1poj: Difference between revisions

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New page: left|200px<br /><applet load="1poj" size="450" color="white" frame="true" align="right" spinBox="true" caption="1poj, resolution 3.3Å" /> '''Isoaspartyl Dipeptida...
 
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[[Image:1poj.jpg|left|200px]]<br /><applet load="1poj" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1poj, resolution 3.3&Aring;" />
'''Isoaspartyl Dipeptidase with bound inhibitor'''<br />


==Overview==
==Isoaspartyl Dipeptidase with bound inhibitor==
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.
<StructureSection load='1poj' size='340' side='right'caption='[[1poj]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1poj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1POJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1POJ FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.3&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AE1:2-{[[(1S)-1-AMINO-2-CARBOXYETHYL](DIHYDROXY)PHOSPHORANYL]METHYL}-4-METHYLPENTANOIC+ACID'>AE1</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1poj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1poj OCA], [https://pdbe.org/1poj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1poj RCSB], [https://www.ebi.ac.uk/pdbsum/1poj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1poj ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/IADA_ECOLI IADA_ECOLI] Catalyzes the hydrolytic cleavage of a subset of L-isoaspartyl (L-beta-aspartyl) dipeptides. Used to degrade proteins damaged by L-isoaspartyl residues formation. The best substrate for the enzyme reported thus far is iso-Asp-Leu.<ref>PMID:7876157</ref> <ref>PMID:4880759</ref> <ref>PMID:12718528</ref> <ref>PMID:15882050</ref>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/po/1poj_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1poj ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1POJ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with ZN and AE1 as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1POJ OCA].
*[[Isoaspartyl dipeptidase|Isoaspartyl dipeptidase]]
 
== References ==
==Reference==
<references/>
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12946361 12946361]
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Bode, W.]]
[[Category: Bode W]]
[[Category: Huber, R.]]
[[Category: Huber R]]
[[Category: Jozic, D.]]
[[Category: Jozic D]]
[[Category: Kaiser, J.T.]]
[[Category: Kaiser JT]]
[[Category: Maskos, K.]]
[[Category: Maskos K]]
[[Category: AE1]]
[[Category: ZN]]
[[Category: hydrolase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 23:58:29 2007''

Latest revision as of 08:57, 17 April 2024

Isoaspartyl Dipeptidase with bound inhibitorIsoaspartyl Dipeptidase with bound inhibitor

Structural highlights

1poj is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.3Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

IADA_ECOLI Catalyzes the hydrolytic cleavage of a subset of L-isoaspartyl (L-beta-aspartyl) dipeptides. Used to degrade proteins damaged by L-isoaspartyl residues formation. The best substrate for the enzyme reported thus far is iso-Asp-Leu.[1] [2] [3] [4]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Gary JD, Clarke S. Purification and characterization of an isoaspartyl dipeptidase from Escherichia coli. J Biol Chem. 1995 Feb 24;270(8):4076-87. PMID:7876157
  2. ↑ Haley EE. Purification and properties of a beta-aspartyl peptidase from Escherichia coli. J Biol Chem. 1968 Nov 10;243(21):5748-52. PMID:4880759
  3. ↑ Thoden JB, Marti-Arbona R, Raushel FM, Holden HM. High-resolution X-ray structure of isoaspartyl dipeptidase from Escherichia coli. Biochemistry. 2003 May 6;42(17):4874-82. PMID:12718528 doi:http://dx.doi.org/10.1021/bi034233p
  4. ↑ Marti-Arbona R, Fresquet V, Thoden JB, Davis ML, Holden HM, Raushel FM. Mechanism of the reaction catalyzed by isoaspartyl dipeptidase from Escherichia coli. Biochemistry. 2005 May 17;44(19):7115-24. PMID:15882050 doi:10.1021/bi050008r

1poj, resolution 3.30Å

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