SMTL ID : 3gai.1

Structure of a F112A variant PduO-type ATP:corrinoid adenosyltransferase from Lactobacillus reuteri complexed with cobalamin and ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

homo-trimer

Ligands

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

ATP.1: 21 residues within 4Å: Chain A: R.138, E.141, R.142, N.162, D.166 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 Ligands: B12.2, MG.3, K.4 24 PLIP interactions: 12 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:T.11, B:K.12, B:G.14, B:Q.18, B:T.19, B:R.20, B:K.29, B:Y.37, A:R.138, A:R.138, A:R.142, A:N.162 Water bridges: B:R.20, B:R.20, A:R.138, A:R.138, A:N.162, A:R.163, A:S.165 Salt bridges: B:K.29, B:K.29, A:R.138 pi-Cation interactions: A:R.138, A:R.138 ATP.11: 21 residues within 4Å: Chain B: 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: B12.12, MG.13, K.14 24 PLIP interactions: 12 interactions with chain B, 12 interactions with chain C Hydrogen bonds: B:R.138, B:R.138, B:R.142, B:N.162, C:T.11, C:K.12, C:G.14, C:Q.18, C:T.19, C:R.20, C:K.29, C:Y.37 Water bridges: B:R.138, B:R.138, B:N.162, B:R.163, B:S.165, C:R.20, C:R.20 Salt bridges: B:R.138, C:K.29, C:K.29 pi-Cation interactions: B:R.138, B:R.138 ATP.21: 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 C: R.138, E.141, R.142, N.162, D.166 Ligands: B12.22, MG.23, K.24 24 PLIP interactions: 12 interactions with chain C, 12 interactions with chain A Hydrogen bonds: C:R.138, C:R.138, C:R.142, C:N.162, A:T.11, A:K.12, A:G.14, A:Q.18, A:T.19, A:R.20, A:K.29, A:Y.37 Water bridges: C:R.138, C:R.138, C:N.162, C:R.163, C:S.165, A:R.20, A:R.20 Salt bridges: C:R.138, A:K.29, A:K.29 pi-Cation interactions: C:R.138, C:R.138

3 x B12: COBALAMIN(Non-covalent)

B12.2: 23 residues within 4Å: Chain A: K.116, K.117, A.118, I.119, R.134, R.138, S.165, D.166, F.169, Y.186 Chain B: K.8, I.9, T.11, R.20, I.22, Y.37, F.73, G.76, H.77, A.80 Ligands: ATP.1, K.4, CL.6 15 PLIP interactions: 6 interactions with chain A, 8 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:F.169, A:F.169, B:I.9, B:I.22, B:Y.37, B:F.73 Hydrogen bonds: A:I.119, A:I.119, A:R.134, A:S.165, B:T.11, B:T.11, B:G.76, B:H.77 Metal complexes: B12.2 B12.12: 23 residues within 4Å: Chain B: K.116, K.117, A.118, I.119, R.134, R.138, S.165, D.166, F.169, Y.186 Chain C: K.8, I.9, T.11, R.20, I.22, Y.37, F.73, G.76, H.77, A.80 Ligands: ATP.11, K.14, CL.16 15 PLIP interactions: 8 interactions with chain C, 6 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: C:I.9, C:I.22, C:Y.37, C:F.73, B:F.169, B:F.169 Hydrogen bonds: C:T.11, C:T.11, C:G.76, C:H.77, B:I.119, B:I.119, B:R.134, B:S.165 Metal complexes: B12.12 B12.22: 23 residues within 4Å: Chain A: K.8, I.9, T.11, R.20, I.22, Y.37, F.73, G.76, H.77, A.80 Chain C: K.116, K.117, A.118, I.119, R.134, R.138, S.165, D.166, F.169, Y.186 Ligands: ATP.21, K.24, CL.26 15 PLIP interactions: 8 interactions with chain A, 6 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: A:I.9, A:I.22, A:Y.37, A:F.73, C:F.169, C:F.169 Hydrogen bonds: A:T.11, A:T.11, A:G.76, A:H.77, C:I.119, C:I.119, C:R.134, C:S.165 Metal complexes: B12.22

