PDBsum entry 3c3i

Hydrolase

PDB id: 3c3i

Contents

Protein chains

127 a.a. *

136 a.a. *

Ligands

DUD ×4

Metals

_MG ×2

Waters ×20

* Residue conservation analysis

PDB id:

3c3i

Name:

Hydrolase

Title:

Evolution of chlorella virus dutpase

Structure:

Deoxyuridine triphosphatase. Chain: a, b, c, d. Engineered: yes. Mutation: yes

Source:

Paramecium bursaria chlorella virus il3a. Strain: mu-22. Expressed in: escherichia coli.

Resolution:

3.00Å R-factor: 0.195 R-free: 0.258

Authors:

M.Yamanishi,K.Homma,Y.Zhang,L.V.J.Etten,H.Moriyama

Key ref:

K.Homma and H.Moriyama (2009). Crystallization and crystal-packing studies of Chlorella virus deoxyuridine triphosphatase. Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 1030-1034. PubMed id: 19851015

Date:

28-Jan-08 Release date: 10-Feb-09

Protein chain

Q5I3E5  (Q5I3E5_PBCVI) -  dUTP diphosphatase from Paramecium bursaria Chlorella virus IL3A

Seq: 141 a.a.

Struc: 127 a.a.*

Protein chains

Q5I3E5  (Q5I3E5_PBCVI) -  dUTP diphosphatase from Paramecium bursaria Chlorella virus IL3A

Seq: 141 a.a.

Struc: 136 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C, D: E.C.3.6.1.23 - dUTP diphosphatase.
• Reaction: dUTP + H2O = dUMP + diphosphate + H⁺

dUTP (Bound ligand (Het Group name = DUD) matches with 85.71% similarity) + H2O = dUMP + diphosphate + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

Acta Crystallogr Sect F Struct Biol Cryst Commun 65:1030-1034 (2009)

PubMed id: 19851015

Crystallization and crystal-packing studies of Chlorella virus deoxyuridine triphosphatase.

K.Homma, H.Moriyama.

ABSTRACT

The 141-amino-acid deoxyuridine triphosphatase (dUTPase) from the algal Chlorella virus IL-3A and its Glu81Ser/Thr84Arg-mutant derivative Mu-22 were crystallized using the hanging-drop vapor-diffusion method at 298 K with polyethylene glycol as the precipitant. An apo IL-3A dUTPase with an amino-terminal T7 epitope tag and a carboxy-terminal histidine tag yielded cubic P2(1)3 crystals with unit-cell parameter a = 106.65 A. In the presence of dUDP, the enzyme produced thin stacked orthorhombic P222 crystals with unit-cell parameters a = 81.0, b = 96.2, c = 132.8 A. T7-histidine-tagged Mu-22 dUTPase formed thin stacked rectangular crystals. Amino-terminal histidine-tagged dUTPases did not crystallize but formed aggregates. Glycyl-seryl-tagged dUTPases yielded cubic P2(1)3 IL-3A crystals with unit-cell parameter a = 105.68 A and hexagonal P6(3) Mu-22 crystals with unit-cell parameters a = 132.07, c = 53.45 A, gamma = 120 degrees . Owing to the Thr84Arg mutation, Mu-22 dUTPase had different monomer-to-monomer interactions to those of IL-3A dUTPase.