SMTL ID : 6zlj.1

Crystal Structure of UDP-Glucuronic acid 4-epimerase Y149F mutant from Bacillus cereus in complex with UDP-4-DEOXY-4-FLUORO-Glucuronic acid and NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 28 residues within 4Å: Chain A: G.7, G.10, F.11, I.12, D.32, H.33, F.34, I.35, K.43, E.61, D.62, I.63, L.81, A.82, A.83, P.85, N.101, V.105, I.124, S.125, T.126, K.153, Y.176, T.178, V.179, R.185, M.188 Ligands: UGF.2 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:Y.176 Hydrogen bonds: A:F.11, A:I.12, A:H.33, A:F.34, A:I.35, A:I.35, A:D.62, A:I.63, A:L.81, A:A.83, A:N.101, A:K.153, A:V.179, A:R.185 Water bridges: A:G.10, A:G.13, A:T.38, A:K.43, A:K.43 Salt bridges: A:K.43, A:R.185, A:R.185 NAD.3: 28 residues within 4Å: Chain B: G.7, G.10, F.11, I.12, D.32, H.33, F.34, I.35, K.43, E.61, D.62, I.63, L.81, A.82, A.83, P.85, N.101, V.105, I.124, S.125, T.126, K.153, Y.176, T.178, V.179, R.185, M.188 Ligands: UGF.4 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:I.12, B:Y.176 Hydrogen bonds: B:F.11, B:I.12, B:H.33, B:F.34, B:I.35, B:I.35, B:D.62, B:I.63, B:L.81, B:A.83, B:K.153, B:V.179, B:R.185 Water bridges: B:G.10, B:G.13, B:K.43, B:K.43, B:K.43, B:N.101 Salt bridges: B:K.43, B:R.185

2 x UGF: (2~{R},3~{S},4~{R},5~{R},6~{R})-6-[[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidany l)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3-fluoranyl-4,5-bis(oxidanyl)oxane-2-carboxylic acid(Non-covalent)

UGF.2: 22 residues within 4Å: Chain A: P.85, V.87, R.88, T.126, S.127, S.128, F.149, Y.176, F.177, T.178, R.185, M.188, A.189, R.192, T.204, I.205, F.206, Q.211, R.213, I.250, E.276 Ligands: NAD.1 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:A.189 Hydrogen bonds: A:P.85, A:R.88, A:S.127, A:S.128, A:T.178, A:T.178, A:T.178, A:R.185, A:R.185, A:A.189, A:R.192, A:T.204, A:F.206, A:Q.211, A:E.276, A:E.276 Water bridges: A:S.127, A:F.190, A:R.213, A:R.213, A:R.213, A:R.213 Salt bridges: A:R.88, A:R.213 pi-Stacking: A:F.206 UGF.4: 22 residues within 4Å: Chain B: P.85, V.87, R.88, T.126, S.127, S.128, F.149, Y.176, F.177, T.178, R.185, M.188, A.189, R.192, T.204, I.205, F.206, Q.211, R.213, I.250, E.276 Ligands: NAD.3 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:A.189 Hydrogen bonds: B:P.85, B:R.88, B:T.126, B:S.127, B:S.128, B:T.178, B:T.178, B:R.185, B:R.185, B:A.189, B:R.192, B:T.204, B:F.206, B:Q.211, B:E.276 Water bridges: B:S.127, B:F.190 Salt bridges: B:R.88, B:R.213 pi-Stacking: B:F.206

Links

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Citation

Iacovino, L.G. et al., Crystallographic snapshots of UDP-glucuronic acid 4-epimerase ligand binding, rotation, and reduction. J.Biol.Chem. (2020)

Release Date

2020-07-29

Peptides

Epimerase domain-containing protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Epimerase domain-containing protein