SMTL ID : 3noj.1 (1 other biounit)

The structure of HMG/CHA aldolase from the protocatechuate degradation pathway of Pseudomonas putida

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.124 Ligands: PYR.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.124, H2O.1, H2O.1, H2O.4 MG.5: 2 residues within 4Å: Chain B: D.124 Ligands: PYR.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.124, H2O.5, H2O.6, H2O.9 MG.9: 2 residues within 4Å: Chain C: D.124 Ligands: PYR.10 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.124, H2O.10, H2O.11, H2O.14 MG.13: 2 residues within 4Å: Chain D: D.124 Ligands: PYR.14 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.124, H2O.15, H2O.16, H2O.19 MG.17: 2 residues within 4Å: Chain E: D.124 Ligands: PYR.18 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.124, H2O.20, H2O.21, H2O.24 MG.21: 2 residues within 4Å: Chain F: D.124 Ligands: PYR.22 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.124, H2O.25, H2O.26, H2O.29

6 x PYR: PYRUVIC ACID(Non-covalent)

PYR.2: 9 residues within 4Å: Chain A: Y.99, F.100, G.101, D.102, L.103, L.104, R.123, D.124 Ligands: MG.1 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.101, A:L.103, A:L.104, A:R.123, A:D.124 Water bridges: B:R.195, B:R.195, B:R.203 PYR.6: 9 residues within 4Å: Chain B: Y.99, F.100, G.101, D.102, L.103, L.104, R.123, D.124 Ligands: MG.5 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:G.101, B:L.103, B:L.104, B:R.123, B:D.124 Water bridges: C:R.195, C:R.195, C:R.203 PYR.10: 9 residues within 4Å: Chain C: Y.99, F.100, G.101, D.102, L.103, L.104, R.123, D.124 Ligands: MG.9 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain C Water bridges: A:R.195, A:R.195, A:R.203 Hydrogen bonds: C:G.101, C:L.103, C:L.104, C:R.123, C:D.124 PYR.14: 9 residues within 4Å: Chain D: Y.99, F.100, G.101, D.102, L.103, L.104, R.123, D.124 Ligands: MG.13 9 PLIP interactions: 3 interactions with chain E, 6 interactions with chain D Water bridges: E:R.195, E:R.195, E:R.203 Hydrogen bonds: D:G.101, D:L.103, D:L.104, D:R.123, D:D.124, D:D.124 PYR.18: 9 residues within 4Å: Chain E: Y.99, F.100, G.101, D.102, L.103, L.104, R.123, D.124 Ligands: MG.17 9 PLIP interactions: 3 interactions with chain F, 6 interactions with chain E Water bridges: F:R.195, F:R.195, F:R.203 Hydrogen bonds: E:G.101, E:L.103, E:L.104, E:R.123, E:D.124, E:D.124 PYR.22: 9 residues within 4Å: Chain F: Y.99, F.100, G.101, D.102, L.103, L.104, R.123, D.124 Ligands: MG.21 9 PLIP interactions: 6 interactions with chain F, 3 interactions with chain D Hydrogen bonds: F:G.101, F:L.103, F:L.104, F:R.123, F:D.124, F:D.124 Water bridges: D:R.195, D:R.195, D:R.203

12 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 6 residues within 4Å: Chain A: R.28, L.29, R.203 Chain C: T.127, D.130, M.131 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.28 Water bridges: A:T.33, A:T.33, A:S.56 PG4.4: 9 residues within 4Å: Chain A: R.49, P.50, I.51, A.137, R.138, A.139, I.140 Chain B: S.46, R.49 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:I.140, B:S.46 Water bridges: B:S.46 PG4.7: 6 residues within 4Å: Chain A: T.127, D.130, M.131 Chain B: R.28, L.29, R.203 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.28 Water bridges: B:T.33, B:T.33, B:S.56 PG4.8: 9 residues within 4Å: Chain B: R.49, P.50, I.51, A.137, R.138, A.139, I.140 Chain C: S.46, R.49 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:I.140, C:S.46 Water bridges: C:S.46 PG4.11: 6 residues within 4Å: Chain B: T.127, D.130, M.131 Chain C: R.28, L.29, R.203 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.28 Water bridges: C:T.33, C:T.33, C:S.56 PG4.12: 9 residues within 4Å: Chain A: S.46, R.49 Chain C: R.49, P.50, I.51, A.137, R.138, A.139, I.140 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:I.140, A:S.46 Water bridges: A:S.46 PG4.15: 6 residues within 4Å: Chain D: R.28, L.29, R.203 Chain F: T.127, D.130, M.131 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:R.28 Water bridges: D:S.56, D:R.203, F:T.127 PG4.16: 9 residues within 4Å: Chain D: R.49, P.50, I.51, A.137, R.138, A.139, I.140 Chain E: S.46, R.49 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:S.46, D:I.140 Water bridges: E:S.46 PG4.19: 6 residues within 4Å: Chain D: T.127, D.130, M.131 Chain E: R.28, L.29, R.203 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:R.28 Water bridges: E:S.56, E:R.203, D:T.127 PG4.20: 9 residues within 4Å: Chain E: R.49, P.50, I.51, A.137, R.138, A.139, I.140 Chain F: S.46, R.49 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:I.140, F:S.46 Water bridges: F:S.46 PG4.23: 6 residues within 4Å: Chain E: T.127, D.130, M.131 Chain F: R.28, L.29, R.203 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:R.28 Water bridges: F:S.56, F:R.203, E:T.127 PG4.24: 9 residues within 4Å: Chain D: S.46, R.49 Chain F: R.49, P.50, I.51, A.137, R.138, A.139, I.140 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:S.46, F:I.140 Water bridges: D:S.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, W. et al., Structural and Kinetic Characterization of 4-Hydroxy-4-methyl-2-oxoglutarate/4-Carboxy-4-hydroxy-2-oxoadipate Aldolase, a Protocatechuate Degradation Enzyme Evolutionarily Convergent with the HpaI and DmpG Pyruvate Aldolases. J.Biol.Chem. (2010)

Release Date

2010-09-15

Peptides

4-carboxy-4-hydroxy-2-oxoadipate aldolase/oxaloacetate decarboxylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

4-carboxy-4-hydroxy-2-oxoadipate aldolase/oxaloacetate decarboxylase

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