SMTL ID : 4uhm.1

Characterization of a Novel Transaminase from Pseudomonas sp. Strain AAC

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.33 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 1 residues within 4Å: Chain A: D.200 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.200, H2O.12, H2O.12 MG.2: 2 residues within 4Å: Chain A: A.124, D.132 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:A.124, H2O.7, H2O.7, H2O.7, H2O.7 MG.13: 1 residues within 4Å: Chain B: D.200 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.200, H2O.34, H2O.34 MG.14: 2 residues within 4Å: Chain B: A.124, D.132 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:A.124, H2O.29, H2O.29, H2O.29, H2O.30

4 x EOH: ETHANOL(Non-functional Binders)

EOH.3: 2 residues within 4Å: Chain A: P.195 Chain B: D.198 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.198 Water bridges: B:D.198, B:D.198, B:D.198 Hydrophobic interactions: A:P.195 EOH.4: 4 residues within 4Å: Chain A: K.259, G.260, F.297 Ligands: CL.12 2 PLIP interactions: 2 interactions with chain A Water bridges: A:P.258, A:L.262 EOH.15: 2 residues within 4Å: Chain A: D.198 Chain B: P.195 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:D.198, A:D.198, A:D.198 Hydrophobic interactions: B:P.195 EOH.16: 4 residues within 4Å: Chain B: K.259, G.260, F.297 Ligands: CL.24 2 PLIP interactions: 2 interactions with chain B Water bridges: B:P.258, B:L.262

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: Y.154, W.155, D.273, L.275, D.302, E.325 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.273, A:D.273 Water bridges: A:D.273, A:D.273, A:I.274, A:S.323 GOL.6: 3 residues within 4Å: Chain A: N.369, Q.372, E.376 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.369, A:N.369 GOL.7: 6 residues within 4Å: Chain A: L.229, R.264, E.267, I.268, A.271, N.272 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.264, A:R.264, A:N.272, A:N.272 GOL.17: 6 residues within 4Å: Chain B: Y.154, W.155, D.273, L.275, D.302, E.325 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.273, B:E.325 Water bridges: B:Y.154, B:D.273, B:D.273, B:I.274, B:S.323 GOL.18: 3 residues within 4Å: Chain B: N.369, Q.372, E.376 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.369, B:N.369 GOL.19: 6 residues within 4Å: Chain B: L.229, R.264, E.267, I.268, A.271, N.272 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.264, B:R.264, B:N.272, B:N.272

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 7 residues within 4Å: Chain A: R.152, R.156, A.161, T.164 Chain B: M.192, F.193, G.194 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:G.194 Hydrogen bonds: A:R.156 EDO.9: 8 residues within 4Å: Chain A: I.100, D.104 Chain B: S.88, R.89, I.92, A.93, N.312, A.314 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.89, B:A.93, B:N.312, B:N.312 EDO.20: 7 residues within 4Å: Chain A: M.192, F.193, G.194 Chain B: R.152, R.156, A.161, T.164 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.156 Water bridges: A:G.194 EDO.21: 8 residues within 4Å: Chain A: S.88, R.89, I.92, A.93, N.312, A.314 Chain B: I.100, D.104 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.104, A:R.89, A:A.93, A:N.312, A:N.312

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.10: 14 residues within 4Å: Chain A: S.139, G.140, S.141, Y.173, H.174, G.175, E.246, S.251, D.279, V.281, I.282, K.308 Chain B: Y.346, T.347 14 PLIP interactions: 4 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:T.347, B:T.347, B:T.347, A:S.139, A:G.140, A:S.141, A:S.251, A:S.251, A:K.308 Water bridges: B:Y.348 Hydrophobic interactions: A:E.246, A:V.281 Salt bridges: A:K.308 pi-Stacking: A:Y.173 PLP.22: 14 residues within 4Å: Chain A: Y.346, T.347 Chain B: S.139, G.140, S.141, Y.173, H.174, G.175, E.246, S.251, D.279, V.281, I.282, K.308 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:E.246, B:V.281 Hydrogen bonds: B:S.139, B:G.140, B:S.141, B:S.251, B:S.251, B:K.308, A:T.347, A:T.347, A:T.347 Water bridges: B:Y.173, B:Y.173, A:Y.348 Salt bridges: B:K.308 pi-Stacking: B:Y.173

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

CL.11: 4 residues within 4Å: Chain A: Y.173, I.186, N.189, S.251 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain A: P.257, P.258, Y.261, L.262 Ligands: EOH.4 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain B: Y.173, I.186, N.189, S.251 Ligand excluded by PLIP CL.24: 5 residues within 4Å: Chain B: P.257, P.258, Y.261, L.262 Ligands: EOH.16 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wilding, M. et al., A Beta-Alanine Catabolism Pathway Containing a Highly Promiscuous Omega-Transaminase in the 12-Aminododecanate-Degrading Pseudomonas Sp. Strain Aac. Appl.Environ.Microbiol. (2016)

Release Date

2016-04-13

Peptides

OMEGA AMINO ACID-PYRUVATE AMINOTRANSFERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

OMEGA AMINO ACID-PYRUVATE AMINOTRANSFERASE

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