PDBsum entry 1poj

Hydrolase

PDB id: 1poj

Contents

Protein chains

388 a.a. *

Ligands

AE1 ×2

Metals

_ZN ×4

Waters ×42

* Residue conservation analysis

PDB id:

1poj

Name:

Hydrolase

Title:

Isoaspartyl dipeptidase with bound inhibitor

Structure:

Isoaspartyl dipeptidase. Chain: a, b. Ec: 3.4.19.-

Source:

Escherichia coli. Organism_taxid: 562

Resolution:

3.30Å R-factor: 0.244 R-free: 0.286

Authors:

D.Jozic,J.T.Kaiser,R.Huber,W.Bode,K.Maskos

Key ref:

D.Jozic et al. (2003). X-ray structure of isoaspartyl dipeptidase from E.coli: a dinuclear zinc peptidase evolved from amidohydrolases. J Mol Biol, 332, 243-256. PubMed id: 12946361 DOI: 10.1016/S0022-2836(03)00845-3

Date:

15-Jun-03 Release date: 22-Jun-04

Protein chains

P39377  (IADA_ECOLI) -  Isoaspartyl dipeptidase from Escherichia coli (strain K12)

Seq: 390 a.a.

Struc: 388 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.4.19.- - ?????

DOI no: 10.1016/S0022-2836(03)00845-3

J Mol Biol 332:243-256 (2003)

PubMed id: 12946361

X-ray structure of isoaspartyl dipeptidase from E.coli: a dinuclear zinc peptidase evolved from amidohydrolases.

D.Jozic, J.T.Kaiser, R.Huber, W.Bode, K.Maskos.

ABSTRACT

L-aspartyl and L-asparaginyl residues in proteins spontaneously undergo intra-residue rearrangements forming isoaspartyl/beta-aspartyl residues linked through their side-chain beta-carboxyl group with the following amino acid. In order to avoid accumulation of isoaspartyl dipeptides left over from protein degradation, some bacteria have developed specialized isoaspartyl/beta-aspartyl zinc dipeptidases sequentially unrelated to other peptidases, which also poorly degrade alpha-aspartyl dipeptides. We have expressed and crystallized the 390 amino acid residue isoaspartyl dipeptidase (IadA) from E.coli, and have determined its crystal structure in the absence and presence of the phosphinic inhibitor Asp-Psi[PO(2)CH(2)]-LeuOH. This structure reveals an octameric particle of 422 symmetry, with each polypeptide chain organized in a (alphabeta)(8) TIM-like barrel catalytic domain attached to a U-shaped beta-sandwich domain. At the C termini of the beta-strands of the beta-barrel, the two catalytic zinc ions are surrounded by four His, a bridging carbamylated Lys and an Asp residue, which seems to act as a proton shuttle. A large beta-hairpin loop protruding from the (alphabeta)(8) barrel is disordered in the free peptidase, but forms a flap that stoppers the barrel entrance to the active center upon binding of the dipeptide mimic. This isoaspartyl dipeptidase shows strong topological homology with the alpha-subunit of the binickel-containing ureases, the dinuclear zinc dihydroorotases, hydantoinases and phosphotriesterases, and the mononuclear adenosine and cytosine deaminases, which all are catalyzing hydrolytic reactions at carbon or phosphorous centers. Thus, nature has adapted an existing fold with catalytic tools suitable for hydrolysis of amide bonds to the binding requirements of a peptidase.

Selected figure(s)

Figure 1.
Figure 1. Stereo view of the quarternary assembly of isoaspartyl dipeptidase (IadA). (a) The octamer can be regarded as a tetramer of dimers with the indicated 422 symmetry. The nomenclature of the monomers as well as the location of the active site zincs (magenta spheres) are given. The monomers in the foreground are colored in light green (A), orange (B), green (C), and blue (D), the monomers in the background are colored in gray. Dimers are formed between molecules A-E, B-F, C-G and D-H, respectively. (b) Surface of isoaspartyl dipeptidase. The electrostatic potential was calculated with GRASP,[48.] using charges according to Weiner and co-workers. [50.]

Figure 5.
Figure 5. Stereo view of the structural comparison of IadA with urease and dihydroorotase. (a) Superposition of the C^a backbones of IadA (beige), urease (blue, PDB code 2UBP) and dihydroorotase (green, PDB code 1J79). The structural alignment was performed using the program TOP.[46.] (b) Superposition of the zinc binding residues. The zinc ions of IdaA (beige) are shown with the corresponding residues of urease (blue, PDB code 2UBP) and dihydroorotase (green, PDB code 1J79). The numbers are according to the numbering of IadA.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 332, 243-256) copyright 2003.

Figures were selected by an automated process.