SMTL ID : 7pt3.1

Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) mutant E493A structure in complex with substrate 2-HIB-CoA and inactive cofactor 3-deaza-ThDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-tetramer

Ligands

4 x TPW: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

TPW.1: 29 residues within 4Å: Chain A: G.420, G.421, D.422, L.423, G.444, L.446, G.470, D.471, G.472, A.473, I.476, N.498, A.500, W.501, N.502, I.503, A.504 Chain B: L.51, Q.52, G.53, G.54, E.76, T.99, P.102, G.103, N.106, Q.139 Ligands: 3KK.2, MG.3 19 PLIP interactions: 15 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.446, A:I.503, B:T.99, B:P.102 Hydrogen bonds: A:G.421, A:D.422, A:D.422, A:L.423, A:G.444, A:G.472, A:A.473, A:N.498, A:N.498, A:N.502, A:I.503, B:Q.139 Water bridges: A:D.471, A:D.471, B:E.76 TPW.5: 29 residues within 4Å: Chain A: L.51, Q.52, G.53, E.76, T.99, P.102, G.103, N.106, Q.139 Chain B: G.420, G.421, D.422, L.423, G.444, L.446, G.470, D.471, G.472, A.473, I.476, S.496, N.498, A.500, W.501, N.502, I.503, A.504 Ligands: 3KK.6, MG.7 20 PLIP interactions: 16 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.446, B:I.503, A:T.99, A:P.102 Hydrogen bonds: B:G.421, B:D.422, B:L.423, B:G.444, B:L.446, B:D.471, B:D.471, B:G.472, B:A.473, B:N.498, B:N.502, B:I.503, A:Q.139 Water bridges: B:S.496, B:N.498, A:E.76 TPW.8: 29 residues within 4Å: Chain C: G.420, G.421, D.422, L.423, G.444, L.446, G.470, D.471, G.472, A.473, I.476, N.498, A.500, W.501, N.502, I.503, A.504 Chain D: L.51, Q.52, G.53, G.54, E.76, T.99, P.102, G.103, N.106, Q.139 Ligands: 3KK.9, MG.10 19 PLIP interactions: 16 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:L.446, C:I.503, D:T.99, D:P.102 Hydrogen bonds: C:G.421, C:D.422, C:D.422, C:D.422, C:L.423, C:G.444, C:G.472, C:A.473, C:N.498, C:N.498, C:N.502, C:I.503, D:Q.139 Water bridges: C:D.471, C:D.471 TPW.12: 29 residues within 4Å: Chain C: L.51, Q.52, G.53, E.76, T.99, P.102, G.103, N.106, Q.139 Chain D: G.420, G.421, D.422, L.423, G.444, L.446, G.470, D.471, G.472, A.473, I.476, S.496, N.498, A.500, W.501, N.502, I.503, A.504 Ligands: 3KK.13, MG.14 18 PLIP interactions: 3 interactions with chain C, 15 interactions with chain D Hydrophobic interactions: C:T.99, C:P.102, D:L.446, D:I.503 Hydrogen bonds: C:Q.139, D:G.421, D:D.422, D:L.423, D:G.444, D:L.446, D:D.471, D:G.472, D:A.473, D:N.498, D:N.502, D:I.503 Water bridges: D:S.496, D:N.498

4 x 3KK: S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} 2-hydroxy-2-methylpropanethioate(Non-covalent)

