SMTL ID : 3ci4.1

Structure of the PduO-type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri complexed with four-coordinate cob(II)inamide and ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

3 x K: POTASSIUM ION(Non-covalent)

K.1: 5 residues within 4Å: Chain A: I.9 Chain B: D.166 Ligands: MG.2, ATP.3, CBY.4 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Metal complexes: A:I.9, B:D.166, B:D.166 K.5: 5 residues within 4Å: Chain B: I.9 Chain C: D.166 Ligands: MG.6, ATP.7, CBY.8 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Metal complexes: C:D.166, C:D.166, B:I.9 K.9: 5 residues within 4Å: Chain A: D.166 Chain C: I.9 Ligands: MG.10, ATP.11, CBY.12 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Metal complexes: A:D.166, A:D.166, C:I.9

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: K.29 Chain B: N.162 Ligands: K.1, ATP.3 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain B: K.29 Chain C: N.162 Ligands: K.5, ATP.7 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain A: N.162 Chain C: K.29 Ligands: K.9, ATP.11 No protein-ligand interaction detected (PLIP)

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 21 residues within 4Å: Chain A: I.9, Y.10, T.11, K.12, N.13, G.14, Q.18, T.19, R.20, K.29, V.34, Y.37, G.38 Chain B: R.138, E.141, R.142, N.162, D.166 Ligands: K.1, MG.2, CBY.4 25 PLIP interactions: 12 interactions with chain A, 13 interactions with chain B Hydrogen bonds: A:T.11, A:K.12, A:G.14, A:Q.18, A:T.19, A:R.20, B:R.138, B:R.138, B:E.141, B:R.142, B:N.162 Water bridges: A:R.20, A:R.20, A:R.20, A:K.29, B:R.138, B:R.138, B:N.162, B:R.163, B:S.165 Salt bridges: A:K.29, A:K.29, B:R.138 pi-Cation interactions: B:R.138, B:R.138 ATP.7: 21 residues within 4Å: Chain B: I.9, Y.10, T.11, K.12, N.13, G.14, Q.18, T.19, R.20, K.29, V.34, Y.37, G.38 Chain C: R.138, E.141, R.142, N.162, D.166 Ligands: K.5, MG.6, CBY.8 25 PLIP interactions: 12 interactions with chain B, 13 interactions with chain C Hydrogen bonds: B:T.11, B:K.12, B:G.14, B:Q.18, B:T.19, B:R.20, C:R.138, C:R.138, C:E.141, C:R.142, C:N.162 Water bridges: B:R.20, B:R.20, B:R.20, B:K.29, C:R.138, C:R.138, C:N.162, C:R.163, C:S.165 Salt bridges: B:K.29, B:K.29, C:R.138 pi-Cation interactions: C:R.138, C:R.138 ATP.11: 21 residues within 4Å: Chain A: R.138, E.141, R.142, N.162, D.166 Chain C: I.9, Y.10, T.11, K.12, N.13, G.14, Q.18, T.19, R.20, K.29, V.34, Y.37, G.38 Ligands: K.9, MG.10, CBY.12 25 PLIP interactions: 12 interactions with chain C, 13 interactions with chain A Hydrogen bonds: C:T.11, C:K.12, C:G.14, C:Q.18, C:T.19, C:R.20, A:R.138, A:R.138, A:E.141, A:R.142, A:N.162 Water bridges: C:R.20, C:R.20, C:R.20, 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 pi-Cation interactions: A:R.138, A:R.138

3 x CBY: COB(II)INAMIDE(Non-covalent)

CBY.4: 23 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, A.80 Chain B: F.118, I.119, R.134, R.138, S.165, D.166, F.169, V.192, F.193 Ligands: K.1, ATP.3 24 PLIP interactions: 10 interactions with chain A, 14 interactions with chain B, Hydrophobic interactions: A:I.22, A:I.22, A:Y.37, A:F.73, B:F.118, B:F.118, B:F.118, B:F.169, B:F.169, B:V.192, B:F.193, B:F.193 Hydrogen bonds: A:K.8, A:I.21, A:G.76, B:I.119, B:I.119, B:R.134, B:R.138, B:S.165 Water bridges: A:T.19, A:T.19, A:H.77, B:R.134 CBY.8: 23 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, A.80 Chain C: F.118, I.119, R.134, R.138, S.165, D.166, F.169, V.192, F.193 Ligands: K.5, ATP.7 24 PLIP interactions: 10 interactions with chain B, 14 interactions with chain C, Hydrophobic interactions: B:I.22, B:I.22, B:Y.37, B:F.73, C:F.118, C:F.118, C:F.118, C:F.169, C:F.169, C:V.192, C:F.193, C:F.193 Hydrogen bonds: B:K.8, B:I.21, B:G.76, C:I.119, C:I.119, C:R.134, C:R.138, C:S.165 Water bridges: B:T.19, B:T.19, B:H.77, C:R.134 CBY.12: 23 residues within 4Å: Chain A: F.118, I.119, R.134, R.138, S.165, D.166, F.169, V.192, F.193 Chain C: K.8, I.9, T.11, R.20, I.21, I.22, Y.37, D.41, F.73, G.76, H.77, A.80 Ligands: K.9, ATP.11 24 PLIP interactions: 14 interactions with chain A, 10 interactions with chain C, Hydrophobic interactions: A:F.118, A:F.118, A:F.118, A:F.169, A:F.169, A:V.192, A:F.193, A:F.193, C:I.22, C:I.22, C:Y.37, C:F.73 Hydrogen bonds: A:I.119, A:I.119, A:R.134, A:R.138, A:S.165, C:K.8, C:I.21, C:G.76 Water bridges: A:R.134, C:T.19, C:T.19, C:H.77

Links

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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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