SMTL ID : 6s83.2 (3 other biounits)

Crystal structure of methionine adenosyltransferase from Pyrococcus furiosus in complex with AMPPCP, SAM, and PCP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

homo-dimer

Ligands

1 x MDN: METHYLENEDIPHOSPHONIC ACID(Non-covalent)

MDN.1: 15 residues within 4Å: Chain A: K.26, H.30, D.32, K.200, R.286 Chain B: D.63, D.159, S.161, E.303, K.308, H.313 Ligands: PO4.2, MG.3, MG.4, MG.5 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:K.26, A:H.30, A:K.200, A:R.286, B:S.161, B:K.308, B:H.313 Water bridges: A:D.281, B:Q.64, B:D.159, B:D.159

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 10 residues within 4Å: Chain A: K.26, D.32, R.286 Chain B: M.302, E.303, A.304, K.308 Ligands: MDN.1, MG.3, MG.4 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Salt bridges: A:K.26, A:R.286, B:K.308 Hydrogen bonds: B:M.302, B:A.304, B:A.304 PO4.7: 10 residues within 4Å: Chain A: M.302, E.303, A.304, K.308 Chain B: K.26, D.32, R.286 Ligands: ACP.6, MG.8, MG.9 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:M.302, A:A.304 Water bridges: A:E.303, A:E.303, B:K.26, B:R.286, B:R.286, B:R.286 Salt bridges: A:K.308, B:K.26, B:R.286

5 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: K.26, H.30, D.32, R.286 Ligands: MDN.1, PO4.2 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.32, H2O.1, H2O.1 MG.4: 7 residues within 4Å: Chain A: K.26 Chain B: S.161, E.303, K.308, H.313 Ligands: MDN.1, PO4.2 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.303, B:E.303, H2O.4 MG.5: 5 residues within 4Å: Chain A: D.281, R.286 Chain B: D.63, Q.64 Ligands: MDN.1 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.63, B:D.63, H2O.1, H2O.2, H2O.4 MG.8: 7 residues within 4Å: Chain A: Q.64 Chain B: K.26, H.30, D.32, R.286 Ligands: ACP.6, PO4.7 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.32, H2O.3, H2O.4, H2O.5 MG.9: 5 residues within 4Å: Chain B: E.24, K.26, K.200 Ligands: ACP.6, PO4.7 No protein-ligand interaction detected (PLIP)

1 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.6: 18 residues within 4Å: Chain A: E.303, K.308, H.313 Chain B: K.26, H.30, P.31, D.32, D.198, K.200, A.215, N.257, A.259, Y.268, S.275, D.280 Ligands: PO4.7, MG.8, MG.9 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.26, B:H.30, B:D.198, B:K.200, B:Y.268, B:D.280, A:E.303, A:H.313 Water bridges: B:A.259, B:D.260 Salt bridges: B:K.200 pi-Stacking: B:Y.268, B:Y.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minici, C. et al., Structures of catalytic cycle intermediates of the Pyrococcus furiosus methionine adenosyltransferase demonstrate negative cooperativity in the archaeal orthologues. J.Struct.Biol. (2020)

Release Date

2020-02-05

Peptides

S-adenosylmethionine synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

S-adenosylmethionine synthase

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