SMTL ID : 1xg3.1

Crystal structure of the C123S 2-methylisocitrate lyase mutant from Escherichia coli in complex with the reaction product, Mg(II)-pyruvate and succinate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: G.46, D.57, D.84, D.86, K.120 Ligands: PYR.2 5 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: A:D.84, PYR.2, H2O.10, H2O.10, H2O.10 MG.4: 6 residues within 4Å: Chain B: G.46, D.57, D.84, D.86, K.120 Ligands: PYR.5 5 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: B:D.84, PYR.5, H2O.21, H2O.21, H2O.21 MG.7: 3 residues within 4Å: Chain C: D.57, D.84 Ligands: PYR.8 5 PLIP interactions: 1 interactions with chain C, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: C:D.84, PYR.8, H2O.31, H2O.31, H2O.31 MG.9: 7 residues within 4Å: Chain D: G.46, D.57, D.84, D.86, K.120, R.157 Ligands: PYR.10 5 PLIP interactions: 1 interactions with chain D, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: D:D.84, PYR.10, H2O.41, H2O.41, H2O.41

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.2: 11 residues within 4Å: Chain A: Y.42, S.44, G.45, G.46, D.57, D.84, R.157, N.209, P.235 Ligands: MG.1, SIN.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.235 Hydrogen bonds: A:Y.42, A:G.45, A:G.46, A:R.157 PYR.5: 11 residues within 4Å: Chain B: Y.42, S.44, G.45, G.46, D.84, H.112, R.157, N.209, P.235 Ligands: MG.4, SIN.6 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.235 Hydrogen bonds: B:Y.42, B:G.45, B:G.46, B:R.157 Water bridges: B:K.120 PYR.8: 10 residues within 4Å: Chain C: Y.42, S.44, G.45, G.46, D.84, H.112, R.157, N.209, P.235 Ligands: MG.7 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.45, C:G.46 Water bridges: C:S.44, C:S.44, C:R.157 PYR.10: 12 residues within 4Å: Chain D: Y.42, S.44, G.45, G.46, D.57, D.84, H.112, R.157, N.209, P.235 Ligands: MG.9, SIN.11 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.45, D:G.46, D:R.157 Water bridges: D:K.120

3 x SIN: SUCCINIC ACID(Non-covalent)

SIN.3: 11 residues within 4Å: Chain A: D.57, S.122, G.123, H.124, R.157, E.187, N.209, T.211, R.240 Chain B: R.269 Ligands: PYR.2 12 PLIP interactions: 1 interactions with chain B, 11 interactions with chain A Salt bridges: B:R.269, A:H.124, A:R.157, A:R.240 Hydrogen bonds: A:S.122, A:G.123, A:E.187, A:N.209 Water bridges: A:D.57, A:K.120, A:R.240, A:R.240 SIN.6: 11 residues within 4Å: Chain A: R.269 Chain B: S.122, G.123, H.124, R.157, E.187, N.209, T.211, L.236, R.240 Ligands: PYR.5 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.122, B:G.123, B:H.124, B:E.187, B:N.209 Water bridges: B:D.57, B:R.157, B:R.240, B:R.240 Salt bridges: B:H.124, B:R.157, B:R.240, A:R.269 SIN.11: 10 residues within 4Å: Chain C: R.269 Chain D: S.122, G.123, H.124, R.157, E.187, N.209, T.211, R.240 Ligands: PYR.10 11 PLIP interactions: 1 interactions with chain C, 10 interactions with chain D Salt bridges: C:R.269, D:R.157, D:R.240 Hydrogen bonds: D:S.122, D:G.123, D:N.209, D:T.211 Water bridges: D:D.57, D:R.157, D:R.240, D:R.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, S. et al., Crystal Structures of 2-Methylisocitrate Lyase in Complex with Product and with Isocitrate Inhibitor Provide Insight into Lyase Substrate Specificity, Catalysis and Evolution. Biochemistry (2005)

Release Date

2005-03-01

Peptides

Probable methylisocitrate lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Probable methylisocitrate lyase

Related Entries With Identical Sequence