: B:R.37, B:F.204, B:V.252, B:V.288, B:K.315 Salt bridges: B:R.37, B:R.323 pi-Cation interactions: B:R.37 PLP.7: 16 residues within 4Å: Chain C: R.37, G.173, G.174, T.175, F.204, Y.207, V.252, N.256, D.286, V.288, Y.289, S.312, S.314, K.315, R.323 Chain D: Y.134 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:R.37, C:F.204, C:V.252, C:V.288, C:K.315 Hydrogen bonds: C:R.37, C:G.174, C:T.175, C:T.175, C:Y.207, C:N.256, C:S.312, C:S.312, C:S.314 Salt bridges: C:R.37, C:R.323 pi-Cation interactions: C:R.37 PLP.10: 16 residues within 4Å: Chain C: Y.134 Chain D: R.37, G.173, G.174, T.175, F.204, Y.207, V.252, N.256, D.286, V.288, Y.289, S.312, S.314, K.315, R.323 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:R.37, D:F.204, D:V.252, D:V.288, D:K.315 Hydrogen bonds: D:R.37, D:G.174, D:T.175, D:T.175, D:Y.207, D:N.256, D:S.312, D:S.312, D:S.314 Salt bridges: D:R.37, D:R.323 pi-Cation interactions: D:R.37 PLP.13: 16 residues within 4Å: Chain E: R.37, G.173, G.174, T.175, F.204, Y.207, V.252, N.256, D.286, V.288, Y.289, S.312, S.314, K.315, R.323 Chain F: Y.134 19 PLIP interactions: 18 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:R.37, E:F.204, E:V.252, E:V.288, E:K.315 Hydrogen bonds: E:R.37, E:G.174, E:T.175, E:T.175, E:Y.207, E:N.256, E:Y.289, E:S.312, E:S.312, E:S.314, F:Y.134 Salt bridges: E:R.37, E:R.323 pi-Cation interactions: E:R.37 PLP.16: 16 residues within 4Å: Chain E: Y.134 Chain F: R.37, G.173, G.174, T.175, F.204, Y.207, V.252, N.256, D.286, V.288, Y.289, S.312, S.314, K.315, R.323 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:R.37, F:F.204, F:V.252, F:V.288, F:K.315 Hydrogen bonds: F:R.37, F:G.174, F:T.175, F:N.256, F:S.312, F:S.312, F:S.314 Salt bridges: F:R.37, F:R.323 pi-Cation interactions: F:R.37 PLP.19: 16 residues within 4Å: Chain G: R.37, G.173, G.174, T.175, F.204, Y.207, V.252, N.256, D.286, V.288, Y.289, S.312, S.314, K.315, R.323 Chain H: Y.134 19 PLIP interactions: 18 interactions with chain G, 1 interactions with chain H Hydrophobic interactions: G:R.37, G:F.204, G:V.252, G:V.288, G:K.315 Hydrogen bonds: G:R.37, G:G.174, G:T.175, G:T.175, G:Y.207, G:N.256, G:Y.289, G:S.312, G:S.312, G:S.314, H:Y.134 Salt bridges: G:R.37, G:R.323 pi-Cation interactions: G:R.37 PLP.22: 16 residues within 4Å: Chain G: Y.134 Chain H: R.37, G.173, G.174, T.175, F.204, Y.207, V.252, N.256, D.286, V.288, Y.289, S.312, S.314, K.315, R.323 15 PLIP interactions: 15 interactions with chain H Hydrophobic interactions: H:R.37, H:F.204, H:V.252, H:V.288, H:K.315 Hydrogen bonds: H:R.37, H:G.174, H:T.175, H:N.256, H:S.312, H:S.312, H:S.314 Salt bridges: H:R.37, H:R.323 pi-Cation interactions: H:R.37 PLP.25: 16 residues within 4Å: Chain I: R.37, G.173, G.174, T.175, F.204, Y.207, V.252, N.256, D.286, V.288, Y.289, S.312, S.314, K.315, R.323 Chain J: Y.134 17 PLIP interactions: 17 interactions with chain I Hydrophobic interactions: I:R.37, I:F.204, I:V.252, I:V.288, I:K.315 Hydrogen bonds: I:R.37, I:G.174, I:T.175, I:T.175, I:Y.207, I:N.256, I:S.312, I:S.312, I:S.314 Salt bridges: I:R.37, I:R.323 pi-Cation interactions: I:R.37 PLP.28: 16 residues within 4Å: Chain I: Y.134 Chain J: R.37, G.173, G.174, T.175, F.204, Y.207, V.252, N.256, D.286, V.288, Y.289, S.312, S.314, K.315, R.323 17 PLIP interactions: 16 interactions with chain J, 1 interactions with chain I Hydrophobic interactions: J:R.37, J:F.204, J:V.252, J:V.288, J:K.315 Hydrogen bonds: J:R.37, J:G.174, J:T.175, J:N.256, J:Y.289, J:S.312, J:S.312, J:S.314, I:Y.134 Salt bridges: J:R.37, J:R.323 pi-Cation interactions: J:R.37 PLP.31: 16 residues within 4Å: Chain K: R.37, G.173, G.174, T.175, F.204, Y.207, V.252, N.256, D.286, V.288, Y.289, S.312, S.314, K.315, R.323 Chain L: Y.134 17 PLIP interactions: 16 interactions with chain K, 1 interactions with chain L Hydrophobic interactions: K:R.37, K:F.204, K:V.252, K:V.288, K:K.315 Hydrogen bonds: K:R.37, K:G.174, K:T.175, K:N.256, K:Y.289, K:S.312, K:S.312, K:S.314, L:Y.134 Salt bridges: K:R.37, K:R.323 pi-Cation interactions: K:R.37 PLP.34: 16 residues within 4Å: Chain K: Y.134 Chain L: R.37, G.173, G.174, T.175, F.204, Y.207, V.252, N.256, D.286, V.288, Y.289, S.312, S.314, K.315, R.323 17 PLIP interactions: 17 interactions with chain L Hydrophobic interactions: L:R.37, L:F.204, L:V.252, L:V.288, L:K.315 Hydrogen bonds: L:R.37, L:G.174, L:T.175, L:T.175, L:Y.207, L:N.256, L:S.312, L:S.312, L:S.314 Salt bridges: L:R.37, L:R.323 pi-Cation interactions: L:R.37

