3c17: Difference between revisions

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New page: left|200px {{Structure |PDB= 3c17 |SIZE=350|CAPTION= <scene name='initialview01'>3c17</scene>, resolution 1.95Å |SITE= <scene name='pdbsite=AC1:Na+Binding+Site+F...
 
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[[Image:3c17.jpg|left|200px]]


{{Structure
==Hexagonal Crystal Structure of Precursor E. coli Isoaspartyl Peptidase/l-Asparaginase (ECAIII) with Active-site T179A mutation==
|PDB= 3c17 |SIZE=350|CAPTION= <scene name='initialview01'>3c17</scene>, resolution 1.95&Aring;
<StructureSection load='3c17' size='340' side='right'caption='[[3c17]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
|SITE= <scene name='pdbsite=AC1:Na+Binding+Site+For+Residue+A+1'>AC1</scene>, <scene name='pdbsite=AC2:Na+Binding+Site+For+Residue+B+322'>AC2</scene>, <scene name='pdbsite=AC3:Na+Binding+Site+For+Residue+A+322'>AC3</scene>, <scene name='pdbsite=AC4:Na+Binding+Site+For+Residue+B+323'>AC4</scene>, <scene name='pdbsite=AC5:Na+Binding+Site+For+Residue+A+323'>AC5</scene>, <scene name='pdbsite=AC6:Na+Binding+Site+For+Residue+B+324'>AC6</scene>, <scene name='pdbsite=AC7:Na+Binding+Site+For+Residue+A+324'>AC7</scene>, <scene name='pdbsite=AC8:Na+Binding+Site+For+Residue+B+325'>AC8</scene>, <scene name='pdbsite=AC9:Na+Binding+Site+For+Residue+B+326'>AC9</scene>, <scene name='pdbsite=BC1:Na+Binding+Site+For+Residue+B+327'>BC1</scene>, <scene name='pdbsite=BC2:Na+Binding+Site+For+Residue+A+325'>BC2</scene>, <scene name='pdbsite=BC3:Cl+Binding+Site+For+Residue+A+326'>BC3</scene>, <scene name='pdbsite=BC4:Cl+Binding+Site+For+Residue+B+328'>BC4</scene>, <scene name='pdbsite=BC5:Cl+Binding+Site+For+Residue+A+327'>BC5</scene>, <scene name='pdbsite=BC6:Cl+Binding+Site+For+Residue+B+329'>BC6</scene>, <scene name='pdbsite=BC7:Cl+Binding+Site+For+Residue+B+330'>BC7</scene>, <scene name='pdbsite=BC8:Cl+Binding+Site+For+Residue+A+328'>BC8</scene>, <scene name='pdbsite=BC9:Cl+Binding+Site+For+Residue+B+331'>BC9</scene>, <scene name='pdbsite=CC1:Cl+Binding+Site+For+Residue+A+329'>CC1</scene>, <scene name='pdbsite=CC2:Cl+Binding+Site+For+Residue+A+330'>CC2</scene>, <scene name='pdbsite=CC3:Cl+Binding+Site+For+Residue+B+332'>CC3</scene>, <scene name='pdbsite=CC4:Cl+Binding+Site+For+Residue+A+331'>CC4</scene>, <scene name='pdbsite=CC5:Cl+Binding+Site+For+Residue+B+333'>CC5</scene>, <scene name='pdbsite=CC6:Cl+Binding+Site+For+Residue+B+334'>CC6</scene>, <scene name='pdbsite=CC7:Cl+Binding+Site+For+Residue+A+332'>CC7</scene>, <scene name='pdbsite=CC8:Cl+Binding+Site+For+Residue+B+335'>CC8</scene>, <scene name='pdbsite=CC9:Cl+Binding+Site+For+Residue+A+333'>CC9</scene> and <scene name='pdbsite=DC1:Cl+Binding+Site+For+Residue+A+334'>DC1</scene>
== Structural highlights ==
|LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>
<table><tr><td colspan='2'>[[3c17]] 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=3C17 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C17 FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95&#8491;</td></tr>
|GENE= ybiK (iaaA) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
<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></td></tr>
|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd04701 Asparaginase_2]</span>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3c17 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c17 OCA], [https://pdbe.org/3c17 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c17 RCSB], [https://www.ebi.ac.uk/pdbsum/3c17 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c17 ProSAT]</span></td></tr>
|RELATEDENTRY=[[2zak|2ZAK]], [[1k2x|1K2X]], [[1jn9|1JN9]], [[2zal|2ZAL]], [[1t3m|1T3M]], [[2gez|2GEZ]], [[9gac|9GAC]], [[9gaf|9GAF]], [[9gaa|9GAA]], [[2gac|2GAC]]
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3c17 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c17 OCA], [http://www.ebi.ac.uk/pdbsum/3c17 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3c17 RCSB]</span>
== Function ==
}}
[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>
== 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/c1/3c17_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=3c17 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Plant l-asparaginases and their bacterial homologs, such as EcAIII found in Escherichia coli, form a subgroup of the N-terminal nucleophile (Ntn)-hydrolase family. In common with all Ntn-hydrolases, they are expressed as inactive precursors that undergo activation in an autocatalytic manner. The maturation process involves intramolecular hydrolysis of a single peptide bond, leading to the formation of two subunits (alpha and beta) folded as one structural domain, with the nucleophilic Thr residue located at the freed N terminus of subunit beta. The mechanism of the autocleavage reaction remains obscure. We have determined the crystal structure of an active site mutant of EcAIII, with the catalytic Thr residue substituted by Ala (T179A). The modification has led to a correctly folded but unprocessed molecule, revealing the geometry and molecular environment of the scissile peptide bond. The autocatalytic reaction is analyzed from the point of view of the Thr(179) side chain rotation, identification of a potential general base residue, and the architecture of the oxyanion hole.


