SMTL ID : 6t8e.1

Crystal structure of native xylose isomerase from Piromyces E2 grown in yeast, in complex with xylose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-tetramer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: E.233, E.269, H.272, D.297, D.340 Ligands: XLS.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.233, A:E.269, A:D.297, A:D.340 CA.2: 6 residues within 4Å: Chain A: E.269, H.272, N.299, D.308, D.310 Ligands: XLS.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.269, A:D.308, A:D.308, A:D.310, H2O.2 CA.10: 5 residues within 4Å: Chain B: E.233, E.269, D.297, D.340 Ligands: XLS.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.233, B:E.269, B:D.297, B:D.340 CA.11: 5 residues within 4Å: Chain B: E.269, H.272, N.299, D.308, D.310 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.269, B:D.308, B:D.308, B:D.310, H2O.20 CA.19: 5 residues within 4Å: Chain C: E.233, E.269, D.297, D.340 Ligands: XLS.21 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.233, C:E.269, C:D.297, C:D.340 CA.20: 6 residues within 4Å: Chain C: E.269, H.272, N.299, D.308, D.310 Ligands: XLS.21 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.269, C:D.308, C:D.308, C:D.310, H2O.38 CA.28: 6 residues within 4Å: Chain D: E.233, E.269, H.272, D.297, D.340 Ligands: XLS.30 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.233, D:E.269, D:D.297, D:D.340 CA.29: 5 residues within 4Å: Chain D: E.269, H.272, N.299, D.308, D.310 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.269, D:D.308, D:D.308, D:D.310, H2O.62

4 x XLS: D-xylose(Non-covalent)

XLS.3: 13 residues within 4Å: Chain A: W.50, H.102, W.140, F.146, W.189, E.233, E.269, H.272, D.297, D.340 Chain B: F.61 Ligands: CA.1, CA.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:H.102, A:E.233, A:H.272 Water bridges: A:W.50, A:T.142, A:E.269, A:D.340, A:D.340 XLS.12: 12 residues within 4Å: Chain A: F.61 Chain B: W.50, H.102, W.140, F.146, W.189, E.233, E.269, H.272, D.297, D.340 Ligands: CA.10 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.102, B:E.233, B:H.272 Water bridges: B:W.50, B:T.142, B:D.340 XLS.21: 13 residues within 4Å: Chain C: W.50, H.102, W.140, F.146, W.189, E.233, E.269, H.272, D.297, D.340 Chain D: F.61 Ligands: CA.19, CA.20 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:H.102, C:E.233, C:D.340 Water bridges: C:W.189, C:E.269, C:D.310, C:D.340, C:D.340 XLS.30: 13 residues within 4Å: Chain C: F.61 Chain D: W.50, H.102, W.140, F.146, W.189, E.233, E.269, H.272, D.297, D.308, D.340 Ligands: CA.28 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:H.102, D:E.233, D:H.272, D:D.340 Water bridges: D:D.310, D:D.340

7 x XYP: beta-D-xylopyranose(Non-covalent)

XYP.4: 6 residues within 4Å: Chain A: E.56, G.64, T.65, K.66, S.67 Chain B: K.149 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.56, A:K.66 Water bridges: A:G.64 Salt bridges: B:K.149 XYP.13: 6 residues within 4Å: Chain A: K.149 Chain B: E.56, G.64, T.65, K.66, S.67 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:G.64 Salt bridges: A:K.149 XYP.17: 7 residues within 4Å: Chain B: Q.8, I.9, Q.10, I.12, N.21, L.23 Ligands: XYS.16 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.10, B:Q.10, B:N.21, B:N.21, B:L.23 XYP.22: 6 residues within 4Å: Chain C: E.56, G.64, T.65, K.66, S.67 Chain D: K.149 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.56, C:E.56, C:K.66 Water bridges: C:G.64, C:S.67 Salt bridges: D:K.149 XYP.31: 6 residues within 4Å: Chain C: K.149 Chain D: E.56, G.64, T.65, K.66, S.67 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:E.56, D:E.56, D:K.66, C:K.149 Water bridges: D:G.64 Salt bridges: C:K.149 XYP.34: 5 residues within 4Å: Chain B: L.428 Chain D: P.22, L.23, E.351 Ligands: XYP.35 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.351 Water bridges: D:N.21 XYP.35: 5 residues within 4Å: Chain D: Q.8, I.9, Q.10, L.23 Ligands: XYP.34 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.10, D:L.23 Water bridges: D:N.21, D:N.21

