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| | <StructureSection load='6vgr' size='340' side='right'caption='[[6vgr]], [[Resolution|resolution]] 2.84Å' scene=''> | | <StructureSection load='6vgr' size='340' side='right'caption='[[6vgr]], [[Resolution|resolution]] 2.84Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6vgr]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VGR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VGR FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6vgr]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VGR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VGR FirstGlance]. <br> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DPEP3, UNQ834/PRO1772 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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]] 2.84Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Membrane_dipeptidase Membrane dipeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.13.19 3.4.13.19] </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=6vgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vgr OCA], [https://pdbe.org/6vgr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vgr RCSB], [https://www.ebi.ac.uk/pdbsum/6vgr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vgr ProSAT]</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=6vgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vgr OCA], [http://pdbe.org/6vgr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vgr RCSB], [http://www.ebi.ac.uk/pdbsum/6vgr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vgr ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DPEP3_HUMAN DPEP3_HUMAN]] Dipeptidase that hydrolyzes cystinyl-bis-glycine. Does not hydrolyze leukotriene D4 (LTD4) into leukotriene E4 (LTE4).[UniProtKB:Q9DA79] | + | [https://www.uniprot.org/uniprot/DPEP3_HUMAN DPEP3_HUMAN] Dipeptidase that hydrolyzes cystinyl-bis-glycine. Does not hydrolyze leukotriene D4 (LTD4) into leukotriene E4 (LTE4).[UniProtKB:Q9DA79] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6vgr" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6vgr" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Antibody 3D structures|Antibody 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Human]] | + | [[Category: Homo sapiens]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Membrane dipeptidase]]
| + | [[Category: Hayashi K]] |
| - | [[Category: Hayashi, K]] | + | [[Category: Longenecker KL]] |
| - | [[Category: Longenecker, K L]] | + | [[Category: Vivona S]] |
| - | [[Category: Vivona, S]] | + | |
| - | [[Category: Antibody drug conjugate]]
| + | |
| - | [[Category: Dipeptidase]]
| + | |
| - | [[Category: Fab]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
DPEP3_HUMAN Dipeptidase that hydrolyzes cystinyl-bis-glycine. Does not hydrolyze leukotriene D4 (LTD4) into leukotriene E4 (LTE4).[UniProtKB:Q9DA79]
Publication Abstract from PubMed
Dipeptidase 3 (DPEP3) is one of three glycosylphosphatidylinositol-anchored metallopeptidases potentially involved in the hydrolytic metabolism of dipeptides. While its exact biological function is not clear, DPEP3 expression is normally limited to testis , but can be elevated in ovarian cancer. Antibody drug conjugates targeting DPEP3 have shown efficacy in preclinical models with a pyrrolobenzodiazepine conjugate, SC-003, dosed in a phase I clinical trial (NCT02539719). Here we reveal the novel atomic structure of DPEP3 alone and in complex with the SC-003 Fab fragment at 1.8 and 2.8 A, respectively. The structure of DPEP3/SC-003 Fab complex reveals an eighteen-residue epitope across the DPEP3 dimerization interface distinct from the enzymatic active site. DPEP1 and DPEP3 extracellular domains share a conserved, dimeric TIM (beta/alpha)8-barrel fold, consistent with 49% sequence identity. However, DPEP3 diverges from DPEP1 and DPEP2 in key positions of its active site: a histidine to tyrosine variation at position 269 reduces affinity for the beta zinc and may cause substrate steric hindrance, whereas an aspartate to asparagine change at position 359 abolishes activation of the nucleophilic water/hydroxide, resulting in no in vitro activity against a variety of dipeptides and biological substrates (imipenem, leukotriene D4 and cystinyl-bis-glycine). Hence DPEP3, unlike DPEP1 and DPEP2, may require an activating co-factor in vivo or may remain an inactive, degenerate enzyme. This report sheds light on the structural discriminants between active and inactive membrane dipeptidases and provides a benchmark to characterize current and future DPEP3-targeted therapeutic approaches.
Structure of human DPEP3 in complex with the SC-003 antibody Fab fragment reveals basis for lack of dipeptidase activity.,Hayashi K, Longenecker KL, Koenig P, Prashar A, Hampl J, Stoll V, Vivona S J Struct Biol. 2020 Apr 20:107512. doi: 10.1016/j.jsb.2020.107512. PMID:32325220[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Hayashi K, Longenecker KL, Koenig P, Prashar A, Hampl J, Stoll V, Vivona S. Structure of human DPEP3 in complex with the SC-003 antibody Fab fragment reveals basis for lack of dipeptidase activity. J Struct Biol. 2020 Apr 20:107512. doi: 10.1016/j.jsb.2020.107512. PMID:32325220 doi:http://dx.doi.org/10.1016/j.jsb.2020.107512
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