2zak

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(New page: 200px {{Structure |PDB= 2zak |SIZE=350|CAPTION= <scene name='initialview01'>2zak</scene>, resolution 2.01&Aring; |SITE= <scene name='pdbsite=AC1:Na+Binding+Site+F...)
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[[Image:2zak.jpg|left|200px]]
 
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{{Structure
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==Orthorhombic crystal structure of precursor E. coli isoaspartyl peptidase/L-asparaginase (EcAIII) with active-site T179A mutation==
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|PDB= 2zak |SIZE=350|CAPTION= <scene name='initialview01'>2zak</scene>, resolution 2.01&Aring;
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<StructureSection load='2zak' size='340' side='right'caption='[[2zak]], [[Resolution|resolution]] 2.01&Aring;' scene=''>
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|SITE= <scene name='pdbsite=AC1:Na+Binding+Site+For+Residue+A+322'>AC1</scene>, <scene name='pdbsite=AC2:Cl+Binding+Site+For+Residue+A+323'>AC2</scene>, <scene name='pdbsite=AC3:Na+Binding+Site+For+Residue+B+322'>AC3</scene>, <scene name='pdbsite=AC4:Cl+Binding+Site+For+Residue+B+323'>AC4</scene> and <scene name='pdbsite=AC5:Trs+Binding+Site+For+Residue+A+1'>AC5</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>
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<table><tr><td colspan='2'>[[2zak]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZAK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZAK FirstGlance]. <br>
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|ACTIVITY=
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.01&#8491;</td></tr>
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|GENE= ybiK (iaaA) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
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|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd04701 Asparaginase_2]</span>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zak OCA], [https://pdbe.org/2zak PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zak RCSB], [https://www.ebi.ac.uk/pdbsum/2zak PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zak ProSAT]</span></td></tr>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zak OCA], [http://www.ebi.ac.uk/pdbsum/2zak PDBsum], [http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1kfv JenaLib], [http://www.rcsb.org/pdb/explore.do?structureId=2zak RCSB]</span>
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</table>
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}}
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== Function ==
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[https://www.uniprot.org/uniprot/IAAA_ECOLI IAAA_ECOLI] Degrades proteins damaged by L-isoaspartyl residue formation (also known as beta-Asp residues). Degrades L-isoaspartyl-containing di- and maybe also tripeptides. Also has L-asparaginase activity, although this may not be its principal function.<ref>PMID:11988085</ref> May be involved in glutathione, and possibly other peptide, transport, although these results could also be due to polar effects of disruption.<ref>PMID:11988085</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/za/2zak_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2zak ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Plant-type L-asparaginases hydrolyze the side-chain amide bond of L-asparagine or its beta-peptides. They belong to the N-terminal nucleophile (Ntn) hydrolases and are synthesized as inactive precursor molecules. Activation occurs via the autoproteolytic release of two subunits, alpha and beta, the latter of which carries the nucleophile at its N-terminus. Crystallographic studies of plant-type asparaginases have focused on an Escherichia coli homologue (EcAIII), which has been crystallized in several crystal forms. Although they all belong to the same P2 1 2 1 2 1 space group with similar unit-cell parameters, they display different crystal-packing arrangements and thus should be classified as separate polymorphs. This variability stems mainly from different positions of the EcAIII molecules within the unit cell, although they also exhibit slight differences in orientation. The intermolecular interactions that trigger different crystal lattice formation are mediated by ions, which represent the most variable component of the crystallization conditions. This behaviour confirms recent observations that small molecules might promote protein crystal lattice formation.
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'''Orthorhombic crystal structure of precursor E. coli isoaspartyl peptidase/L-asparaginase (EcAIII) with active-site T179A mutation'''
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Crystal packing of plant-type L-asparaginase from Escherichia coli.,Michalska K, Borek D, Hernandez-Santoyo A, Jaskolski M Acta Crystallogr D Biol Crystallogr. 2008 Mar;64(Pt 3):309-20. Epub 2008, Feb 20. PMID:18323626<ref>PMID:18323626</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2zak" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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Plant-type L-asparaginases hydrolyze the side-chain amide bond of L-asparagine or its beta-peptides. They belong to the N-terminal nucleophile (Ntn) hydrolases and are synthesized as inactive precursor molecules. Activation occurs via the autoproteolytic release of two subunits, alpha and beta, the latter of which carries the nucleophile at its N-terminus. Crystallographic studies of plant-type asparaginases have focused on an Escherichia coli homologue (EcAIII), which has been crystallized in several crystal forms. Although they all belong to the same P2(1)2(1)2(1) space group with similar unit-cell parameters, they display different crystal-packing arrangements and thus should be classified as separate polymorphs. This variability stems mainly from different positions of the EcAIII molecules within the unit cell, although they also exhibit slight differences in orientation. The intermolecular interactions that trigger different crystal lattice formation are mediated by ions, which represent the most variable component of the crystallization conditions. This behaviour confirms recent observations that small molecules might promote protein crystal lattice formation.
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*[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]]
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*[[Asparaginase 3D structures|Asparaginase 3D structures]]
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==About this Structure==
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== References ==
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2ZAK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZAK OCA].
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<references/>
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__TOC__
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==Reference==
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</StructureSection>
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Crystal packing of plant-type L-asparaginase from Escherichia coli., Michalska K, Borek D, Hernandez-Santoyo A, Jaskolski M, Acta Crystallogr D Biol Crystallogr. 2008 Mar;64(Pt 3):309-20. Epub 2008, Feb 20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18323626 18323626]
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[[Category: Escherichia coli K-12]]
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[[Category: Escherichia coli]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Hernandez-Santoyo A]]
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[[Category: Hernandez-Santoyo, A.]]
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[[Category: Jaskolski M]]
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[[Category: Jaskolski, M.]]
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[[Category: Michalska K]]
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[[Category: Michalska, K.]]
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[[Category: asparaginase]]
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[[Category: autoproteolysis]]
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[[Category: isoaspartyl peptidase]]
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[[Category: ntn-hydrolase]]
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[[Category: precursor]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 26 09:55:14 2008''
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Current revision

Orthorhombic crystal structure of precursor E. coli isoaspartyl peptidase/L-asparaginase (EcAIII) with active-site T179A mutation

PDB ID 2zak

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