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: N.162 Chain B: K.29 Ligands: ATP.1, K.4 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain B: N.162 Chain C: K.29 Ligands: ATP.11, K.14 No protein-ligand interaction detected (PLIP) MG.23: 4 residues within 4Å: Chain A: K.29 Chain C: N.162 Ligands: ATP.21, K.24 No protein-ligand interaction detected (PLIP)

6 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain A: D.166 Chain B: I.9 Ligands: ATP.1, B12.2, MG.3 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Metal complexes: B:I.9, A:D.166, A:D.166 K.5: 5 residues within 4Å: Chain A: T.81, P.82, A.83, D.85, H.88 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.83, A:D.85, A:H.88, H2O.3, H2O.3 K.14: 5 residues within 4Å: Chain B: D.166 Chain C: I.9 Ligands: ATP.11, B12.12, MG.13 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Metal complexes: C:I.9, B:D.166, B:D.166 K.15: 5 residues within 4Å: Chain B: T.81, P.82, A.83, D.85, H.88 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.83, B:D.85, B:H.88, H2O.9, H2O.9 K.24: 5 residues within 4Å: Chain A: I.9 Chain C: D.166 Ligands: ATP.21, B12.22, MG.23 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Metal complexes: C:D.166, C:D.166, A:I.9 K.25: 5 residues within 4Å: Chain C: T.81, P.82, A.83, D.85, H.88 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:A.83, C:D.85, C:H.88, H2O.15, H2O.15

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 4 residues within 4Å: Chain A: K.117, A.118, Y.186 Ligands: B12.2 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: R.87 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain B: K.117, A.118, Y.186 Ligands: B12.12 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain B: R.87 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain C: K.117, A.118, Y.186 Ligands: B12.22 Ligand excluded by PLIP CL.27: 1 residues within 4Å: Chain C: R.87 Ligand excluded by PLIP

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 6 residues within 4Å: Chain A: E.67, L.71, Q.96, P.97, W.100 Chain C: R.187 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:E.67, A:E.67, C:R.187 GOL.9: 5 residues within 4Å: Chain A: R.142, Q.143, Q.146 Chain B: N.30, A.35 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.30, A:R.142, A:R.142, A:Q.143 GOL.10: 5 residues within 4Å: Chain A: A.114, V.115, K.116, K.117, L.185 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.116, A:K.117, A:K.117, A:K.117 GOL.18: 6 residues within 4Å: Chain A: R.187 Chain B: E.67, L.71, Q.96, P.97, W.100 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.67, B:E.67, A:R.187 GOL.19: 5 residues within 4Å: Chain B: R.142, Q.143, Q.146 Chain C: N.30, A.35 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.142, B:R.142, B:Q.143, C:N.30 GOL.20: 5 residues within 4Å: Chain B: A.114, V.115, K.116, K.117, L.185 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.116, B:K.117, B:K.117, B:K.117 GOL.28: 6 residues within 4Å: Chain B: R.187 Chain C: E.67, L.71, Q.96, P.97, W.100 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.187, C:E.67, C:E.67 GOL.29: 5 residues within 4Å: Chain A: N.30, A.35 Chain C: R.142, Q.143, Q.146 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.142, C:R.142, C:Q.143, A:N.30 GOL.30: 5 residues within 4Å: Chain C: A.114, V.115, K.116, K.117, L.185 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.116, C:K.117, C:K.117, C:K.117

Links

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Citation

Mera, P.E. et al., Residue Phe112 of the human-type corrinoid adenosyltransferase (PduO) enzyme of Lactobacillus reuteri is critical to the formation of the four-coordinate Co(II) corrinoid substrate and to the activity of the enzyme. Biochemistry (2009)

Release Date

2009-07-07

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