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5yq8

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Crystal structure of retroviral protease-like domain of Ddi1 from Leishmania major

Structural highlights

5yq8 is a 4 chain structure with sequence from Leishmania major. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.25Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DDI1_LEIMA Aspartic protease (PubMed:22933181, PubMed:21266539).^[1] ^[2]

Publication Abstract from PubMed

DNA damage-inducible 1 (Ddi1) is a multidomain protein with one of the domains being retropepsin-like. HIV-1 protease inhibitors were found to reduce opportunistic infections caused by pathogens like Leishmania and Plasmodium, and some of them were shown to inhibit the growth of these parasites. In Leishmania, Ddi1 was identified as a likely target of the inhibitors. We report the crystal structure of the retropepsin-like domain of Ddi1 from Leishmania major as a dimer with clear density for the critical 'flap' region. We have characterized binding with one of the HIV-1 protease inhibitors in solution using bio-layer interferometry and by docking. Further, we have performed molecular dynamics (MD) simulation studies that show that the protein undergoes a conformational change from open to semi-open and closed forms with the closing of the flexible flap over the active site.

Crystal structure of the retroviral protease-like domain of a protozoal DNA damage-inducible 1 protein.,Kumar S, Suguna K FEBS Open Bio. 2018 Aug 3;8(9):1379-1394. doi: 10.1002/2211-5463.12491., eCollection 2018 Sep. PMID:30186740^[3]

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

References

↑ Perteguer MJ, Gómez-Puertas P, Cañavate C, Dagger F, Gárate T, Valdivieso E. Ddi1-like protein from Leishmania major is an active aspartyl proteinase. Cell Stress Chaperones. 2013 Mar;18(2):171-81. PMID:22933181 doi:10.1007/s12192-012-0368-9
↑ White RE, Powell DJ, Berry C. HIV proteinase inhibitors target the Ddi1-like protein of Leishmania parasites. FASEB J. 2011 May;25(5):1729-36. PMID:21266539 doi:10.1096/fj.10-178947
↑ Kumar S, Suguna K. Crystal structure of the retroviral protease-like domain of a protozoal DNA damage-inducible 1 protein. FEBS Open Bio. 2018 Aug 3;8(9):1379-1394. doi: 10.1002/2211-5463.12491., eCollection 2018 Sep. PMID:30186740 doi:http://dx.doi.org/10.1002/2211-5463.12491

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5yq8"

Categories: Large Structures | Leishmania major | Kumar S | Suguna K

@@ Line 3: / Line 3: @@
 <StructureSection load='5yq8' size='340' side='right'caption='[[5yq8]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5yq8]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YQ8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YQ8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5yq8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Leishmania_major Leishmania major]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YQ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YQ8 FirstGlance]. <br>
-</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=5yq8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yq8 OCA], [http://pdbe.org/5yq8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yq8 RCSB], [http://www.ebi.ac.uk/pdbsum/5yq8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yq8 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]] 2.25&#8491;</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=5yq8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yq8 OCA], [https://pdbe.org/5yq8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yq8 RCSB], [https://www.ebi.ac.uk/pdbsum/5yq8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yq8 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/DDI1_LEIMA DDI1_LEIMA] Aspartic protease (PubMed:22933181, PubMed:21266539).<ref>PMID:22933181</ref> <ref>PMID:21266539</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 23: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Kumar, S]]
+[[Category: Leishmania major]]
-[[Category: Suguna, K]]
+[[Category: Kumar S]]
-[[Category: Aspartic protease]]
+[[Category: Suguna K]]
-[[Category: Cytoplasmic]]
-[[Category: Hydrolase]]
-[[Category: Retropepsin]]

5yq8

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Current revision

Crystal structure of retroviral protease-like domain of Ddi1 from Leishmania major

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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