SMTL ID : 3tq4.1

Crystal structure of M-PMV dUTPase with a mixed population of substrate (dUPNPP) and post-inversion product (dUMP) in the active sites

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-trimer

Ligands

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

UMP.1: 15 residues within 4Å: Chain A: I.76, G.92, V.93, I.94, D.95, Y.98, E.101, I.102, K.103, M.105 Chain C: R.79, S.80, Q.123 Ligands: MG.2, DUP.3 11 PLIP interactions: 5 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:S.80, C:S.80, C:Q.123, A:V.93, A:D.95, A:D.95, A:K.103 Water bridges: C:S.81, C:S.81, A:M.105 Hydrophobic interactions: A:Y.98 UMP.5: 15 residues within 4Å: Chain A: R.79, S.80, Q.123 Chain B: I.76, G.92, V.93, I.94, D.95, Y.98, E.101, I.102, K.103, M.105 Ligands: MG.6, DUP.7 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Y.98 Hydrogen bonds: B:V.93, B:D.95, B:D.95, B:K.103, A:S.80, A:S.80, A:Q.123 Water bridges: B:M.105, A:S.81, A:S.81 UMP.9: 15 residues within 4Å: Chain B: R.79, S.80, Q.123 Chain C: I.76, G.92, V.93, I.94, D.95, Y.98, E.101, I.102, K.103, M.105 Ligands: MG.10, DUP.11 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:S.80, B:S.80, B:Q.123, C:V.93, C:D.95, C:D.95, C:K.103 Water bridges: B:S.81, B:S.81, C:M.105 Hydrophobic interactions: C:Y.98

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain C: R.79 Ligands: UMP.1, DUP.3 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain A: R.79 Ligands: UMP.5, DUP.7 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain B: R.79 Ligands: UMP.9, DUP.11 No protein-ligand interaction detected (PLIP)

3 x DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE(Non-covalent)

DUP.3: 15 residues within 4Å: Chain A: G.92, V.93, I.94, D.95, Y.98, E.101, K.103, M.105 Chain C: G.78, R.79, S.80, S.81, Q.123 Ligands: UMP.1, MG.2 12 PLIP interactions: 7 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:R.79, C:S.80, C:S.80, C:S.80, C:S.81, C:Q.123, A:D.95, A:K.103 Salt bridges: C:R.79 Hydrophobic interactions: A:I.94, A:Y.98 Water bridges: A:M.105 DUP.7: 15 residues within 4Å: Chain A: G.78, R.79, S.80, S.81, Q.123 Chain B: G.92, V.93, I.94, D.95, Y.98, E.101, K.103, M.105 Ligands: UMP.5, MG.6 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:I.94, B:Y.98 Hydrogen bonds: B:D.95, B:K.103, A:R.79, A:S.80, A:S.80, A:S.80, A:S.81, A:Q.123 Water bridges: B:M.105 Salt bridges: A:R.79 DUP.11: 15 residues within 4Å: Chain B: G.78, R.79, S.80, S.81, Q.123 Chain C: G.92, V.93, I.94, D.95, Y.98, E.101, K.103, M.105 Ligands: UMP.9, MG.10 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:R.79, B:S.80, B:S.80, B:S.80, B:S.81, B:Q.123, C:D.95, C:K.103 Salt bridges: B:R.79 Hydrophobic interactions: C:I.94, C:Y.98 Water bridges: C:M.105

3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 13 residues within 4Å: Chain A: Q.88, V.89, Y.90, P.91 Chain B: Q.88, V.89, P.91 Chain C: Q.88, V.89, Y.90, P.91 Ligands: TRS.8, TRS.12 6 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:Q.88, A:Q.88, B:Q.88 Water bridges: C:T.83, C:V.89, C:V.89 TRS.8: 13 residues within 4Å: Chain A: Q.88, V.89, Y.90, P.91 Chain B: Q.88, V.89, Y.90, P.91 Chain C: Q.88, V.89, P.91 Ligands: TRS.4, TRS.12 6 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: A:Q.88, C:Q.88, B:Q.88 Water bridges: A:T.83, A:V.89, A:V.89 TRS.12: 13 residues within 4Å: Chain A: Q.88, V.89, P.91 Chain B: Q.88, V.89, Y.90, P.91 Chain C: Q.88, V.89, Y.90, P.91 Ligands: TRS.4, TRS.8 6 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: A:Q.88, B:Q.88, C:Q.88 Water bridges: B:T.83, B:V.89, B:V.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barabas, O. et al., Structural Snapshots of Enzyme-Catalysed Phosphate Ester Hydrolysis Directly Visualize In-line Attack and Inversion. to be published

Release Date

2011-10-12

Peptides

DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE

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