SMTL ID : 8urk.1 (1 other biounit)

Crystal structure of DNA N6-Adenine Methyltransferase M.BceJIV from Burkholderia cenocepacia in complex with duplex DNA substrates

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-dimer

Ligands

2 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose

GLC-FRU.1: 7 residues within 4Å: Chain A: G.76, W.106, Q.107, Y.108 Chain D: K.117, T.121, M.122 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:Q.107, A:Q.107, D:K.117, D:M.122 Water bridges: A:G.76 GLC-FRU.2: 11 residues within 4Å: Chain A: L.181 Chain D: M.135, G.136, G.137 Chain E: T.4, T.5, A.6, T.9 Chain F: G.8, T.9, T.10 29 PLIP interactions: 24 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: D:L.63, A:L.181, A:F.182 Hydrogen bonds: D:Q.107, D:R.130, D:S.134, D:S.134, D:T.138, D:T.138, D:S.144, D:D.147, D:R.202, D:Q.206, D:Q.206, D:Q.216, A:R.179 Water bridges: D:R.130, D:R.130, D:M.135, D:H.146, D:L.203, D:L.203, D:Q.206, A:K.180 Salt bridges: D:K.65, D:R.141, D:R.205, D:R.210 pi-Cation interactions: A:R.179

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

EPE.3: 9 residues within 4Å: Chain A: M.135, G.136 Chain B: T.5, A.6, T.9 Chain C: G.8, T.9, T.10 Chain D: L.181 No protein-ligand interaction detected (PLIP)

2 x SFG: SINEFUNGIN

SFG.4: 23 residues within 4Å: Chain A: R.38, D.39, F.40, L.41, D.58, Y.67, N.69, S.71, H.213, T.215, Q.216, K.217, P.239, F.240, M.241, G.242, S.243, T.245, Y.260, E.261, I.262, Y.266 Chain B: A.7 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.67 Hydrogen bonds: A:D.39, A:D.39, A:F.40, A:D.58, A:D.58, A:N.69, A:H.213, A:T.215, A:K.217, A:S.243, A:T.245, A:I.262 Salt bridges: A:H.213 pi-Stacking: A:F.240, A:F.240 SFG.5: 22 residues within 4Å: Chain D: R.38, D.39, F.40, D.58, Y.67, N.69, S.71, H.213, T.215, Q.216, K.217, P.239, F.240, M.241, G.242, S.243, T.245, Y.260, E.261, I.262, Y.266 Chain E: A.7 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:D.39, D:D.39, D:F.40, D:D.58, D:D.58, D:N.69, D:H.213, D:T.215, D:K.217, D:S.243, D:T.245, D:I.262 Water bridges: D:F.240, D:M.241 Salt bridges: D:H.213 pi-Stacking: D:F.240, D:F.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Quintana-Feliciano, R. et al., Burkholderia cenocepacia epigenetic regulator M.BceJIV simultaneously engages two DNA recognition sequences for methylation. Nat Commun (2024)

Release Date

2024-09-11

Peptides

Methyltransferase: AD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

Methyltransferase

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