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| | <StructureSection load='1zlp' size='340' side='right'caption='[[1zlp]], [[Resolution|resolution]] 2.70Å' scene=''> | | <StructureSection load='1zlp' size='340' side='right'caption='[[1zlp]], [[Resolution|resolution]] 2.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1zlp]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Carnation Carnation]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZLP OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1ZLP FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1zlp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Dianthus_caryophyllus Dianthus caryophyllus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZLP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZLP FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GAQ:5-HYDROXYPENTANAL'>GAQ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.7Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PSR132 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3570 Carnation])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GAQ:5-HYDROXYPENTANAL'>GAQ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=1zlp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zlp OCA], [http://pdbe.org/1zlp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1zlp RCSB], [http://www.ebi.ac.uk/pdbsum/1zlp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1zlp ProSAT]</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=1zlp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zlp OCA], [https://pdbe.org/1zlp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zlp RCSB], [https://www.ebi.ac.uk/pdbsum/1zlp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zlp ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PDP_DIACA PDP_DIACA]] Catalyzes cleavage of the C(2)-C(3) bond in oxaloacetate and in (2R)-alkyl malate derivatives to form oxalate and acetate, and alkyl carboxylates and R-ketocarboxylates, respectively.<ref>PMID:16342929</ref> | + | [https://www.uniprot.org/uniprot/PDP_DIACA PDP_DIACA] Catalyzes cleavage of the C(2)-C(3) bond in oxaloacetate and in (2R)-alkyl malate derivatives to form oxalate and acetate, and alkyl carboxylates and R-ketocarboxylates, respectively.<ref>PMID:16342929</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Carnation]] | + | [[Category: Dianthus caryophyllus]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Dunaway-Mariano, D]] | + | [[Category: Dunaway-Mariano D]] |
| - | [[Category: Herzberg, O]] | + | [[Category: Herzberg O]] |
| - | [[Category: Howard, A]] | + | [[Category: Howard A]] |
| - | [[Category: Liu, S]] | + | [[Category: Liu S]] |
| - | [[Category: Lu, Z]] | + | [[Category: Lu Z]] |
| - | [[Category: Teplyakov, A]] | + | [[Category: Teplyakov A]] |
| - | [[Category: 2-ethyl-3-methylmalate lyase]]
| + | |
| - | [[Category: 2-propyl-3-methylmalate lyase]]
| + | |
| - | [[Category: Helix swapping]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Lyase/pep mutase superfamily]]
| + | |
| - | [[Category: Tim-barrel]]
| + | |
| Structural highlights
Function
PDP_DIACA Catalyzes cleavage of the C(2)-C(3) bond in oxaloacetate and in (2R)-alkyl malate derivatives to form oxalate and acetate, and alkyl carboxylates and R-ketocarboxylates, respectively.[1]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Expression of the PSR132 protein from Dianthus caryophyllus (carnation, clover pink) is induced in response to ethylene production associated with petal senescence, and thus the protein is named petal death protein (PDP). Recent work has established that despite the annotation of PDP in sequence databases as carboxyphosphoenolpyruvate mutase, the enzyme is actually a C-C bond cleaving lyase exhibiting a broad substrate profile. The crystal structure of PDP has been determined at 2.7 A resolution, revealing a dimer-of-dimers oligomeric association. Consistent with sequence homology, the overall alpha/beta barrel fold of PDP is the same as that of other isocitrate lyase/PEP mutase superfamily members, including a swapped eighth helix within a dimer. Moreover, Mg(2+) binds in the active site of PDP with a coordination pattern similar to that seen in other superfamily members. A compound, covalently bound to the catalytic residue, Cys144, was interpreted as a thiohemiacetal adduct resulting from the reaction of glutaraldehyde used to cross-link the crystals. The Cys144-carrying flexible loop that gates access to the active site is in the closed conformation. Models of bound substrates and comparison with the closed conformation of isocitrate lyase and 2-methylisocitrate lyase revealed the structural basis for the broad substrate profile of PDP.
Crystal structure of the petal death protein from carnation flower.,Teplyakov A, Liu S, Lu Z, Howard A, Dunaway-Mariano D, Herzberg O Biochemistry. 2005 Dec 20;44(50):16377-84. PMID:16342930[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Lu Z, Feng X, Song L, Han Y, Kim A, Herzberg O, Woodson WR, Martin BM, Mariano PS, Dunaway-Mariano D. Diversity of function in the isocitrate lyase enzyme superfamily: the Dianthus caryophyllus petal death protein cleaves alpha-keto and alpha-hydroxycarboxylic acids. Biochemistry. 2005 Dec 20;44(50):16365-76. PMID:16342929 doi:http://dx.doi.org/10.1021/bi051776l
- ↑ Teplyakov A, Liu S, Lu Z, Howard A, Dunaway-Mariano D, Herzberg O. Crystal structure of the petal death protein from carnation flower. Biochemistry. 2005 Dec 20;44(50):16377-84. PMID:16342930 doi:10.1021/bi051779y
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