SMTL ID : 8fo0.1

The structure of a crystallizable variant of E. coli pyruvate formate-lyase activating enzyme bound to a partially cleaved SAM molecule

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

monomer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: C.29, M.31, R.32, C.33, Y.35, C.36, T.41, W.42, G.78, N.106, K.131 Ligands: SAM.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.29, A:C.33, A:C.36, SAM.2

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.2: 25 residues within 4Å: Chain A: C.29, Y.35, C.36, H.37, N.38, S.76, G.77, G.78, E.79, D.104, T.105, N.106, D.129, K.131, R.166, V.168, L.199, P.200, Y.201, H.202, E.203, L.204, Y.216 Ligands: SF4.1, K.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:H.37, A:G.78, A:T.105, A:D.129, A:K.131, A:R.166, A:R.166, A:H.202, A:H.202 Water bridges: A:H.202, A:H.202, A:Y.216 Salt bridges: A:D.104, A:K.131 pi-Stacking: A:Y.35, A:H.37, A:H.202

1 x K: POTASSIUM ION(Non-covalent)

K.3: 7 residues within 4Å: Chain A: D.104, T.105, M.127, L.128, D.129, R.166 Ligands: SAM.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.104, A:T.105, A:D.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moody, J.D. et al., Computational engineering of previously crystallized pyruvate formate-lyase activating enzyme reveals insights into SAM binding and reductive cleavage. J.Biol.Chem. (2023)

Release Date

2023-05-24

Peptides

Pyruvate formate-lyase 1-activating enzyme: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Pyruvate formate-lyase 1-activating enzyme

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