3KK.2: 39 residues within 4Å: Chain A: Q.266, R.269, G.281, S.282, A.283, R.284, S.285, Y.303, Q.304, R.373, A.374, Y.377, G.420, G.421, L.424, R.428, L.429, T.432, A.440, G.441, G.444, L.446, I.503, P.571, D.572, K.575, L.577, G.578, V.580, A.585, L.586, W.589 Chain B: G.53, G.54, H.55, T.99, L.138, Q.139 Ligands: TPW.1 36 PLIP interactions: 31 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Q.304, A:L.577, A:L.586, A:W.589, B:L.138 Hydrogen bonds: A:Q.266, A:G.281, A:R.284, A:S.285, A:Q.304, A:R.373, A:R.428, B:G.54, B:Q.139 Water bridges: A:R.269, A:R.269, A:R.284, A:R.284, A:R.373, A:R.378, A:R.428, A:R.428, A:D.572, A:D.572, A:K.575, A:K.575, A:K.575, A:K.575, B:T.99, B:T.99 Salt bridges: A:R.284, A:R.284, A:R.373, A:R.428, A:K.575, A:K.575 3KK.6: 41 residues within 4Å: Chain A: G.53, G.54, H.55, T.99, L.138, Q.139 Chain B: Q.266, R.269, G.281, S.282, A.283, R.284, S.285, A.286, M.288, Y.303, Q.304, R.373, A.374, Y.377, G.420, G.421, L.424, R.428, L.429, T.432, A.440, G.441, G.444, L.446, I.503, P.571, D.572, K.575, L.577, G.578, V.580, A.585, L.586, W.589 Ligands: TPW.5 39 PLIP interactions: 34 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Q.304, B:L.577, B:L.586, A:L.138 Hydrogen bonds: B:Q.266, B:G.281, B:S.282, B:R.284, B:S.285, B:Q.304, B:R.373, B:R.428, A:G.54, A:Q.139 Water bridges: B:R.269, B:R.269, B:R.269, B:R.284, B:R.284, B:A.286, B:R.373, B:R.373, B:R.373, B:R.373, B:R.373, B:R.378, B:R.428, B:D.572, B:K.575, B:K.575, B:K.575, A:T.99, A:T.99 Salt bridges: B:R.284, B:R.284, B:R.373, B:R.428, B:K.575, B:K.575 3KK.9: 39 residues within 4Å: Chain C: Q.266, R.269, G.281, S.282, A.283, R.284, S.285, Y.303, Q.304, R.373, A.374, Y.377, G.420, G.421, L.424, R.428, L.429, T.432, A.440, G.441, G.444, L.446, I.503, P.571, D.572, K.575, L.577, G.578, V.580, A.585, L.586, W.589 Chain D: G.53, G.54, H.55, T.99, L.138, Q.139 Ligands: TPW.8 36 PLIP interactions: 31 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:Q.304, C:L.577, C:L.586, C:W.589, D:L.138 Hydrogen bonds: C:Q.266, C:G.281, C:R.284, C:S.285, C:Q.304, C:R.373, C:R.428, D:G.54, D:Q.139 Water bridges: C:R.269, C:R.269, C:R.284, C:R.284, C:R.373, C:R.378, C:R.428, C:R.428, C:D.572, C:K.575, C:K.575, C:K.575, C:K.575, C:K.575, D:T.99, D:T.99 Salt bridges: C:R.284, C:R.284, C:R.373, C:R.428, C:K.575, C:K.575 3KK.13: 41 residues within 4Å: Chain C: G.53, G.54, H.55, T.99, L.138, Q.139 Chain D: Q.266, R.269, G.281, S.282, A.283, R.284, S.285, A.286, M.288, Y.303, Q.304, R.373, A.374, Y.377, G.420, G.421, L.424, R.428, L.429, T.432, A.440, G.441, G.444, L.446, I.503, P.571, D.572, K.575, L.577, G.578, V.580, A.585, L.586, W.589 Ligands: TPW.12 39 PLIP interactions: 34 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:Q.304, D:L.577, D:L.586, C:L.138 Hydrogen bonds: D:Q.266, D:G.281, D:S.282, D:R.284, D:S.285, D:Q.304, D:R.373, D:R.428, C:G.54, C:Q.139 Water bridges: D:R.269, D:R.269, D:R.269, D:R.284, D:R.284, D:A.286, D:R.373, D:R.373, D:R.373, D:R.373, D:R.373, D:R.378, D:R.428, D:D.572, D:K.575, D:K.575, D:K.575, C:T.99, C:T.99 Salt bridges: D:R.284, D:R.284, D:R.373, D:R.428, D:K.575, D:K.575

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 7 residues within 4Å: Chain A: D.471, G.472, N.498, A.500, W.501, N.502 Ligands: TPW.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.471, A:A.500, H2O.4 MG.4: 1 residues within 4Å: Chain B: D.75 No protein-ligand interaction detected (PLIP) MG.7: 7 residues within 4Å: Chain B: D.471, G.472, N.498, A.500, W.501, N.502 Ligands: TPW.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.471, B:A.500, H2O.24 MG.10: 7 residues within 4Å: Chain C: D.471, G.472, N.498, A.500, W.501, N.502 Ligands: TPW.8 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.471, C:A.500, H2O.41 MG.11: 1 residues within 4Å: Chain D: D.75 No protein-ligand interaction detected (PLIP) MG.14: 7 residues within 4Å: Chain D: D.471, G.472, N.498, A.500, W.501, N.502 Ligands: TPW.12 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.471, D:A.500, H2O.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zahn, M. et al., Mechanistic details of the actinobacterial lyase-catalyzed degradation reaction of 2-hydroxyisobutyryl-CoA. J.Biol.Chem. (2022)

Release Date

2022-02-02

Peptides

2-hydroxyacyl-CoA lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

2-hydroxyacyl-CoA lyase