12 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 10 residues within 4Å: Chain A: N.41, F.42, R.419, N.504 Chain B: S.65, Y.66, S.67, Y.68, G.75 Chain E: Q.113 6 PLIP interactions: 3 interactions with chain B, 1 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: B:Y.66, B:Y.68 Hydrogen bonds: B:S.65, E:Q.113, A:N.504 Salt bridges: A:R.419 ACT.5: 10 residues within 4Å: Chain A: S.65, Y.66, S.67, Y.68, G.75 Chain B: N.41, F.42, R.419, N.504 Chain G: Q.113 6 PLIP interactions: 1 interactions with chain G, 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: G:Q.113, B:N.504, A:S.65 Salt bridges: B:R.419 Hydrophobic interactions: A:Y.66, A:Y.68 ACT.8: 10 residues within 4Å: Chain C: N.41, F.42, R.419, N.504 Chain D: S.65, Y.66, S.67, Y.68, G.75 Chain H: Q.113 6 PLIP interactions: 1 interactions with chain H, 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: H:Q.113, C:N.504, D:S.65 Salt bridges: C:R.419 Hydrophobic interactions: D:Y.66, D:Y.68 ACT.11: 10 residues within 4Å: Chain C: S.65, Y.66, S.67, Y.68, G.75 Chain D: N.41, F.42, R.419, N.504 Chain F: Q.113 6 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C, 1 interactions with chain F Hydrogen bonds: D:N.504, C:S.65, F:Q.113 Salt bridges: D:R.419 Hydrophobic interactions: C:Y.66, C:Y.68 ACT.14: 10 residues within 4Å: Chain E: N.41, F.42, R.419, N.504 Chain F: S.65, Y.66, S.67, Y.68, G.75 Chain I: Q.113 6 PLIP interactions: 3 interactions with chain F, 1 interactions with chain I, 2 interactions with chain E Hydrophobic interactions: F:Y.66, F:Y.68 Hydrogen bonds: F:S.65, I:Q.113, E:N.504 Salt bridges: E:R.419 ACT.17: 10 residues within 4Å: Chain E: S.65, Y.66, S.67, Y.68, G.75 Chain F: N.41, F.42, R.419, N.504 Chain K: Q.113 6 PLIP interactions: 1 interactions with chain K, 3 interactions with chain E, 2 interactions with chain F Hydrogen bonds: K:Q.113, E:S.65, F:N.504 Hydrophobic interactions: E:Y.66, E:Y.68 Salt bridges: F:R.419 ACT.20: 10 residues within 4Å: Chain G: N.41, F.42, R.419, N.504 Chain H: S.65, Y.66, S.67, Y.68, G.75 Chain L: Q.113 6 PLIP interactions: 1 interactions with chain L, 2 interactions with chain G, 3 interactions with chain H Hydrogen bonds: L:Q.113, G:N.504, H:S.65 Salt bridges: G:R.419 Hydrophobic interactions: H:Y.66, H:Y.68 ACT.23: 10 residues within 4Å: Chain G: S.65, Y.66, S.67, Y.68, G.75 Chain H: N.41, F.42, R.419, N.504 Chain J: Q.113 6 PLIP interactions: 2 interactions with chain H, 3 interactions with chain G, 1 interactions with chain J Hydrogen bonds: H:N.504, G:S.65, J:Q.113 Salt bridges: H:R.419 Hydrophobic interactions: G:Y.66, G:Y.68 ACT.26: 10 residues within 4Å: Chain A: Q.113 Chain I: N.41, F.42, R.419, N.504 Chain J: S.65, Y.66, S.67, Y.68, G.75 6 PLIP interactions: 1 interactions with chain A, 3 interactions with chain J, 2 interactions with chain I Hydrogen bonds: A:Q.113, J:S.65, I:N.504 Hydrophobic interactions: J:Y.66, J:Y.68 Salt bridges: I:R.419 ACT.29: 10 residues within 4Å: Chain C: Q.113 Chain I: S.65, Y.66, S.67, Y.68, G.75 Chain J: N.41, F.42, R.419, N.504 6 PLIP interactions: 3 interactions with chain I, 2 interactions with chain J, 1 interactions with chain C Hydrophobic interactions: I:Y.66, I:Y.68 Hydrogen bonds: I:S.65, J:N.504, C:Q.113 Salt bridges: J:R.419 ACT.32: 10 residues within 4Å: Chain D: Q.113 Chain K: N.41, F.42, R.419, N.504 Chain L: S.65, Y.66, S.67, Y.68, G.75 6 PLIP interactions: 3 interactions with chain L, 1 interactions with chain D, 2 interactions with chain K Hydrophobic interactions: L:Y.66, L:Y.68 Hydrogen bonds: L:S.65, D:Q.113, K:N.504 Salt bridges: K:R.419 ACT.35: 10 residues within 4Å: Chain B: Q.113 Chain K: S.65, Y.66, S.67, Y.68, G.75 Chain L: N.41, F.42, R.419, N.504 6 PLIP interactions: 3 interactions with chain K, 2 interactions with chain L, 1 interactions with chain B Hydrophobic interactions: K:Y.66, K:Y.68 Hydrogen bonds: K:S.65, L:N.504, B:Q.113 Salt bridges: L:R.419

