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1pok

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{{STRUCTURE_1pok| PDB=1pok | SCENE= }}
{{STRUCTURE_1pok| PDB=1pok | SCENE= }}
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'''Crystal structure of Isoaspartyl Dipeptidase'''
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===Crystal structure of Isoaspartyl Dipeptidase===
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==Overview==
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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.
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(as it appears on PubMed at http://www.pubmed.gov), where 12946361 is the PubMed ID number.
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{{ABSTRACT_PUBMED_12946361}}
==About this Structure==
==About this Structure==
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[[Category: Maskos, K.]]
[[Category: Maskos, K.]]
[[Category: Hydrolase]]
[[Category: Hydrolase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 05:18:44 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 14:21:02 2008''

Revision as of 11:21, 27 July 2008

Image:1pok.png

Template:STRUCTURE 1pok

Crystal structure of Isoaspartyl Dipeptidase

Template:ABSTRACT PUBMED 12946361

About this Structure

1POK is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.

Reference

X-ray structure of isoaspartyl dipeptidase from E.coli: a dinuclear zinc peptidase evolved from amidohydrolases., Jozic D, Kaiser JT, Huber R, Bode W, Maskos K, J Mol Biol. 2003 Sep 5;332(1):243-56. PMID:12946361

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