SMTL ID : 7pd1.1 (1 other biounit)

Crystal structure of the L-tyrosine-bound radical SAM tyrosine lyase ThiH (2-iminoacetate synthase) from Thermosinus carboxydivorans

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.27 Å

Oligo State

monomer

Ligands

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

SF4.1: 10 residues within 4Å: Chain A: C.95, N.97, C.99, C.102, F.104, Q.105, G.140, K.209, Q.346 Ligands: MET.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Salt bridges: A:E.193 Metal complexes: A:C.95, A:C.99, A:C.102, MET.3

1 x 5AD: 5'-DEOXYADENOSINE(Non-covalent)

5AD.2: 16 residues within 4Å: Chain A: Y.101, C.102, E.168, Y.191, E.193, R.215, L.235, R.270, M.271, R.272, H.274, R.310, Q.346, F.347 Ligands: MET.3, TYR.4 9 PLIP interactions: 8 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:E.193, A:R.215, A:R.272, A:R.272, A:R.310, A:Q.346, Y.4 Water bridges: A:E.168 pi-Stacking: A:F.347

1 x MET: METHIONINE(Non-covalent)

MET.3: 11 residues within 4Å: Chain A: T.139, G.140, E.141, E.168, I.169, Y.170, K.209, R.215, Q.346 Ligands: SF4.1, 5AD.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:I.169 Water bridges: A:R.215, M.3 Salt bridges: A:K.209, A:R.215

1 x TYR: TYROSINE(Non-covalent)

TYR.4: 15 residues within 4Å: Chain A: Y.86, P.88, Y.90, L.136, L.138, E.168, Y.191, S.308, T.309, R.310, S.328, S.331, F.347 Ligands: 5AD.2, SO4.7 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:P.88, A:P.88, A:L.136, A:L.138 Hydrogen bonds: A:Y.90, A:Y.90, A:Y.191, A:T.309, A:R.310, A:R.310, A:S.328, A:S.328, A:S.331 Water bridges: A:Y.86, A:Y.86, A:S.267, A:S.267 Salt bridges: A:R.310 pi-Cation interactions: A:R.310

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 2 residues within 4Å: Chain A: R.39, R.43 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.39, A:R.40, A:R.43 Salt bridges: A:R.39, A:R.43 SO4.6: 3 residues within 4Å: Chain A: H.72, R.81 Ligands: BR.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.321 Water bridges: A:R.81 Salt bridges: A:H.72, A:R.81 SO4.7: 8 residues within 4Å: Chain A: Y.86, L.136, E.168, T.189, Y.191, S.308, R.310 Ligands: TYR.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.86, A:E.168, A:Y.191 Water bridges: A:T.189, A:S.267, A:R.310 Salt bridges: A:R.310

1 x K: POTASSIUM ION(Non-covalent)

K.8: 2 residues within 4Å: Chain A: T.116, A.118 No protein-ligand interaction detected (PLIP)

6 x BR: BROMIDE ION(Non-covalent)

BR.9: 4 residues within 4Å: Chain A: T.130, G.330, T.354, V.355 Ligand excluded by PLIP BR.10: 3 residues within 4Å: Chain A: V.96, E.141, R.143 Ligand excluded by PLIP BR.11: 3 residues within 4Å: Chain A: M.300, P.301, R.302 Ligand excluded by PLIP BR.12: 3 residues within 4Å: Chain A: T.34, D.35, S.36 Ligand excluded by PLIP BR.13: 3 residues within 4Å: Chain A: H.72, R.321 Ligands: SO4.6 Ligand excluded by PLIP BR.14: 1 residues within 4Å: Chain A: G.345 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Amara, P. et al., L-tyrosine-bound ThiH structure reveals C-C bond break differences within radical SAM aromatic amino acid lyases. Nat Commun (2022)

Release Date

2022-05-11

Peptides

Thiazole biosynthesis protein ThiH: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Thiazole biosynthesis protein ThiH

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