'''Hexagonal Crystal Structure of Precursor E. coli Isoaspartyl Peptidase/l-Asparaginase (ECAIII) with Active-site T179A mutation'''
The mechanism of autocatalytic activation of plant-type L-asparaginases.,Michalska K, Hernandez-Santoyo A, Jaskolski M J Biol Chem. 2008 May 9;283(19):13388-97. Epub 2008 Mar 10. PMID:18334484<ref>PMID:18334484</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3c17" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
Plant L-asparaginases and their bacterial homologs, such as EcAIII found in E. coli, form a subgroup of the Ntn-hydrolase family. In common with all Ntn-hydrolases, they are expressed as inactive precursors that undergo activation in an autocatalytic manner. The maturation process involves intramolecular hydrolysis of a single peptide bond, leading to the formation of two subunits (alpha and beta) folded as one structural domain, with the nucleophilic Thr residue located at the freed N-terminus of subunit beta. The mechanism of the autocleavage reaction remains obscure. We have determined the crystal structure of an active-site mutant of EcAIII, with the catalytic Thr residue substituted by Ala (T179A). The modification has led to a correctly folded but unprocessed molecule, revealing the geometry and molecular environment of the scissile peptide bond. The autocatalytic reaction is analyzed from the point of view of the Thr179 side chain rotation, identification of a potential general-base residue, and the architecture of the oxyanion hole.
*[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]]
 
*[[Asparaginase 3D structures|Asparaginase 3D structures]]
==About this Structure==
== References ==
3C17 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=3C17 OCA].
<references/>
 
__TOC__
==Reference==
</StructureSection>
The mechanism of autocatalytic activation of plant-type L-asparaginases., Michalska K, Hernandez-Santoyo A, Jaskolski M, J Biol Chem. 2008 Mar 10;. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18334484 18334484]
[[Category: Escherichia coli K-12]]
[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Hernandez-Santoyo A]]
[[Category: Hernandez-Santoyo, A.]]
[[Category: Jaskolski M]]
[[Category: Jaskolski, M.]]
[[Category: Michalska K]]
[[Category: Michalska, K.]]
[[Category: asparaginase]]
[[Category: autoproteolysis]]
[[Category: isoaspartyl peptidase]]
[[Category: ntn-hydrolase]]
[[Category: precursor]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr  2 11:59:51 2008''

Latest revision as of 17:54, 1 November 2023

Hexagonal Crystal Structure of Precursor E. coli Isoaspartyl Peptidase/l-Asparaginase (ECAIII) with Active-site T179A mutationHexagonal Crystal Structure of Precursor E. coli Isoaspartyl Peptidase/l-Asparaginase (ECAIII) with Active-site T179A mutation

Structural highlights

3c17 is a 2 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.95Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[1] May be involved in glutathione, and possibly other peptide, transport, although these results could also be due to polar effects of disruption.[2]

Evolutionary Conservation

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

Publication Abstract from PubMed

Plant l-asparaginases and their bacterial homologs, such as EcAIII found in Escherichia coli, form a subgroup of the N-terminal nucleophile (Ntn)-hydrolase family. In common with all Ntn-hydrolases, they are expressed as inactive precursors that undergo activation in an autocatalytic manner. The maturation process involves intramolecular hydrolysis of a single peptide bond, leading to the formation of two subunits (alpha and beta) folded as one structural domain, with the nucleophilic Thr residue located at the freed N terminus of subunit beta. The mechanism of the autocleavage reaction remains obscure. We have determined the crystal structure of an active site mutant of EcAIII, with the catalytic Thr residue substituted by Ala (T179A). The modification has led to a correctly folded but unprocessed molecule, revealing the geometry and molecular environment of the scissile peptide bond. The autocatalytic reaction is analyzed from the point of view of the Thr(179) side chain rotation, identification of a potential general base residue, and the architecture of the oxyanion hole.

The mechanism of autocatalytic activation of plant-type L-asparaginases.,Michalska K, Hernandez-Santoyo A, Jaskolski M J Biol Chem. 2008 May 9;283(19):13388-97. Epub 2008 Mar 10. PMID:18334484[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Hejazi M, Piotukh K, Mattow J, Deutzmann R, Volkmer-Engert R, Lockau W. Isoaspartyl dipeptidase activity of plant-type asparaginases. Biochem J. 2002 May 15;364(Pt 1):129-36. PMID:11988085
  2. ↑ Hejazi M, Piotukh K, Mattow J, Deutzmann R, Volkmer-Engert R, Lockau W. Isoaspartyl dipeptidase activity of plant-type asparaginases. Biochem J. 2002 May 15;364(Pt 1):129-36. PMID:11988085
  3. ↑ Michalska K, Hernandez-Santoyo A, Jaskolski M. The mechanism of autocatalytic activation of plant-type L-asparaginases. J Biol Chem. 2008 May 9;283(19):13388-97. Epub 2008 Mar 10. PMID:18334484 doi:10.1074/jbc.M800746200

3c17, resolution 1.95Å

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