SMTL ID : 1dlj.1

THE FIRST STRUCTURE OF UDP-GLUCOSE DEHYDROGENASE (UDPGDH) REVEALS THE CATALYTIC RESIDUES NECESSARY FOR THE TWO-FOLD OXIDATION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.144, K.147 Ligands: GOL.8 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.144 Salt bridges: A:R.144, A:K.147 SO4.2: 4 residues within 4Å: Chain A: L.363, V.364, N.365, D.366 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.365, A:D.366, A:N.369 SO4.3: 5 residues within 4Å: Chain A: F.326, R.327, E.328, K.332 Ligands: GOL.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.328 Water bridges: A:E.328, A:E.328, A:K.332, A:K.332 Salt bridges: A:K.332 SO4.9: 3 residues within 4Å: Chain B: R.144, K.147 Ligands: GOL.16 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.144 Salt bridges: B:R.144, B:K.147 SO4.10: 4 residues within 4Å: Chain B: L.363, V.364, N.365, D.366 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.365, B:D.366, B:N.369 SO4.11: 5 residues within 4Å: Chain B: F.326, R.327, E.328, K.332 Ligands: GOL.15 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.328 Water bridges: B:E.328, B:K.332, B:K.332 Salt bridges: B:K.332

2 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.4: 26 residues within 4Å: Chain A: G.7, S.8, G.9, Y.10, V.11, V.28, D.29, I.30, L.31, K.34, A.80, T.81, P.82, T.83, T.99, V.100, S.117, T.118, E.141, L.143, E.145, Y.259, K.263, R.327 Ligands: UGA.5, GOL.7 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:V.11, A:E.141, A:L.143 Hydrogen bonds: A:S.8, A:Y.10, A:V.11, A:I.30, A:K.34, A:T.81, A:T.83, A:T.118, A:E.145, A:E.145, A:K.263, A:K.263, A:R.327 Water bridges: A:G.9, A:G.12, A:K.34, A:E.103, A:E.103, A:T.118 Salt bridges: A:K.34, A:R.327, A:R.327 NAI.12: 26 residues within 4Å: Chain B: G.7, S.8, G.9, Y.10, V.11, V.28, D.29, I.30, L.31, K.34, A.80, T.81, P.82, T.83, T.99, V.100, S.117, T.118, E.141, L.143, E.145, Y.259, K.263, R.327 Ligands: UGA.13, GOL.15 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:V.11, B:E.141, B:L.143 Hydrogen bonds: B:S.8, B:Y.10, B:V.11, B:I.30, B:K.34, B:T.81, B:T.83, B:T.118, B:T.118, B:E.145, B:E.145, B:E.145, B:K.263, B:K.263, B:R.327 Water bridges: B:G.9, B:G.12, B:K.34, B:Y.71, B:E.103, B:E.103 Salt bridges: B:K.34, B:R.327, B:R.327

2 x UGA: URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID(Non-covalent)

UGA.5: 23 residues within 4Å: Chain A: E.141, F.142, L.143, R.144, E.145, K.204, N.208, L.211, V.215, Y.249, N.250, N.251, S.253, Y.256, G.257, S.260, L.261, M.319, K.320, R.381, D.402 Chain B: R.244 Ligands: NAI.4 28 PLIP interactions: 26 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.215, A:Y.249, A:D.402 Hydrogen bonds: A:F.142, A:E.145, A:K.204, A:N.208, A:N.251, A:N.251, A:S.253, A:G.257, A:G.257, A:S.260, A:M.319, A:R.381, B:R.244, B:R.244 Water bridges: A:Y.249, A:Y.259, A:S.260, A:S.260, A:L.261, A:N.380, A:N.380, A:D.402 Salt bridges: A:K.204, A:K.320, A:K.320 UGA.13: 23 residues within 4Å: Chain A: R.244 Chain B: E.141, F.142, L.143, R.144, E.145, K.204, N.208, L.211, V.215, Y.249, N.250, N.251, S.253, Y.256, G.257, S.260, L.261, M.319, K.320, R.381, D.402 Ligands: NAI.12 29 PLIP interactions: 27 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.215, B:Y.249, B:D.402 Hydrogen bonds: B:F.142, B:E.145, B:K.204, B:N.208, B:Y.249, B:N.251, B:N.251, B:S.253, B:G.257, B:G.257, B:S.260, B:M.319, B:R.381, B:D.402, A:R.244, A:R.244 Water bridges: B:Y.249, B:Y.259, B:S.260, B:S.260, B:L.261, B:N.380, B:N.380 Salt bridges: B:K.204, B:K.320, B:K.320

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: P.276, Q.277 Chain B: V.289 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.277 GOL.7: 6 residues within 4Å: Chain A: P.82, N.84, Y.259, R.327 Ligands: SO4.3, NAI.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.327 Water bridges: A:N.84, A:E.328 GOL.8: 6 residues within 4Å: Chain A: F.142, R.144, P.155, S.156 Chain B: R.244 Ligands: SO4.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.144, A:S.156, A:S.156 Water bridges: A:R.144, A:D.151 GOL.14: 3 residues within 4Å: Chain A: V.289 Chain B: P.276, Q.277 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.277 GOL.15: 6 residues within 4Å: Chain B: P.82, N.84, Y.259, R.327 Ligands: SO4.11, NAI.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.327 Water bridges: B:N.84, B:E.328 GOL.16: 6 residues within 4Å: Chain A: R.244 Chain B: F.142, R.144, P.155, S.156 Ligands: SO4.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.144, B:S.156, B:S.156 Water bridges: B:R.144, B:D.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Campbell, R.E. et al., The first structure of UDP-glucose dehydrogenase reveals the catalytic residues necessary for the two-fold oxidation. Biochemistry (2000)

Release Date

2000-05-31

Peptides

UDP-GLUCOSE DEHYDROGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

UDP-GLUCOSE DEHYDROGENASE