PDBsum entry 3cl6

Hydrolase

PDB id: 3cl6

Contents

Protein chains

302 a.a. *

Waters ×292

* Residue conservation analysis

PDB id:

3cl6

Name:

Hydrolase

Title:

Crystal structure of puue allantoinase

Structure:

Puue allantoinase. Chain: a, b. Engineered: yes

Source:

Pseudomonas fluorescens. Organism_taxid: 294. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.58Å R-factor: 0.209 R-free: 0.232

Authors:

I.Ramazzina,L.Cendron,C.Folli,R.Berni,D.Monteverdi,G.Zanotti, R.Percudani

Key ref:

I.Ramazzina et al. (2008). Logical Identification of an Allantoinase Analog (puuE) Recruited from Polysaccharide Deacetylases. J Biol Chem, 283, 23295-23304. PubMed id: 18550550 DOI: 10.1074/jbc.M801195200

Date:

18-Mar-08 Release date: 10-Jun-08

Protein chains

Q3KFK7  (Q3KFK7_PSEPF) -  NodB homology domain-containing protein from Pseudomonas fluorescens (strain Pf0-1)

Seq: 308 a.a.

Struc: 302 a.a.*

* PDB and UniProt seqs differ at 11 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.5.2.5 - allantoinase.
• Pathway: AMP Catabolism
• Reaction: (S)-allantoin + H2O = allantoate + H⁺

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

Added reference

DOI no: 10.1074/jbc.M801195200

J Biol Chem 283:23295-23304 (2008)

PubMed id: 18550550

Logical Identification of an Allantoinase Analog (puuE) Recruited from Polysaccharide Deacetylases.

I.Ramazzina, L.Cendron, C.Folli, R.Berni, D.Monteverdi, G.Zanotti, R.Percudani.

ABSTRACT

The hydrolytic cleavage of the hydantoin ring of allantoin, catalyzed by allantoinase, is required for the utilization of the nitrogen present in purine-derived compounds. The allantoinase gene (DAL1), however, is missing in many completely sequenced organisms able to use allantoin as a nitrogen source. Here we show that an alternative allantoinase gene (puuE) can be precisely identified by analyzing its logic relationship with three other genes of the pathway. The novel allantoinase is annotated in structure and sequence data bases as polysaccharide deacetylase for its homology with enzymes that catalyze hydrolytic reactions on chitin or peptidoglycan substrates. The recombinant PuuE protein from Pseudomonas fluorescens exhibits metal-independent allantoinase activity and stereospecificity for the S enantiomer of allantoin. The crystal structures of the protein and of protein-inhibitor complexes reveal an overall similarity with the polysaccharide deacetylase beta/alpha barrel and remarkable differences in oligomeric assembly and active site geometry. The conserved Asp-His-His metal-binding triad is replaced by Glu-His-Trp, a configuration that is distinctive of PuuE proteins within the protein family. An extra domain at the top of the barrel offers a scaffold for protein tetramerization and forms a small substrate-binding cleft by hiding the large binding groove of polysaccharide deacetylases. Substrate positioning at the active site suggests an acid/base mechanism of catalysis in which only one member of the catalytic pair of polysaccharide deacetylases has been conserved. These data provide a structural rationale for the shifting of substrate specificity that occurred during evolution.

Selected figure(s)

Figure 3.
FIGURE 3. Sequence and structure of PuuE. A, the PuuE sequence is aligned with a hypothetical polysaccharide deacetylase from P. aeruginosa (Protein Data Bank code 1Z7A), a putative chitin deacetylase from S. pombe (SpCDA), a peptidoglycan deacetylase from B. subtilis (Protein Data Bank code 1W17), acetyl xylan esterases from S. lividans (Protein Data Bank code 2CC0), and a chitin deacetylase from C. lindemuthianum (Protein Data Bank code 2IW0). Secondary structure elements deriving from Protein Data Bank coordinates are drawn over the alignment. Residues involved in metal-binding or in catalysis (38) are denoted by cyan (metal-binding) and magenta (catalysis) arrowheads. B, cartoon drawing of the structure of the PuuE monomer alongside its topological representation. The helices are colored red, and the strands are blue, except for helix 1(orange) and strands β6 and β7(light blue), which do not fit the canonical PsDA fold. C, cartoon drawing of the PuuE tetramer. Subunits A and C are colored as in B; subunits B and D are colored green.

Figure 4.
FIGURE 4. Substrate binding and reaction mechanism of PuuE. A, surface drawing of hydantoin-bound PuuE (left panel) compared with a zinc-bound chitin deacetylase (Protein Data Bank code 2IW0; right panel). The inserted segments IS1 and IS2 of PuuE are colored orange and light blue, respectively. The positions of sugar-binding subsites in 2IW0 are indicated. B, stereo view comparison of the metal-binding site of 2IW0 (cyan) and the corresponding region of PuuE (yellow). Metal-binding residues of 2IW0 and superimposable residues of PuuE are shown as sticks. C, the PuuE active site in complex with hydantoin. Key residues and ligands are represented in stick mode. D, proposed catalytic mechanism for (S)-allantoin hydrolysis.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 23295-23304) copyright 2008.

Figures were selected by the author.