8bkf: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[8bkf]] is a 4 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=8BKF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BKF FirstGlance]. <br>
<table><tr><td colspan='2'>[[8bkf]] is a 4 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=8BKF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BKF FirstGlance]. <br>
</td></tr><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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.221&#8491;</td></tr>
<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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=8bkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8bkf OCA], [https://pdbe.org/8bkf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8bkf RCSB], [https://www.ebi.ac.uk/pdbsum/8bkf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8bkf ProSAT]</span></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=8bkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8bkf OCA], [https://pdbe.org/8bkf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8bkf RCSB], [https://www.ebi.ac.uk/pdbsum/8bkf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8bkf ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== 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>  
[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>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The Escherichia coli enzyme EcAIII catalyzes the hydrolysis of L-Asn to L-Asp and ammonia. Using a nature-inspired mutagenesis approach, we designed and produced five new EcAIII variants (M200I, M200L, M200K, M200T, M200W). The modified proteins were characterized by spectroscopic and crystallographic methods. All new variants were enzymatically active, confirming that the applied mutagenesis procedure has been successful. The determined crystal structures revealed new conformational states of the EcAIII molecule carrying the M200W mutation and allowed a high-resolution observation of an acyl-enzyme intermediate with the M200L mutant. In addition, we performed structure prediction, substrate docking, and molecular dynamics simulations for 25 selected bacterial orthologs of EcAIII, to gain insights into how mutations at the M200 residue affect the active site and substrate binding mode. This comprehensive strategy, including both experimental and computational methods, can be used to guide further enzyme engineering and can be applied to the study of other proteins of medicinal or biotechnological importance. This article is protected by copyright. All rights reserved.
The effects of nature-inspired amino acid substitutions on structural and biochemical properties of the E. coli L-asparaginase EcAIII.,Janicki M, Sciuk A, Zielezinski A, Ruszkowski M, Ludwikow A, Karlowski WM, Jaskolski M, Loch JI Protein Sci. 2023 Apr 24:e4647. doi: 10.1002/pro.4647. PMID:37095066<ref>PMID:37095066</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8bkf" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>

Latest revision as of 11:18, 7 February 2024

Structure of E. coli Class 2 L-asparaginase EcAIII, mutant M200T (crystal M200T#o)Structure of E. coli Class 2 L-asparaginase EcAIII, mutant M200T (crystal M200T#o)

Structural highlights

8bkf is a 4 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 1.221Å
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]

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

8bkf, resolution 1.22Å

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