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| | ==Structural and kinetic bases for the metal preference of the M18 aminopeptidase from Pseudomonas aeruginosa== | | ==Structural and kinetic bases for the metal preference of the M18 aminopeptidase from Pseudomonas aeruginosa== |
| - | <StructureSection load='3wt4' size='340' side='right' caption='[[3wt4]], [[Resolution|resolution]] 2.30Å' scene=''> | + | <StructureSection load='3wt4' size='340' side='right'caption='[[3wt4]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3wt4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WT4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WT4 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3wt4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WT4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WT4 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4njq|4njq]], [[4oid|4oid]], [[4oiw|4oiw]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">apeB, PA3247 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</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=3wt4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wt4 OCA], [https://pdbe.org/3wt4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wt4 RCSB], [https://www.ebi.ac.uk/pdbsum/3wt4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wt4 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3wt4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wt4 OCA], [http://pdbe.org/3wt4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wt4 RCSB], [http://www.ebi.ac.uk/pdbsum/3wt4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wt4 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/APEB_PSEAE APEB_PSEAE] |
| - | The peptidases in clan MH are known as cocatalytic zinc peptidases that have two zinc ions in the active site, but their metal preference has not been rigorously investigated. In this study, the molecular basis for metal preference is provided from the structural and biochemical analyses. Kinetic studies of Pseudomonas aeruginosa aspartyl aminopeptidase (PaAP) which belongs to peptidase family M18 in clan MH revealed that its peptidase activity is dependent on Co2+ rather than Zn2+: the kcat (s-1) values of PaAP were 0.006, 5.10 and 0.43 in no-metal, Co2+, and Zn2+conditions, respectively. Consistently, addition of low concentrations of Co2+ to PaAP previously saturated with Zn2+ greatly enhanced the enzymatic activity, suggesting that Co2+may be the physiologically relevant cocatalytic metal ion of PaAP. The crystal structures of PaAP complexes with Co2+ or Zn2+ commonly showed two metal ions in the active site coordinated with three conserved residues and a bicarbonate ion in a tetragonal geometry. However, Co2+- and Zn2+-bound structures showed no noticeable alterations relevant to differential effects of metal species, except the relative orientation of Glu-265, a general base in the active site. The characterization of mutant PaAP revealed that the first metal binding site is primarily responsible for metal preference. Similar to PaAP, Streptococcus pneumonia glutamyl aminopeptidase (SpGP), belonging to aminopeptidase family M42 in clan MH, also showed requirement for Co2+ for maximum activity. These results proposed that clan MH peptidases might be a cocatalytic cobalt peptidase rather than a zinc-dependent peptidase.
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| - | Structural and kinetic bases for the metal preference of the M18 aminopeptidase from Pseudomonas aeruginosa.,Nguyen DD, Pandian R, Kim D, Ha SC, Yoon HJ, Kim KS, Yun KH, Kim JH, Kim KK Biochem Biophys Res Commun. 2014 Apr 1. pii: S0006-291X(14)00561-0. doi:, 10.1016/j.bbrc.2014.03.109. PMID:24704201<ref>PMID:24704201</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
| + | |
| - | <div class="pdbe-citations 3wt4" style="background-color:#fffaf0;"></div>
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| - | == References ==
| + | |
| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Pseae]] | + | [[Category: Large Structures]] |
| - | [[Category: Ha, S C]] | + | [[Category: Pseudomonas aeruginosa PAO1]] |
| - | [[Category: Kim, D D]] | + | [[Category: Ha SC]] |
| - | [[Category: Kim, J H]] | + | [[Category: Kim DD]] |
| - | [[Category: Kim, K K]] | + | [[Category: Kim JH]] |
| - | [[Category: Kim, K S]] | + | [[Category: Kim KK]] |
| - | [[Category: Nguyen, D D]] | + | [[Category: Kim KS]] |
| - | [[Category: Pandian, R]] | + | [[Category: Nguyen DD]] |
| - | [[Category: Yoon, H J]] | + | [[Category: Pandian R]] |
| - | [[Category: Yun, K H]] | + | [[Category: Yoon HJ]] |
| - | [[Category: Aspartyl aminopeptidase]]
| + | [[Category: Yun KH]] |
| - | [[Category: Dodecameric peptidase]]
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| - | [[Category: Dodecameric tetraheral shape]]
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| - | [[Category: Hydrolase]]
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| - | [[Category: Tet shape protease]]
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