SMTL ID : 4njj.1

Crystal Structure of QueE from Burkholderia multivorans in complex with AdoMet, 6-carboxy-5,6,7,8-tetrahydropterin, and Manganese(II)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 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: 9 residues within 4Å: Chain B: C.51, 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, 2K8.3 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:E.136, A:S.153, A:K.155, A:K.155, A:K.169, A:Q.193, A:D.196, A:D.196 Water bridges: A:T.137, A:S.153 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, 2K8.8 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:D.70, B:E.113, B:E.113, B:E.136, B:E.136, B:T.137, 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:V.171 Salt bridges: B:K.155 pi-Stacking: B:F.68 pi-Cation interactions: B:K.225

2 x 2K8: (6R)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridine-6-carboxylic acid(Non-covalent)

2K8.3: 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, MN.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.33, A:G.34, A:R.47, A:P.230, A:P.230 Water bridges: A:Q.222 Salt bridges: A:R.47 pi-Stacking: A:H.224 pi-Cation interactions: A:H.224 2K8.8: 12 residues within 4Å: Chain B: L.32, Q.33, G.34, E.35, F.45, R.47, T.110, E.136, H.224, P.230 Ligands: SAM.7, MN.9 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:Q.33, B:G.34, B:R.47, B:T.110, B:E.136, B:P.230, B:P.230 Water bridges: B:P.230 Salt bridges: B:R.47 pi-Stacking: B:H.224 pi-Cation interactions: B:H.224

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.4: 3 residues within 4Å: Chain A: R.47, T.71 Ligands: 2K8.3 No protein-ligand interaction detected (PLIP) MN.5: 1 residues within 4Å: Chain A: D.72 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.72 MN.9: 3 residues within 4Å: Chain B: D.70, T.71 Ligands: 2K8.8 No protein-ligand interaction detected (PLIP) MN.10: 1 residues within 4Å: Chain B: D.72 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.72

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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