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 5 residues within 4Å: Chain A: R.49, R.53, Q.97, E.98, G.99 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain B: R.49, R.53, Q.97, E.98, G.99 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain C: R.49, R.53, Q.97, E.98, G.99 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain D: R.49, R.53, Q.97, E.98, G.99 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain E: R.49, R.53, Q.97, E.98, G.99 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain F: R.49, R.53, Q.97, E.98, G.99 Ligand excluded by PLIP CL.21: 5 residues within 4Å: Chain G: R.49, R.53, Q.97, E.98, G.99 Ligand excluded by PLIP CL.24: 5 residues within 4Å: Chain H: R.49, R.53, Q.97, E.98, G.99 Ligand excluded by PLIP CL.27: 5 residues within 4Å: Chain I: R.49, R.53, Q.97, E.98, G.99 Ligand excluded by PLIP CL.30: 5 residues within 4Å: Chain J: R.49, R.53, Q.97, E.98, G.99 Ligand excluded by PLIP CL.33: 5 residues within 4Å: Chain K: R.49, R.53, Q.97, E.98, G.99 Ligand excluded by PLIP CL.36: 5 residues within 4Å: Chain L: R.49, R.53, Q.97, E.98, G.99 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lima, S. et al., The crystal structure of the Pseudomonas dacunhae aspartate-beta-decarboxylase dodecamer reveals an unknown oligomeric assembly for a pyridoxal-5'-phosphate-dependent enzyme. J.Mol.Biol. (2009)

Release Date

2009-03-17

Peptides

L-aspartate-beta-decarboxylase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

L-aspartate-beta-decarboxylase