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| | <StructureSection load='4re5' size='340' side='right'caption='[[4re5]], [[Resolution|resolution]] 1.90Å' scene=''> | | <StructureSection load='4re5' size='340' side='right'caption='[[4re5]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4re5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aerpe Aerpe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RE5 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=4RE5 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4re5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix_K1 Aeropyrum pernix K1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RE5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RE5 FirstGlance]. <br> |
| | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=Y3A:N-[(BENZYLOXY)CARBONYL]GLYCYL-N-[(2S,3R)-4-CHLORO-3-HYDROXY-1-PHENYLBUTAN-2-YL]GLYCINAMIDE'>Y3A</scene></td></tr> | | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=Y3A:N-[(BENZYLOXY)CARBONYL]GLYCYL-N-[(2S,3R)-4-CHLORO-3-HYDROXY-1-PHENYLBUTAN-2-YL]GLYCINAMIDE'>Y3A</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4re6|4re6]]</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=4re5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4re5 OCA], [https://pdbe.org/4re5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4re5 RCSB], [https://www.ebi.ac.uk/pdbsum/4re5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4re5 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">APE_1547.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272557 AERPE])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Acylaminoacyl-peptidase Acylaminoacyl-peptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.19.1 3.4.19.1] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=4re5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4re5 OCA], [http://pdbe.org/4re5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4re5 RCSB], [http://www.ebi.ac.uk/pdbsum/4re5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4re5 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/APEH_AERPE APEH_AERPE]] This enzyme catalyzes the hydrolysis of the N-terminal peptide bond of an N-acetylated peptide to generate an N-acetylated amino acid and a peptide with a free N-terminus. | + | [https://www.uniprot.org/uniprot/APEH_AERPE APEH_AERPE] This enzyme catalyzes the hydrolysis of the N-terminal peptide bond of an N-acetylated peptide to generate an N-acetylated amino acid and a peptide with a free N-terminus. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Acylaminoacyl-peptidase]] | + | [[Category: Aeropyrum pernix K1]] |
| - | [[Category: Aerpe]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Harmat, V]] | + | [[Category: Harmat V]] |
| - | [[Category: Menyhard, D K]] | + | [[Category: Menyhard DK]] |
| - | [[Category: Orgovan, Z]] | + | [[Category: Orgovan Z]] |
| - | [[Category: Szamosi, I]] | + | [[Category: Szamosi I]] |
| - | [[Category: Szeltner, Z]] | + | [[Category: Szeltner Z]] |
| - | [[Category: Alpha-beta-hydrolase fold]]
| + | |
| - | [[Category: Beta-propeller]]
| + | |
| - | [[Category: Chloromethyl-ketone inhibitor]]
| + | |
| - | [[Category: Hydrolase-hydrolase inhibitor complex]]
| + | |
| Structural highlights
Function
APEH_AERPE This enzyme catalyzes the hydrolysis of the N-terminal peptide bond of an N-acetylated peptide to generate an N-acetylated amino acid and a peptide with a free N-terminus.
Publication Abstract from PubMed
Acylaminoacyl peptidase (AAP) is an oligopeptidase that only cleaves short peptides or protein segments. In the case of AAP from Aeropyrum pernix (ApAAP), previous studies have led to a model in which the clamshell-like opening and closing of the enzyme provides the means of substrate-size selection. The closed form of the enzyme is catalytically active, while opening deactivates the catalytic triad. The crystallographic results presented here show that the open form of ApAAP is indeed functionally disabled. The obtained crystal structures also reveal that the closed form is penetrable to small ligands: inhibitor added to the pre-formed crystal was able to reach the active site of the rigidified protein, which is only possible through the narrow channel of the propeller domain. Molecular-dynamics simulations investigating the structure of the complexes formed with longer peptide substrates showed that their binding within the large crevice of the closed form of ApAAP leaves the enzyme structure unperturbed; however, their accessing the binding site seems more probable when assisted by opening of the enzyme. Thus, the open form of ApAAP corresponds to a scavenger of possible substrates, the actual cleavage of which only takes place if the enzyme is able to re-close.
Catalytically distinct states captured in a crystal lattice: the substrate-bound and scavenger states of acylaminoacyl peptidase and their implications for functionality.,Menyhard DK, Orgovan Z, Szeltner Z, Szamosi I, Harmat V Acta Crystallogr D Biol Crystallogr. 2015 Mar 1;71(Pt 3):461-72. doi:, 10.1107/S1399004714026819. Epub 2015 Feb 26. PMID:25760596[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Menyhard DK, Orgovan Z, Szeltner Z, Szamosi I, Harmat V. Catalytically distinct states captured in a crystal lattice: the substrate-bound and scavenger states of acylaminoacyl peptidase and their implications for functionality. Acta Crystallogr D Biol Crystallogr. 2015 Mar 1;71(Pt 3):461-72. doi:, 10.1107/S1399004714026819. Epub 2015 Feb 26. PMID:25760596 doi:http://dx.doi.org/10.1107/S1399004714026819
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