11 x XYS: alpha-D-xylopyranose(Non-covalent)

XYS.5: 6 residues within 4Å: Chain A: K.204, K.207, F.254, H.258 Chain D: D.289, A.290 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:H.258 Water bridges: D:D.289 XYS.6: 6 residues within 4Å: Chain A: K.40, D.41, R.44, P.97, Y.98, K.137 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.98 Water bridges: A:K.40, A:K.40, A:R.44 Salt bridges: A:R.44, A:K.137 XYS.7: 4 residues within 4Å: Chain A: P.22, L.23, E.351 Chain C: L.428 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.351 Water bridges: A:E.351 XYS.14: 6 residues within 4Å: Chain B: K.204, K.207, F.254, H.258 Chain C: D.289, A.290 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:H.258 Water bridges: C:D.289 XYS.15: 6 residues within 4Å: Chain B: K.40, D.41, R.44, P.97, Y.98, K.137 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Y.98 Water bridges: B:K.40, B:K.40, B:R.44, B:R.44, B:K.137, B:K.137, B:K.137 Salt bridges: B:R.44, B:K.137 XYS.16: 4 residues within 4Å: Chain B: P.22, E.351 Chain D: L.428 Ligands: XYP.17 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.351 Water bridges: B:N.21, B:E.351 XYS.23: 6 residues within 4Å: Chain B: D.289, A.290 Chain C: K.204, K.207, F.254, H.258 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:H.258 Water bridges: B:K.256, B:D.289 XYS.24: 5 residues within 4Å: Chain C: K.40, D.41, P.97, Y.98, K.137 8 PLIP interactions: 8 interactions with chain C Water bridges: C:K.40, C:K.40, C:R.44, C:R.44, C:Y.98, C:K.137 Salt bridges: C:R.44, C:K.137 XYS.25: 4 residues within 4Å: Chain A: L.428 Chain C: P.22, L.23, E.351 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.351 XYS.32: 6 residues within 4Å: Chain A: D.289, A.290 Chain D: K.204, K.207, F.254, H.258 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain D Water bridges: A:K.256 Hydrogen bonds: D:K.204, D:K.204, D:H.258 Salt bridges: D:K.204 XYS.33: 6 residues within 4Å: Chain D: K.40, D.41, R.44, P.97, Y.98, K.137 6 PLIP interactions: 6 interactions with chain D Water bridges: D:R.44, D:Y.98, D:G.135, D:K.137 Salt bridges: D:R.44, D:K.137

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 4 residues within 4Å: Chain A: S.112, I.113 Chain D: G.417, E.418 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain D Hydrogen bonds: A:I.113 Water bridges: A:E.114, A:E.114, A:R.166, D:K.414, D:G.417, D:G.417, D:E.418, D:E.418 SO4.9: 3 residues within 4Å: Chain A: D.349, L.350, E.351 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.350, A:E.351 Water bridges: A:D.349, A:E.351, A:E.351, A:E.351 SO4.18: 3 residues within 4Å: Chain B: D.349, L.350, E.351 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.350, B:E.351 Water bridges: B:E.351, B:E.351 SO4.26: 4 residues within 4Å: Chain B: G.417, E.418 Chain C: S.112, I.113 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C Water bridges: B:E.418, B:E.418, C:E.114, C:E.114, C:R.166 Hydrogen bonds: C:I.113 SO4.27: 3 residues within 4Å: Chain C: D.349, L.350, E.351 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.350, C:E.351 SO4.36: 5 residues within 4Å: Chain A: G.417, E.418 Chain D: S.112, I.113, E.114 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:I.113 Water bridges: D:R.166, A:G.417, A:E.418 SO4.37: 4 residues within 4Å: Chain D: Q.8, D.349, L.350, E.351 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:L.350, D:E.351 Water bridges: D:Q.8, D:Q.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, M. et al., Structure-based directed evolution improves S. cerevisiae growth on xylose by influencing in vivo enzyme performance. Biotechnol Biofuels (2020)

Release Date

2020-01-29

Peptides

Xylose isomerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Xylose isomerase

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