SMTL ID : 3hk9.3 (3 other biounits)

Crystal structure of uronate isomerase from Bacillus halodurans complexed with zinc and D-Glucuronate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-octamer

Ligands

8 x REL: D-glucuronic acid(Non-covalent)

REL.1: 12 residues within 4Å: Chain A: H.26, H.28, H.49, Y.50, R.170, S.223, M.258, W.325, W.326, D.355, R.357 Ligands: ZN.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.50, A:S.223, A:R.357, A:R.357 Water bridges: A:H.49, A:N.329 Salt bridges: A:H.26, A:H.28, A:R.170 REL.3: 12 residues within 4Å: Chain B: H.26, H.28, H.49, Y.50, R.170, S.223, M.258, W.325, W.326, D.355, R.357 Ligands: ZN.5 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:Y.50, B:S.223, B:R.357, B:R.357 Water bridges: B:H.49, B:K.263, B:K.263, B:D.274, B:N.329 Salt bridges: B:H.26, B:H.28, B:R.170 REL.6: 12 residues within 4Å: Chain C: H.26, H.28, H.49, Y.50, R.170, S.223, M.258, W.325, W.326, D.355, R.357 Ligands: ZN.8 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:Y.50, C:S.223, C:R.357, C:R.357 Water bridges: C:Y.48, C:K.263, C:K.263, C:K.263, C:K.263, C:D.274, C:N.329 Salt bridges: C:H.26, C:H.28, C:R.170 REL.10: 13 residues within 4Å: Chain D: H.26, H.28, H.49, Y.50, R.170, S.223, M.258, K.263, W.325, W.326, D.355, R.357 Ligands: ZN.12 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:S.223, D:K.263, D:R.357, D:R.357 Water bridges: D:H.49, D:Y.50, D:N.329 Salt bridges: D:H.26, D:H.28, D:R.170 REL.13: 12 residues within 4Å: Chain E: H.26, H.28, H.49, Y.50, R.170, S.223, M.258, W.325, W.326, D.355, R.357 Ligands: ZN.15 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:S.223, E:K.263, E:R.357, E:R.357 Water bridges: E:Y.48, E:H.49, E:R.170, E:K.263, E:K.263, E:N.329 Salt bridges: E:H.26, E:H.28, E:R.170 REL.17: 12 residues within 4Å: Chain F: H.26, H.28, H.49, Y.50, R.170, S.223, M.258, W.325, W.326, D.355, R.357 Ligands: ZN.19 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:S.223, F:K.263, F:R.357, F:R.357 Water bridges: F:H.49, F:Y.50, F:K.263, F:K.263, F:N.329 Salt bridges: F:H.26, F:H.28, F:R.170 REL.20: 12 residues within 4Å: Chain G: H.26, H.28, H.49, Y.50, R.170, S.223, M.258, W.325, W.326, D.355, R.357 Ligands: ZN.22 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:S.223, G:R.357, G:R.357 Water bridges: G:H.49, G:Y.50, G:K.263, G:K.263, G:N.329 Salt bridges: G:H.26, G:H.28, G:R.170 REL.23: 12 residues within 4Å: Chain H: H.26, H.28, H.49, Y.50, R.170, S.223, M.258, W.325, W.326, D.355, R.357 Ligands: ZN.25 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:S.223, H:R.357, H:R.357 Water bridges: H:H.49, H:Y.50, H:K.263, H:K.263, H:K.263, H:N.329 Salt bridges: H:H.26, H:H.28, H:R.170

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.26, H.28, D.355 Ligands: REL.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.26, A:H.28, A:D.355 ZN.5: 4 residues within 4Å: Chain B: H.26, H.28, D.355 Ligands: REL.3 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.26, B:H.28, B:D.355 ZN.8: 4 residues within 4Å: Chain C: H.26, H.28, D.355 Ligands: REL.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.26, C:H.28, C:D.355 ZN.12: 4 residues within 4Å: Chain D: H.26, H.28, D.355 Ligands: REL.10 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.26, D:H.28, D:D.355 ZN.15: 4 residues within 4Å: Chain E: H.26, H.28, D.355 Ligands: REL.13 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.26, E:H.28, E:D.355 ZN.19: 4 residues within 4Å: Chain F: H.26, H.28, D.355 Ligands: REL.17 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.26, F:H.28, F:D.355 ZN.22: 4 residues within 4Å: Chain G: H.26, H.28, D.355 Ligands: REL.20 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:H.26, G:H.28, G:D.355 ZN.25: 4 residues within 4Å: Chain H: H.26, H.28, D.355 Ligands: REL.23 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:H.26, H:H.28, H:D.355

7 x CO3: CARBONATE ION(Non-functional Binders)

CO3.4: 8 residues within 4Å: Chain A: H.49, Y.50, A.53, A.272, W.326, F.327 Chain B: R.314, K.315 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.49, A:W.326, B:R.314, B:K.315 CO3.7: 2 residues within 4Å: Chain C: R.314, K.315 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.314, C:K.315 CO3.11: 8 residues within 4Å: Chain D: R.314, K.315 Chain F: H.49, Y.50, A.53, A.272, W.326, F.327 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain D Hydrogen bonds: F:H.49, D:R.314, D:K.315, D:K.315 CO3.14: 8 residues within 4Å: Chain D: H.49, Y.50, A.53, A.272, W.326, F.327 Chain E: R.314, K.315 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:R.314, E:K.315, D:H.49 CO3.18: 8 residues within 4Å: Chain E: H.49, Y.50, A.53, A.272, W.326, F.327 Chain F: R.314, K.315 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:H.49, E:W.326, F:R.314, F:K.315 CO3.21: 8 residues within 4Å: Chain G: R.314, K.315 Chain H: H.49, Y.50, A.53, A.272, W.326, F.327 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:R.314, G:K.315, H:H.49, H:W.326 CO3.24: 2 residues within 4Å: Chain H: R.314, K.315 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:R.314, H:K.315

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

CL.9: 2 residues within 4Å: Chain C: K.278, E.304 Ligand excluded by PLIP CL.16: 6 residues within 4Å: Chain D: K.278, E.304 Chain E: K.278, E.304 Chain F: K.278, E.304 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, T.T. et al., The mechanism of the reaction catalyzed by uronate isomerase illustrates how an isomerase may have evolved from a hydrolase within the amidohydrolase superfamily. Biochemistry (2009)

Release Date

2009-08-25

Peptides

Uronate isomerase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
F

D
G

E
H

F
I

G
J

H
L

Uronate isomerase

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