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7lji
From Proteopedia
(Difference between revisions)
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==Structure of poly(aspartic acid) hydrolase PahZ2 with Gd+3 bound== | ==Structure of poly(aspartic acid) hydrolase PahZ2 with Gd+3 bound== | ||
| - | <StructureSection load='7lji' size='340' side='right'caption='[[7lji]]' scene=''> | + | <StructureSection load='7lji' size='340' side='right'caption='[[7lji]], [[Resolution|resolution]] 1.85Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LJI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LJI FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7lji]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingomonas_sp._KT-1 Sphingomonas sp. KT-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LJI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LJI FirstGlance]. <br> |
| - | </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=7lji FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lji OCA], [https://pdbe.org/7lji PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lji RCSB], [https://www.ebi.ac.uk/pdbsum/7lji PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lji ProSAT]</span></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]] 1.85Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GD3:GADOLINIUM+ION'>GD3</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=7lji FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lji OCA], [https://pdbe.org/7lji PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lji RCSB], [https://www.ebi.ac.uk/pdbsum/7lji PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lji ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/Q769D3_9SPHN Q769D3_9SPHN] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Poly(aspartic acid) (PAA) is a common water-soluble polycarboxylate used in a broad range of applications. PAA biodegradation and environmental assimilation were first identified in river water bacterial strains, Sphingomonas sp. KT-1 and Pedobacter sp. KP-2. Within Sphingomonas sp. KT-1, PahZ1KT-1 cleaves beta-amide linkages to oligo(aspartic acid) and then is degraded by PahZ2KT-1. Recently, we reported the first structure for PahZ1KT-1. Here, we report novel structures for PahZ2KT-1 bound to either Gd(3+)/Sm(3+) or Zn(2+) cations in a dimeric state consistent with M28 metallopeptidase family members. PahZ2KT-1 monomers include a dimerization domain and a catalytic domain with dual Zn(2+) cations. MD methods predict the putative substrate binding site to span across the dimerization and catalytic domains, where NaCl promotes the transition from an open conformation to a closed conformation that positions the substrate adjacent to catalytic zinc ions. Structural knowledge of PahZ1KT-1 and PahZ2KT-1 will allow for protein engineering endeavors to develop novel biodegradation reagents. | ||
| + | |||
| + | Sphingomonas sp. KT-1 PahZ2 Structure Reveals a Role for Conformational Dynamics in Peptide Bond Hydrolysis.,Brambley CA, Yared TJ, Gonzalez M, Jansch AL, Wallen JR, Weiland MH, Miller JM J Phys Chem B. 2021 Jun 10;125(22):5722-5739. doi: 10.1021/acs.jpcb.1c01216. Epub, 2021 Jun 1. PMID:34060838<ref>PMID:34060838</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7lji" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| + | [[Category: Sphingomonas sp. KT-1]] | ||
[[Category: Brambley CA]] | [[Category: Brambley CA]] | ||
[[Category: Gonzalez M]] | [[Category: Gonzalez M]] | ||
Current revision
Structure of poly(aspartic acid) hydrolase PahZ2 with Gd+3 bound
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