SMTL ID : 6wtf.1 (1 other biounit)

Structure of radical S-adenosylmethionine methyltransferase, TsrM, from Kitasatospora setae with tryptophan substrate and SAM analog (aza-SAM) bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

monomer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: C.227, C.231, H.233, C.234, E.236, P.237, S.272, E.273, L.276, Q.310, Y.354 Ligands: SA8.3 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: 48 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, V.102, G.103, G.104, G.105, I.106, G.107, T.110, V.125, G.127, P.128, G.129, E.130, L.218, G.219, S.220, C.234, V.235, E.236, K.240, H.268, T.269, T.270, D.271, S.272, Y.308, F.414, N.528, Y.529, A.530, F.547 Ligands: SA8.3, TRP.4 50 PLIP interactions: 47 interactions with chain A, 2 Ligand-Ligand interactions, 1 Ligand-Water interactions Hydrophobic interactions: A:I.17, A:Y.20, A:L.25, A:I.106, A:I.106, A:V.125, A:V.235, A:H.268, A:Y.308, A:F.547, W.4, W.4 Hydrogen bonds: A:N.11, A:P.15, A:I.17, A:R.69, A:N.70, A:T.71, A:T.71, A:G.105, A:I.106, A:T.110, A:G.129, A:E.130, A:S.220, A:E.236, A:E.236, A:K.240, A:K.240, A:T.270, A:N.528, A:Y.529, A:A.530 Water bridges: A:A.18, A:Y.20, A:A.21, A:R.69, A:R.69, A:S.109, A:G.127, A:G.127, A:L.218, A:S.220, A:S.220, A:V.235, A:S.272, A:S.272, A:S.272 Salt bridges: A:K.240 Metal complexes: H2O.3

1 x SA8: S-5'-AZAMETHIONINE-5'-DEOXYADENOSINE(Non-covalent)

SA8.3: 16 residues within 4Å: Chain A: V.74, H.233, E.236, S.272, E.273, Y.308, D.335, E.377, L.379, S.408, G.410, L.411, R.412 Ligands: SF4.1, B12.2, TRP.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.308 Hydrogen bonds: A:E.236, A:D.335, A:S.408, A:S.408, A:R.412, A:R.412 Water bridges: A:Y.308, A:E.377, A:A.378 Salt bridges: A:E.377

1 x TRP: TRYPTOPHAN(Non-covalent)

TRP.4: 10 residues within 4Å: Chain A: V.74, Y.308, N.331, M.375, E.377, N.527, Y.529, W.548 Ligands: B12.2, SA8.3 7 PLIP interactions: 2 Ligand-Ligand interactions, 5 interactions with chain A Hydrogen bonds: W.4, W.4, A:E.377, A:N.527, A:N.527 Hydrophobic interactions: A:Y.529 Water bridges: A:S.408

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

Tryptophan-C2-methyltransferase containing B12-binding domain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Tryptophan-C2-methyltransferase containing B12-binding domain

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