SMTL ID : 8fsi.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

monomer

Ligands

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

SF4.1: 11 residues within 4Å: Chain A: C.29, M.31, R.32, C.33, Y.35, C.36, 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: 24 residues within 4Å: Chain A: 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, Y.216 Ligands: SF4.1, K.3, K.5 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Y.35, A:Y.35, A:Y.35, A:H.37, A:G.78, A:K.131, A:H.202 Salt bridges: A:D.104, A:K.131 pi-Stacking: A:Y.35, A:H.37, A:H.202

2 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain A: D.104, T.105, M.127, L.128, D.129 Ligands: SAM.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.104, A:T.105, A:M.127, A:D.129 K.5: 8 residues within 4Å: Chain A: Y.35, C.36, H.37, E.203, L.204, W.209, Y.216 Ligands: SAM.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:Y.35, A:L.204, A:Y.216

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 7 residues within 4Å: Chain A: C.29, L.30, M.31, E.79, L.82, N.106, F.108 Ligand excluded by PLIP

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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