SMTL ID : 5vz0.1

Crystal structure of Lactococcus lactis pyruvate carboxylase G746A mutant in complex with cyclic-di-AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: D.541, K.710, H.739, H.741 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.541, A:H.739, A:H.741, H2O.3 MN.5: 4 residues within 4Å: Chain B: D.541, K.710, H.739, H.741 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.541, B:H.739, B:H.741, H2O.15 MN.8: 4 residues within 4Å: Chain C: D.541, K.710, H.739, H.741 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.541, C:H.739, C:H.741, H2O.27 MN.10: 4 residues within 4Å: Chain D: D.541, K.710, H.739, H.741 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.541, D:H.739, D:H.741, H2O.39

3 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 19 residues within 4Å: Chain A: K.123, I.138, M.162, K.164, G.168, M.174, E.206, K.207, Y.208, I.209, H.214, Q.238, N.241, E.281, L.283, I.292, E.293, T.449 Ligands: MG.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:E.206, A:K.207, A:I.209, A:H.214, A:Q.238, A:N.241, A:T.449, A:T.449 Water bridges: A:Y.208 Salt bridges: A:K.123, A:K.123, A:K.164 ADP.6: 18 residues within 4Å: Chain B: K.123, I.138, M.162, K.164, M.174, E.206, K.207, Y.208, I.209, H.214, Q.238, N.241, E.281, L.283, I.292, E.293, T.449 Ligands: MG.7 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:E.206, B:K.207, B:I.209, B:H.214, B:Q.238, B:N.241, B:E.293, B:T.449, B:T.449 Salt bridges: B:K.123, B:K.123, B:K.164 ADP.11: 18 residues within 4Å: Chain D: K.123, I.138, M.162, K.164, M.174, E.206, K.207, Y.208, I.209, H.214, Q.238, N.241, E.281, L.283, I.292, E.293, T.449 Ligands: MG.12 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:E.206, D:I.209, D:H.214, D:Q.238, D:N.241, D:T.449 Salt bridges: D:K.123, D:K.123, D:K.164

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: E.281, E.293 Ligands: ADP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.281, A:E.293 MG.7: 3 residues within 4Å: Chain B: E.281, E.293 Ligands: ADP.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.281, B:E.293, H2O.11 MG.12: 3 residues within 4Å: Chain D: E.281, E.293 Ligands: ADP.11 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.281, D:E.293, H2O.34

2 x 2BA: (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide(Non-covalent)

2BA.4: 14 residues within 4Å: Chain A: P.718, Q.719, Y.722, I.749, S.752, A.753, Q.756 Chain B: P.718, Q.719, Y.722, I.749, S.752, A.753, Q.756 19 PLIP interactions: 8 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:S.752, A:S.752, A:Q.756, B:S.752, B:Q.756 Water bridges: A:Q.719, A:Q.719, A:A.784, B:Q.719, B:Q.719, B:Y.722, B:Y.722, B:R.723, B:S.752, B:Q.756 pi-Stacking: A:Y.722, A:Y.722, B:Y.722, B:Y.722 2BA.9: 14 residues within 4Å: Chain C: P.718, Q.719, Y.722, I.749, S.752, A.753, Q.756 Chain D: P.718, Q.719, Y.722, I.749, S.752, A.753, Q.756 17 PLIP interactions: 8 interactions with chain C, 9 interactions with chain D Hydrogen bonds: C:S.752, C:Q.756, D:Y.722, D:S.752, D:S.752, D:Q.756 Water bridges: C:Q.719, C:Q.719, C:S.752, C:A.784, D:Q.719, D:Q.719, D:A.784 pi-Stacking: C:Y.722, C:Y.722, D:Y.722, D:Y.722

Links

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Citation

Choi, P.H. et al., Structural and functional studies of pyruvate carboxylase regulation by cyclic di-AMP in lactic acid bacteria. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-08-16

Peptides

Pyruvate carboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate carboxylase