4s2r: Difference between revisions

Revision as of 10:40, 15 March 2023

Crystal structure of X-prolyl aminopeptidase from Caenorhabditis elegans: a cytosolic enzyme with a di-nuclear active site

Structural highlights

4s2r is a 2 chain structure with sequence from Caenorhabditis elegans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

XPP_CAEEL Catalyzes the removal of a penultimate prolyl residue from the N-termini of peptides, such as Arg-Pro-Pro (PubMed:11606206, PubMed:25905034). Has activity towards the flp-9 neuropeptide KPSFVRF-amide (PubMed:11606206).^[1] ^[2]

Publication Abstract from PubMed

Eukaryotic aminopeptidase P1 (APP1), also known as X-prolyl aminopeptidase (XPNPEP1) in human tissues, is a cytosolic exopeptidase that preferentially removes amino acids from the N-terminus of peptides possessing a penultimate N-terminal proline residue. The enzyme has an important role in the catabolism of proline containing peptides since peptide bonds adjacent to the imino acid proline are resistant to cleavage by most peptidases. We show that recombinant and catalytically active Caenorhabditis elegans APP-1 is a dimer that uses dinuclear zinc at the active site and, for the first time, we provide structural information for a eukaryotic APP-1 in complex with the inhibitor, apstatin. Our analysis reveals that C. elegans APP-1 shares similar mode of substrate binding and a common catalytic mechanism with other known X-prolyl aminopeptidases.

Crystal structure of X-prolyl aminopeptidase from Caenorhabditis elegans: A cytosolic enzyme with a di-nuclear active site.,Iyer S, La-Borde PJ, Payne KA, Parsons MR, Turner AJ, Isaac RE, Acharya KR FEBS Open Bio. 2015 Apr 2;5:292-302. doi: 10.1016/j.fob.2015.03.013. eCollection , 2015. PMID:25905034^[3]

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

References

↑ Laurent V, Brooks DR, Coates D, Isaac RE. Functional expression and characterization of the cytoplasmic aminopeptidase P of Caenorhabditis elegans. Eur J Biochem. 2001 Oct;268(20):5430-8. PMID:11606206 doi:10.1046/j.0014-2956.2001.02483.x
↑ Iyer S, La-Borde PJ, Payne KA, Parsons MR, Turner AJ, Isaac RE, Acharya KR. Crystal structure of X-prolyl aminopeptidase from Caenorhabditis elegans: A cytosolic enzyme with a di-nuclear active site. FEBS Open Bio. 2015 Apr 2;5:292-302. doi: 10.1016/j.fob.2015.03.013. eCollection , 2015. PMID:25905034 doi:https://dx.doi.org/10.1016/j.fob.2015.03.013
↑ Iyer S, La-Borde PJ, Payne KA, Parsons MR, Turner AJ, Isaac RE, Acharya KR. Crystal structure of X-prolyl aminopeptidase from Caenorhabditis elegans: A cytosolic enzyme with a di-nuclear active site. FEBS Open Bio. 2015 Apr 2;5:292-302. doi: 10.1016/j.fob.2015.03.013. eCollection , 2015. PMID:25905034 doi:https://dx.doi.org/10.1016/j.fob.2015.03.013

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Laurent V, Brooks DR, Coates D, Isaac RE. Functional expression and characterization of the cytoplasmic aminopeptidase P of Caenorhabditis elegans. Eur J Biochem. 2001 Oct;268(20):5430-8. PMID:11606206 doi:10.1046/j.0014-2956.2001.02483.x

[2] Iyer S, La-Borde PJ, Payne KA, Parsons MR, Turner AJ, Isaac RE, Acharya KR. Crystal structure of X-prolyl aminopeptidase from Caenorhabditis elegans: A cytosolic enzyme with a di-nuclear active site. FEBS Open Bio. 2015 Apr 2;5:292-302. doi: 10.1016/j.fob.2015.03.013. eCollection , 2015. PMID:25905034 doi:https://dx.doi.org/10.1016/j.fob.2015.03.013

[3] Iyer S, La-Borde PJ, Payne KA, Parsons MR, Turner AJ, Isaac RE, Acharya KR. Crystal structure of X-prolyl aminopeptidase from Caenorhabditis elegans: A cytosolic enzyme with a di-nuclear active site. FEBS Open Bio. 2015 Apr 2;5:292-302. doi: 10.1016/j.fob.2015.03.013. eCollection , 2015. PMID:25905034 doi:https://dx.doi.org/10.1016/j.fob.2015.03.013

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='4s2r' size='340' side='right'caption='[[4s2r]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4s2r]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Caeel Caeel]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4S2R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4S2R FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4s2r]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4S2R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4S2R FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4s2t|4s2t]]</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=4s2r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4s2r OCA], [https://pdbe.org/4s2r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4s2r RCSB], [https://www.ebi.ac.uk/pdbsum/4s2r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4s2r ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">app-1, CELE_W03G9.4, W03G9.4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6239 CAEEL])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xaa-Pro_aminopeptidase Xaa-Pro aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.9 3.4.11.9] </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=4s2r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4s2r OCA], [http://pdbe.org/4s2r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4s2r RCSB], [http://www.ebi.ac.uk/pdbsum/4s2r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4s2r ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/XPP_CAEEL XPP_CAEEL] Catalyzes the removal of a penultimate prolyl residue from the N-termini of peptides, such as Arg-Pro-Pro (PubMed:11606206, PubMed:25905034). Has activity towards the flp-9 neuropeptide KPSFVRF-amide (PubMed:11606206).<ref>PMID:11606206</ref> <ref>PMID:25905034</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 25: @@
 __TOC__
 </StructureSection>
-[[Category: Caeel]]
+[[Category: Caenorhabditis elegans]]
 [[Category: Large Structures]]
-[[Category: Xaa-Pro aminopeptidase]]
+[[Category: Acharya KR]]
-[[Category: Acharya, K R]]
+[[Category: Isaac RE]]
-[[Category: Isaac, R E]]
+[[Category: Iyer S]]
-[[Category: Iyer, S]]
+[[Category: La-Borde P]]
-[[Category: La-Borde, P]]
+[[Category: Parsons MR]]
-[[Category: Parsons, M R]]
+[[Category: Payne KAP]]
-[[Category: Payne, K A.P]]
+[[Category: Turner AJ]]
-[[Category: Turner, A J]]
-[[Category: Hydrolase]]
-[[Category: Metalloprotease]]
-[[Category: Pitta-bread fold]]
-[[Category: Zinc binding]]

4s2r: Difference between revisions

Revision as of 10:40, 15 March 2023

Crystal structure of X-prolyl aminopeptidase from Caenorhabditis elegans: a cytosolic enzyme with a di-nuclear active site

Structural highlights

Function

Publication Abstract from PubMed

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References

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