PDBsum entry 2fvm

Hydrolase

PDB id: 2fvm

Contents

Protein chains

532 a.a. *

Ligands

URP ×2

Metals

_ZN ×8

Waters ×795

* Residue conservation analysis

PDB id:

2fvm

Name:

Hydrolase

Title:

Crystal structure of dihydropyrimidinase from saccharomyces kluyveri in complex with the reaction product n-carbamyl-beta-alanine

Structure:

Dihydropyrimidinase. Chain: a, b, c, d. Engineered: yes

Source:

Lachancea kluyveri. Organism_taxid: 4934. Gene: pyd2. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.45Å R-factor: 0.185 R-free: 0.237

Authors:

D.Dobritzsch,B.Lohkamp

Key ref:

B.Lohkamp et al. (2006). The crystal structures of dihydropyrimidinases reaffirm the close relationship between cyclic amidohydrolases and explain their substrate specificity. J Biol Chem, 281, 13762-13776. PubMed id: 16517602 DOI: 10.1074/jbc.M513266200

Date:

31-Jan-06 Release date: 14-Mar-06

Protein chains

Q9P903  (DPYS_LACK1) -  Dihydropyrimidinase from Lachancea kluyveri (strain ATCC 58438 / CBS 3082 / BCRC 21498 / NBRC 1685 / JCM 7257 / NCYC 543 / NRRL Y-12651)

Seq: 542 a.a.

Struc: 532 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.5.2.2 - dihydropyrimidinase.
• Reaction: 5,6-dihydrouracil + H2O = 3-(carbamoylamino)propanoate + H⁺

5,6-dihydrouracil (Bound ligand (Het Group name = URP) matches with 88.89% similarity) + H2O = 3-(carbamoylamino)propanoate + H(+)

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

Key reference

DOI no: 10.1074/jbc.M513266200

J Biol Chem 281:13762-13776 (2006)

PubMed id: 16517602

The crystal structures of dihydropyrimidinases reaffirm the close relationship between cyclic amidohydrolases and explain their substrate specificity.

B.Lohkamp, B.Andersen, J.Piskur, D.Dobritzsch.

ABSTRACT

In eukaryotes, dihydropyrimidinase catalyzes the second step of the reductive pyrimidine degradation, the reversible hydrolytic ring opening of dihydropyrimidines. Here we describe the three-dimensional structures of dihydropyrimidinase from two eukaryotes, the yeast Saccharomyces kluyveri and the slime mold Dictyostelium discoideum, determined and refined to 2.4 and 2.05 angstroms, respectively. Both enzymes have a (beta/alpha)8-barrel structural core embedding the catalytic di-zinc center, which is accompanied by a smaller beta-sandwich domain. Despite loop-forming insertions in the sequence of the yeast enzyme, the overall structures and architectures of the active sites of the dihydropyrimidinases are strikingly similar to each other, as well as to those of hydantoinases, dihydroorotases, and other members of the amidohydrolase superfamily of enzymes. However, formation of the physiologically relevant tetramer shows subtle but nonetheless significant differences. The extension of one of the sheets of the beta-sandwich domain across a subunit-subunit interface in yeast dihydropyrimidinase underlines its closer evolutionary relationship to hydantoinases, whereas the slime mold enzyme shows higher similarity to the noncatalytic collapsin-response mediator proteins involved in neuron development. Catalysis is expected to follow a dihydroorotase-like mechanism but in the opposite direction and with a different substrate. Complexes with dihydrouracil and N-carbamyl-beta-alanine obtained for the yeast dihydropyrimidinase reveal the mode of substrate and product binding and allow conclusions about what determines substrate specificity, stereoselectivity, and the reaction direction among cyclic amidohydrolases.

Selected figure(s)

Figure 1.
FIGURE 1. Subunit structures. a, stereo view of the subunit of ^SkDHPase. The following color coding is used for the secondary structure elements: green and dark green, barrel strands and helices, respectively; blue and light blue, strands of the larger and smaller sheets of the -sandwich domain, respectively; yellow, additional -strands; orange and dark orange, additional - and 3[10]-helices, respectively. Spheres in magenta represent the zinc ions of the metal center. b, stereo view of the subunit of ^DdDHPase. The same color coding as in a is used. c, stereo view of the superimposed subunits of ^SkDHPase (light blue), ^DdDHPase (blue), CRMP1 (gold), and ^B9D-Hyd (magenta). The orientation is changed for better visualization of the structural differences, especially at the C terminus, and is related to that from a and b by a 45° upward rotation around a horizontal axis lying within the paper plane.

Figure 3.
FIGURE 3. Structures of the tetramers showing the intersubunit interfaces. a, tetramer of ^SkDHPase in two orientations related by a 90° rotation around a 2-fold axis lying within the paper plane (as indicated), with subunits A, B, C, and D shown in gold, magenta, blue, and light green. b, corresponding view of the ^DdDHPase tetramer. Here the subunits are shown in yellow (A), red (B), light blue (C), and green (D). The rigid body movement of the dimer pairs in relation to the corresponding pairs in ^SkDHPase is indicated by an arrow. c, tetramer of ^B9D-Hyd, with the subunits colored in correspondence to ^SkDHPase. d, tetramer of CRMP1. The subunit color code corresponds to that of ^DdDHPase.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 13762-13776) copyright 2006.

Figures were selected by an automated process.