SMTL ID : 6wte.2 (1 other biounit)

Structure of radical S-adenosylmethionine methyltransferase, TsrM, from Kitasatospora setae with cobalamin and [4Fe-4S] cluster bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

monomer

Ligands

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 11 residues within 4Å: Chain A: C.227, Y.229, C.231, H.233, C.234, P.237, S.272, E.273, L.276, Q.310, Y.354 8 PLIP interactions: 8 interactions with chain A, Salt bridges: A:E.236, A:E.273, A:E.273, A:E.273 Metal complexes: A:C.227, A:C.231, A:C.234, A:E.273

1 x B12: COBALAMIN(Non-covalent)

B12.2: 37 residues within 4Å: Chain A: N.11, V.13, P.15, I.17, Y.20, A.21, V.24, L.25, G.65, V.66, T.67, R.69, N.70, T.71, T.73, V.74, Y.75, V.102, G.103, G.104, G.105, I.106, G.107, V.125, G.127, P.128, G.129, E.130, L.218, S.220, V.235, E.236, K.240, T.270, D.271, S.272, F.414 41 PLIP interactions: 40 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:I.17, A:I.17, A:Y.20, A:L.25, A:V.102, A:I.106, A:I.106, A:V.125 Hydrogen bonds: A:N.11, A:P.15, A:I.17, A:R.69, A:N.70, A:T.71, A:T.71, A:T.73, A:G.105, A:I.106, A:G.129, A:E.130, A:L.218, A:E.236, A:E.236, A:E.236, A:K.240, A:K.240, A:T.270 Water bridges: A:A.18, A:A.18, A:Y.20, A:A.21, A:R.69, A:G.105, A:S.109, A:G.127, A:L.218, A:S.220, A:V.235, A:S.272 Salt bridges: A:K.240 Metal complexes: H2O.9

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 3 residues within 4Å: Chain A: Y.118, F.465, G.469 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.461 EDO.4: 4 residues within 4Å: Chain A: P.383, M.419, E.422, Q.426 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.426, A:Q.426 Water bridges: A:P.418 EDO.5: 6 residues within 4Å: Chain A: Y.229, N.275, L.276, S.277, I.278, P.313 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.277, A:I.278 Water bridges: A:Y.229, A:A.279 EDO.6: 3 residues within 4Å: Chain A: L.373, S.549, H.550 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.550 EDO.7: 3 residues within 4Å: Chain A: L.373, T.403, R.552 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.402, A:R.552 EDO.8: 5 residues within 4Å: Chain A: K.12, V.13, R.80, F.82, E.85 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.80 Water bridges: A:K.12 EDO.9: 3 residues within 4Å: Chain A: F.184, R.230, I.421 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.230

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Knox, H.L. et al., Structural basis for non-radical catalysis by TsrM, a radical SAM methylase. Nat.Chem.Biol. (2021)

Release Date

2020-12-23

Peptides

B12-binding domain-containing protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B12-binding domain-containing protein

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