SMTL ID : 6h9e.1

Structure of glutamate mutase reconstituted with homo-coenzyme B12

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

hetero-2-2-mer

Ligands

2 x B12: COBALAMIN(Non-covalent)

B12.1: 47 residues within 4Å: Chain A: S.13, D.14, C.15, H.16, A.17, V.18, G.19, I.22, L.23, L.59, S.61, L.63, Y.64, G.65, Y.89, G.91, G.92, N.93, V.95, V.96, G.97, Y.117, T.121, P.123, G.126 Chain B: T.94, I.95, A.97, R.100, N.123, P.180, Y.181, L.219, T.220, M.294, G.295, G.296, F.297, H.329, E.330, A.331, G.333, I.334, P.410, F.471 Ligands: FWK.2, TAR.3 33 PLIP interactions: 21 interactions with chain A, 12 interactions with chain B, Hydrophobic interactions: A:I.22, A:L.23, A:L.59, A:Y.64, A:Y.89, B:Y.181, B:I.334, B:I.334, B:F.471 Hydrogen bonds: A:S.13, A:D.14, A:C.15, A:A.17, A:V.18, A:G.19, A:L.63, A:G.97, B:N.123, B:N.123, B:P.180, B:F.297, B:E.330, B:I.334 Water bridges: A:N.93, A:N.93, A:V.95, A:V.95, A:G.120, A:T.121, B:Q.101, B:A.331 pi-Stacking: A:H.16 Metal complexes: A:H.16 B12.6: 49 residues within 4Å: Chain C: S.13, D.14, C.15, H.16, A.17, V.18, G.19, I.22, L.23, L.59, V.60, S.61, L.63, Y.64, G.65, Y.89, G.91, G.92, N.93, V.95, V.96, G.97, Y.117, T.121, P.123, G.126 Chain D: T.94, I.95, A.97, R.100, N.123, P.180, Y.181, F.216, L.219, T.220, M.294, G.295, G.296, F.297, H.329, E.330, A.331, G.333, I.334, P.410, F.471 Ligands: FWK.8, TAR.9 33 PLIP interactions: 21 interactions with chain C, 12 interactions with chain D, Hydrophobic interactions: C:I.22, C:L.23, C:L.23, C:L.59, C:Y.64, C:Y.89, C:Y.117, D:Y.181, D:F.216, D:I.334, D:I.334, D:F.471 Hydrogen bonds: C:S.13, C:C.15, C:A.17, C:V.18, C:G.19, C:L.63, C:G.97, D:N.123, D:P.180, D:F.297, D:E.330, D:I.334 Water bridges: C:G.92, C:N.93, C:N.93, C:V.95, C:G.120, D:Q.101, D:A.331 pi-Stacking: C:H.16 Metal complexes: C:H.16

2 x FWK: (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol(Non-covalent)

FWK.2: 12 residues within 4Å: Chain B: R.66, A.67, G.68, T.94, N.123, G.124, K.326, E.330, I.334, P.335 Ligands: B12.1, TAR.3 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.68, B:G.68, B:K.326, B:K.326, B:E.330 Water bridges: B:R.66, B:E.330, B:E.330 FWK.8: 12 residues within 4Å: Chain D: R.66, A.67, G.68, T.94, N.123, G.124, K.326, E.330, I.334, P.335 Ligands: B12.6, TAR.9 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.68, D:G.68, D:K.326, D:K.326, D:E.330 Water bridges: D:R.66

2 x TAR: D(-)-TARTARIC ACID(Non-covalent)

TAR.3: 13 residues within 4Å: Chain B: R.66, T.94, R.100, R.149, H.150, E.171, Y.177, Y.181, F.216, H.291, M.294 Ligands: B12.1, FWK.2 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:H.150, B:Y.177, B:Y.181 Water bridges: B:R.66 Salt bridges: B:R.66, B:R.100, B:R.149, B:H.291 TAR.9: 13 residues within 4Å: Chain D: R.66, T.94, R.100, R.149, H.150, E.171, Y.177, Y.181, F.216, H.291, M.294 Ligands: B12.6, FWK.8 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:Y.181, D:Y.181, D:Y.181 Salt bridges: D:R.66, D:R.100, D:R.149, D:H.291

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: K.21 Chain B: P.407, F.408, G.416, M.418, M.419, P.420, F.463 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:F.408, B:G.416 Water bridges: A:K.21 GOL.5: 2 residues within 4Å: Chain B: E.274, A.278 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.274, B:Y.279, B:Y.279 Water bridges: B:Y.275, B:K.377, B:K.377, B:D.381 GOL.7: 5 residues within 4Å: Chain C: P.122, P.123, E.124 Chain D: F.471, K.475 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.475, D:K.475 GOL.10: 7 residues within 4Å: Chain D: P.407, F.408, G.416, M.418, M.419, P.420, F.463 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:F.408, D:G.416 Water bridges: D:I.406, D:M.418 GOL.11: 4 residues within 4Å: Chain D: M.1, K.15, Q.16, E.19 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:M.1, D:M.1, D:K.15, D:E.19 Water bridges: D:Q.16, D:Q.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gruber, K. et al., Structure-Based Demystification of Radical Catalysis by a Coenzyme B 12 Dependent Enzyme-Crystallographic Study of Glutamate Mutase with Cofactor Homologues. Angew.Chem.Int.Ed.Engl. (2022)

Release Date

2019-08-14

Peptides

Glutamate mutase sigma subunit: AC
Glutamate mutase epsilon subunit: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Glutamate mutase sigma subunit

Glutamate mutase epsilon subunit

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