SMTL ID : 3ci3.1

Structure of the PduO-type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri complexed with partial adenosylcobalamin and PPPi

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.11 Å

Oligo State

homo-trimer

Ligands

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

NA.1: 6 residues within 4Å: Chain A: I.9, Y.10 Chain B: D.166 Ligands: MG.2, 3PO.3, B12.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.166 Water bridges: B:D.166 NA.6: 6 residues within 4Å: Chain B: I.9, Y.10 Chain C: D.166 Ligands: MG.7, 3PO.8, B12.10 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.166 Water bridges: C:D.166 NA.11: 6 residues within 4Å: Chain A: D.166 Chain C: I.9, Y.10 Ligands: MG.12, 3PO.13, B12.15 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:I.9 Water bridges: A:D.166

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: K.29 Chain B: R.138, N.162 Ligands: NA.1, 3PO.3 No protein-ligand interaction detected (PLIP) MG.7: 5 residues within 4Å: Chain B: K.29 Chain C: R.138, N.162 Ligands: NA.6, 3PO.8 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain A: R.138, N.162 Chain C: K.29 Ligands: NA.11, 3PO.13 No protein-ligand interaction detected (PLIP)

3 x 3PO: TRIPHOSPHATE(Non-covalent)

3PO.3: 16 residues within 4Å: Chain A: I.9, Y.10, T.11, K.12, N.13, G.14, Q.18, T.19, K.29 Chain B: R.138, N.162, D.166 Ligands: NA.1, MG.2, 5AD.4, B12.5 18 PLIP interactions: 7 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:N.162, A:I.9, A:T.11, A:T.11, A:K.12, A:G.14, A:D.15, A:T.19, A:T.19 Water bridges: B:R.138, B:R.138, B:N.162, B:R.163, B:S.165, A:K.29 Salt bridges: B:R.138, A:K.29, A:K.29 3PO.8: 16 residues within 4Å: Chain B: I.9, Y.10, T.11, K.12, N.13, G.14, Q.18, T.19, K.29 Chain C: R.138, N.162, D.166 Ligands: NA.6, MG.7, 5AD.9, B12.10 18 PLIP interactions: 7 interactions with chain C, 11 interactions with chain B Hydrogen bonds: C:N.162, B:I.9, B:T.11, B:T.11, B:K.12, B:G.14, B:D.15, B:T.19, B:T.19 Water bridges: C:R.138, C:R.138, C:N.162, C:R.163, C:S.165, B:K.29 Salt bridges: C:R.138, B:K.29, B:K.29 3PO.13: 16 residues within 4Å: Chain A: R.138, N.162, D.166 Chain C: I.9, Y.10, T.11, K.12, N.13, G.14, Q.18, T.19, K.29 Ligands: NA.11, MG.12, 5AD.14, B12.15 18 PLIP interactions: 11 interactions with chain C, 7 interactions with chain A Hydrogen bonds: C:I.9, C:T.11, C:T.11, C:K.12, C:G.14, C:D.15, C:T.19, C:T.19, A:N.162 Water bridges: C:K.29, A:R.138, A:R.138, A:N.162, A:R.163, A:S.165 Salt bridges: C:K.29, C:K.29, A:R.138

3 x 5AD: 5'-DEOXYADENOSINE(Non-covalent)

5AD.4: 11 residues within 4Å: Chain A: T.19, R.20, K.29, V.34, Y.37, G.38 Chain B: R.138, E.141, R.142 Ligands: 3PO.3, B12.5 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.138, B:R.138, B:E.141, B:R.142 Water bridges: B:R.142, B:S.165, A:K.29 pi-Cation interactions: B:R.138 5AD.9: 11 residues within 4Å: Chain B: T.19, R.20, K.29, V.34, Y.37, G.38 Chain C: R.138, E.141, R.142 Ligands: 3PO.8, B12.10 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:R.138, C:R.138, C:E.141, C:R.142 Water bridges: C:R.142, C:S.165, B:K.29 pi-Cation interactions: C:R.138 5AD.14: 11 residues within 4Å: Chain A: R.138, E.141, R.142 Chain C: T.19, R.20, K.29, V.34, Y.37, G.38 Ligands: 3PO.13, B12.15 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.138, A:R.138, A:E.141, A:R.142 Water bridges: A:R.142, A:S.165, C:K.29 pi-Cation interactions: A:R.138

3 x B12: COBALAMIN(Non-covalent)

B12.5: 26 residues within 4Å: Chain A: K.8, I.9, T.11, R.20, I.21, I.22, Y.37, D.41, F.73, G.76, H.77, H.88 Chain B: F.118, I.119, R.134, R.138, S.165, D.166, F.169, K.190, V.192, F.193, R.194 Ligands: NA.1, 3PO.3, 5AD.4 25 PLIP interactions: 10 interactions with chain A, 14 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: A:I.9, A:Y.37, A:F.73, B:F.118, B:F.169, B:F.169, B:V.192, B:F.193, B:F.193 Hydrogen bonds: A:R.20, A:I.21, A:G.76, B:I.119, B:I.119, B:R.134, B:D.166, B:D.166, B:R.194, B:R.194 Water bridges: A:K.8, A:T.11, A:H.77, B:R.134 Salt bridges: A:H.88 Metal complexes: H2O.7 B12.10: 26 residues within 4Å: Chain B: K.8, I.9, T.11, R.20, I.21, I.22, Y.37, D.41, F.73, G.76, H.77, H.88 Chain C: F.118, I.119, R.134, R.138, S.165, D.166, F.169, K.190, V.192, F.193, R.194 Ligands: NA.6, 3PO.8, 5AD.9 25 PLIP interactions: 10 interactions with chain B, 14 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: B:I.9, B:Y.37, B:F.73, C:F.118, C:F.169, C:F.169, C:V.192, C:F.193, C:F.193 Hydrogen bonds: B:R.20, B:I.21, B:G.76, C:I.119, C:I.119, C:R.134, C:D.166, C:D.166, C:R.194, C:R.194 Water bridges: B:K.8, B:T.11, B:H.77, C:R.134 Salt bridges: B:H.88 Metal complexes: H2O.14 B12.15: 26 residues within 4Å: Chain A: F.118, I.119, R.134, R.138, S.165, D.166, F.169, K.190, V.192, F.193, R.194 Chain C: K.8, I.9, T.11, R.20, I.21, I.22, Y.37, D.41, F.73, G.76, H.77, H.88 Ligands: NA.11, 3PO.13, 5AD.14 25 PLIP interactions: 14 interactions with chain A, 10 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: A:F.118, A:F.169, A:F.169, A:V.192, A:F.193, A:F.193, C:I.9, C:Y.37, C:F.73 Hydrogen bonds: A:I.119, A:I.119, A:R.134, A:D.166, A:D.166, A:R.194, A:R.194, C:R.20, C:I.21, C:G.76 Water bridges: A:R.134, C:K.8, C:T.11, C:H.77 Salt bridges: C:H.88 Metal complexes: H2O.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

St Maurice, M. et al., Structural characterization of a human-type corrinoid adenosyltransferase confirms that coenzyme B12 is synthesized through a four-coordinate intermediate. Biochemistry (2008)

Release Date

2008-05-27

Peptides

Cobalamin adenosyltransferase PduO-like protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Cobalamin adenosyltransferase PduO-like protein

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