SMTL ID : 7r3b.2 (1 other biounit)

S-adenosylmethionine synthetase from Lactobacillus plantarum complexed with AMPPNP, methionine and SAM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.82 Å

Oligo State

homo-tetramer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 17 residues within 4Å: Chain A: H.16, P.17, D.18, D.174, K.176, S.198, T.239, F.242, G.246, D.250, A.251, K.257 Chain B: G.272, K.277, D.283 Ligands: MG.2, MG.4 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.198, A:T.239, A:D.250, A:D.250, A:K.257, B:K.277, B:K.277, B:D.283, B:D.283 Salt bridges: A:H.16, A:K.176, A:K.257 ANP.3: 18 residues within 4Å: Chain A: E.57, G.271, G.272, A.273, K.277, D.283 Chain B: H.16, D.18, D.174, K.176, G.249, D.250, A.251, R.256, K.257 Ligands: MG.5, MG.6, K.7 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:A.273, A:K.277, A:D.283, B:H.16, B:G.246, B:R.256, B:K.257 Salt bridges: A:K.281, B:H.16, B:K.176, B:K.257

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.250, A.251 Chain B: E.44 Ligands: ANP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:A.251 MG.4: 5 residues within 4Å: Chain A: E.10, K.176 Chain B: D.129, D.283 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.5: 6 residues within 4Å: Chain A: E.44 Chain B: D.18, A.251, R.256 Ligands: ANP.3, K.7 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain A: D.129, D.283 Chain B: E.10 Ligands: ANP.3 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain C: E.10 Chain D: D.283 Ligands: PPK.8 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain C: D.129, D.283 Chain D: E.10 Ligands: PPK.14 No protein-ligand interaction detected (PLIP) MG.15: 6 residues within 4Å: Chain C: D.18, A.251, L.253, R.256 Chain D: E.44 Ligands: PPK.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.44 MG.16: 5 residues within 4Å: Chain D: D.250, A.251 Ligands: SAM.12, PPK.14, K.17 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.250, D:A.251

2 x K: POTASSIUM ION(Non-covalent)

K.7: 5 residues within 4Å: Chain A: E.44 Chain B: D.250, A.251 Ligands: ANP.3, MG.5 No protein-ligand interaction detected (PLIP) K.17: 6 residues within 4Å: Chain C: E.44 Chain D: D.18, A.251, R.256 Ligands: PPK.14, MG.16 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.44

2 x PPK: (DIPHOSPHONO)AMINOPHOSPHONIC ACID(Non-covalent)

PPK.8: 15 residues within 4Å: Chain C: E.10, H.16, D.18, K.176, D.250, A.251, R.256, K.257 Chain D: G.272, A.273, K.277, D.283 Ligands: SAM.9, MG.10, MG.15 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:A.273, D:K.277, D:D.283, C:D.18, C:R.256, C:K.257 Salt bridges: C:H.16, C:K.176, C:K.257 PPK.14: 16 residues within 4Å: Chain C: G.272, A.273, K.277, D.283 Chain D: E.10, H.16, D.18, K.176, D.250, A.251, R.256, K.257 Ligands: MG.11, SAM.12, MG.16, K.17 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:D.18, D:R.256, D:K.257, C:A.273, C:K.277 Salt bridges: D:H.16, D:K.176, D:K.257

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

SAM.9: 6 residues within 4Å: Chain C: D.174, K.176, F.242, G.249, D.250 Ligands: PPK.8 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:E.57, C:D.174 Salt bridges: D:K.281, C:D.250 SAM.12: 13 residues within 4Å: Chain C: A.42, E.57, D.129 Chain D: H.16, P.17, D.174, K.176, G.245, G.246, G.249, D.250 Ligands: PPK.14, MG.16 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:H.16, D:G.249, D:G.249, D:D.250, D:D.250, C:E.57, C:E.57 Salt bridges: C:K.281

1 x PHE: PHENYLALANINE(Non-covalent)

PHE.13: 6 residues within 4Å: Chain D: L.302, V.332, A.340, L.390, K.391, A.393 5 PLIP interactions: 5 interactions with chain D, Hydrophobic interactions: D:L.302, D:V.332, D:V.332, D:A.340, D:A.393

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kleiner, D. et al., Evolution of homo-oligomerization of methionine S-adenosyltransferases is replete with structure-function constrains. Protein Sci. (2022)

Release Date

2022-07-13

Peptides

S-adenosylmethionine synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

S-adenosylmethionine synthase

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