SMTL ID : 7ayg.1 (1 other biounit)

oxalyl-CoA decarboxylase from Methylorubrum extorquens with bound TPP and ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 25 residues within 4Å: Chain A: F.391, G.414, A.415, N.416, T.417, G.440, M.442, G.465, D.466, S.467, A.468, F.471, N.493, G.495, I.496, Y.497 Chain B: P.46, G.47, E.70, V.93, P.96, G.97, N.100, E.135 Ligands: MG.3 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.471, A:F.471, A:I.496 Hydrogen bonds: A:A.415, A:N.416, A:N.416, A:T.417, A:T.417, A:G.440, A:M.442, A:D.466, A:S.467, A:S.467, A:A.468, A:N.493, A:Y.497 Water bridges: B:E.135 TPP.4: 25 residues within 4Å: Chain A: P.46, G.47, E.70, V.93, P.96, G.97, N.100, E.135 Chain B: F.391, G.414, A.415, N.416, T.417, G.440, M.442, G.465, D.466, S.467, A.468, F.471, N.493, G.495, I.496, Y.497 Ligands: MG.6 19 PLIP interactions: 17 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.471, B:F.471, B:I.496 Hydrogen bonds: B:A.415, B:N.416, B:N.416, B:T.417, B:T.417, B:G.440, B:M.442, B:D.466, B:S.467, B:S.467, B:A.468, B:N.493, B:G.495, B:Y.497 Water bridges: A:Y.134, A:E.135 TPP.7: 25 residues within 4Å: Chain C: F.391, G.414, A.415, N.416, T.417, G.440, M.442, G.465, D.466, S.467, A.468, F.471, N.493, G.495, I.496, Y.497 Chain D: P.46, G.47, E.70, V.93, P.96, G.97, N.100, E.135 Ligands: MG.9 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.471, C:I.496, D:V.93 Hydrogen bonds: C:A.415, C:N.416, C:N.416, C:T.417, C:G.440, C:M.442, C:D.466, C:S.467, C:S.467, C:A.468, C:N.493, C:N.493, C:Y.497 Water bridges: C:T.417, C:T.417 TPP.10: 25 residues within 4Å: Chain C: P.46, G.47, E.70, V.93, P.96, G.97, N.100, E.135 Chain D: F.391, G.414, A.415, N.416, T.417, G.440, M.442, G.465, D.466, S.467, A.468, F.471, N.493, G.495, I.496, Y.497 Ligands: MG.12 18 PLIP interactions: 16 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.471, D:I.496, C:V.93 Hydrogen bonds: D:A.415, D:N.416, D:N.416, D:T.417, D:T.417, D:G.440, D:M.442, D:D.466, D:S.467, D:S.467, D:A.468, D:Y.497 Water bridges: D:T.417, D:T.417, C:Y.134

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 19 residues within 4Å: Chain A: C.112, R.174, P.175, G.235, K.236, G.237, Y.240, M.261, G.294, A.295, R.296, N.298, L.300, D.321, I.322, G.339, D.340, I.341, T.438 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:R.174, A:R.174, A:K.236, A:R.296, A:R.296, A:N.298, A:I.322, A:I.341, A:T.438, A:T.438 Water bridges: A:A.241, A:R.296, A:R.296 Salt bridges: A:K.236, A:K.236, A:R.296 ADP.5: 20 residues within 4Å: Chain B: C.112, R.174, P.175, G.235, K.236, G.237, Y.240, M.261, G.294, A.295, R.296, N.298, L.300, D.321, I.322, E.323, G.339, D.340, I.341, T.438 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:R.174, B:R.174, B:K.236, B:R.296, B:R.296, B:N.298, B:I.322, B:I.341, B:T.438, B:T.438 Water bridges: B:A.241, B:R.296, B:R.296, B:D.340 Salt bridges: B:K.236, B:K.236, B:R.296 ADP.8: 20 residues within 4Å: Chain C: C.112, R.174, P.175, G.235, K.236, G.237, Y.240, M.261, G.294, A.295, R.296, N.298, L.300, D.321, I.322, E.323, G.339, D.340, I.341, T.438 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:R.174, C:R.174, C:K.236, C:R.296, C:R.296, C:N.298, C:I.322, C:I.341 Water bridges: C:K.236, C:K.236, C:R.296, C:N.298, C:T.438 Salt bridges: C:K.236, C:K.236, C:R.296 ADP.11: 20 residues within 4Å: Chain D: C.112, R.174, G.235, K.236, G.237, Y.240, A.241, M.261, G.294, A.295, R.296, N.298, L.300, D.321, I.322, E.323, G.339, D.340, I.341, T.438 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:R.174, D:R.174, D:K.236, D:R.296, D:N.298, D:I.322, D:I.341 Water bridges: D:A.241, D:R.296, D:R.296, D:R.296, D:N.298, D:T.438 Salt bridges: D:K.236, D:K.236, D:R.296

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.466, N.493, G.495 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.466, A:G.495, H2O.3 MG.6: 4 residues within 4Å: Chain B: D.466, N.493, G.495 Ligands: TPP.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.466, B:G.495, H2O.23 MG.9: 4 residues within 4Å: Chain C: D.466, N.493, G.495 Ligands: TPP.7 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.466, C:G.495, H2O.38 MG.12: 4 residues within 4Å: Chain D: D.466, N.493, G.495 Ligands: TPP.10 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.466, D:G.495, H2O.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nattermann, M. et al., Engineering a Highly Efficient Carboligase for Synthetic One-Carbon Metabolism. Acs Catalysis (2021)

Release Date

2021-04-28

Peptides

Putative oxalyl-CoA decarboxylase (Oxc, yfdU): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Putative oxalyl-CoA decarboxylase (Oxc, yfdU)

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