SMTL ID : 3f4f.1

Crystal structure of dUT1p, a dUTPase from Saccharomyces cerevisiae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

3 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Non-covalent)

UMP.1: 16 residues within 4Å: Chain A: G.100, A.101, G.102, V.103, V.104, D.105, Y.108, E.111, V.112, K.113 Chain B: R.157, G.161, F.162, G.163 Chain C: S.89 Ligands: PEG.7 18 PLIP interactions: 7 interactions with chain A, 6 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: A:A.101, A:V.104, A:Y.108 Hydrogen bonds: A:G.102, A:D.105, A:K.113, C:S.89, C:S.89, B:F.162, B:G.163 Water bridges: A:V.115, C:R.88, C:R.88, C:R.88, C:S.89, B:R.157, B:G.163 Salt bridges: B:R.157 UMP.3: 17 residues within 4Å: Chain A: S.89 Chain B: I.85, G.100, A.101, G.102, V.103, V.104, D.105, Y.108, E.111, V.112, K.113 Chain C: R.157, G.160, G.161, F.162, G.163 15 PLIP interactions: 4 interactions with chain C, 7 interactions with chain B, 4 interactions with chain A Hydrogen bonds: C:F.162, C:G.163, B:G.102, B:D.105, B:K.113, B:K.113, A:S.89 Water bridges: C:R.157, B:D.105, A:S.89, A:S.89, A:G.90 Salt bridges: C:R.157 Hydrophobic interactions: B:A.101, B:Y.108 UMP.6: 17 residues within 4Å: Chain A: R.157, G.161, F.162, G.163 Chain B: S.89 Chain C: G.100, A.101, G.102, V.103, V.104, D.105, Y.108, E.111, V.112, K.113, V.115 Ligands: EDO.4 19 PLIP interactions: 8 interactions with chain C, 6 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: C:A.101, C:Y.108 Hydrogen bonds: C:G.102, C:D.105, C:D.105, C:K.113, C:K.113, B:S.89, B:S.89, B:S.89, A:F.162, A:G.163 Water bridges: C:V.115, B:R.88, B:R.88, B:G.90, A:R.157, A:R.157 Salt bridges: A:R.157

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 2 residues within 4Å: Chain A: R.157 Chain B: G.44 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.160

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

EDO.4: 5 residues within 4Å: Chain A: R.157 Chain B: A.48, D.52, Q.134 Ligands: UMP.6 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.52, A:R.157 Water bridges: B:G.44, B:D.52 EDO.5: 3 residues within 4Å: Chain A: K.139 Chain B: K.139 Chain C: K.139 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: C:K.139, C:K.139, B:K.139, B:K.139 Water bridges: A:K.139

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 11 residues within 4Å: Chain A: V.103, D.105 Chain B: R.157 Chain C: T.42, K.43, G.44, A.48, G.50, D.52, Q.134 Ligands: UMP.1 7 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:T.42, C:G.44, C:D.52, C:Q.134, A:V.103, B:R.157 Water bridges: C:G.50 PEG.8: 4 residues within 4Å: Chain A: D.150 Chain C: Q.32, L.33, R.34 1 PLIP interactions: 1 interactions with chain C Water bridges: C:L.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tchigvintsev, A. et al., Structure and activity of the Saccharomyces cerevisiae dUTP pyrophosphatase DUT1, an essential housekeeping enzyme. Biochem.J. (2011)

Release Date

2008-11-11

Peptides

Deoxyuridine 5'-triphosphate nucleotidohydrolase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Deoxyuridine 5'-triphosphate nucleotidohydrolase

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