SMTL ID : 4njk.1

Crystal Structure of QueE from Burkholderia multivorans in complex with AdoMet, 7-carboxy-7-deazaguanine, and Mg2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

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

SF4.1: 10 residues within 4Å: Chain A: C.51, L.53, W.54, C.66, C.69, F.73, G.112, N.138, K.155 Ligands: SAM.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.51, A:C.66, A:C.69, SAM.2 SF4.6: 10 residues within 4Å: Chain B: C.51, L.53, W.54, C.66, C.69, F.73, G.112, N.138, K.155 Ligands: SAM.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:C.51, B:C.66, B:C.69, SAM.7

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

SAM.2: 23 residues within 4Å: Chain A: E.35, F.68, C.69, D.70, T.71, T.110, G.111, G.112, E.113, E.136, T.137, N.138, S.153, K.155, K.169, V.171, Q.193, P.194, M.195, D.196, Q.222 Ligands: SF4.1, 2KA.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:E.136 Hydrogen bonds: A:D.70, A:E.113, A:E.136, A:S.153, A:K.155, A:K.169, A:Q.193, A:D.196, A:D.196 Water bridges: A:T.137, A:C.151, A:V.171, A:Q.222 Salt bridges: A:K.155 pi-Stacking: A:F.68 pi-Cation interactions: A:K.225 SAM.7: 23 residues within 4Å: Chain B: E.35, F.68, C.69, D.70, T.71, T.110, G.111, G.112, E.113, E.136, T.137, N.138, S.153, K.155, K.169, V.171, Q.193, P.194, M.195, D.196, Q.222 Ligands: SF4.6, 2KA.8 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:E.136 Hydrogen bonds: B:D.70, B:E.113, B:E.113, B:E.136, B:E.136, B:E.136, B:S.153, B:K.155, B:K.155, B:K.169, B:Q.193, B:D.196, B:D.196 Water bridges: B:T.137, B:Q.222 Salt bridges: B:K.155 pi-Stacking: B:F.68 pi-Cation interactions: B:K.225

2 x 2KA: 2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carboxylic acid(Non-covalent)

2KA.3: 13 residues within 4Å: Chain A: T.31, L.32, Q.33, G.34, E.35, F.45, R.47, T.110, E.136, H.224, P.230 Ligands: SAM.2, MG.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.45 Hydrogen bonds: A:Q.33, A:Q.33, A:G.34, A:R.47, A:P.230, A:P.230 Salt bridges: A:R.47 pi-Stacking: A:H.224 pi-Cation interactions: A:H.224 2KA.8: 13 residues within 4Å: Chain B: T.31, L.32, Q.33, G.34, E.35, F.45, R.47, T.110, E.136, H.224, P.230 Ligands: SAM.7, MG.9 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.45 Hydrogen bonds: B:Q.33, B:Q.33, B:G.34, B:R.47, B:T.110, B:P.230, B:P.230 Water bridges: B:P.230, B:P.230 Salt bridges: B:R.47 pi-Stacking: B:H.224 pi-Cation interactions: B:H.224

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: R.47, D.70, T.71 Ligands: 2KA.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.71, H2O.1, H2O.2, H2O.8 MG.9: 4 residues within 4Å: Chain B: R.47, D.70, T.71 Ligands: 2KA.8 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.71, H2O.10

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

PO4.5: 2 residues within 4Å: Chain A: R.41, H.104 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.41, A:H.104 Salt bridges: A:R.41, A:H.104 PO4.10: 2 residues within 4Å: Chain B: R.41, H.104 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.41, B:H.104

1 x NA: SODIUM ION(Non-functional Binders)

NA.11: 1 residues within 4Å: Chain B: Q.174 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.174 Water bridges: B:Q.174, B:D.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dowling, D.P. et al., Radical SAM enzyme QueE defines a new minimal core fold and metal-dependent mechanism. Nat.Chem.Biol. (2014)

Release Date

2013-12-25

Peptides

7-carboxy-7-deazaguanine synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

7-carboxy-7-deazaguanine synthase

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