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| | <StructureSection load='1tuf' size='340' side='right'caption='[[1tuf]], [[Resolution|resolution]] 2.40Å' scene=''> | | <StructureSection load='1tuf' size='340' side='right'caption='[[1tuf]], [[Resolution|resolution]] 2.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1tuf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TUF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1TUF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1tuf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TUF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TUF FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZ1:AZELAIC+ACID'>AZ1</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]] 2.4Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZ1:AZELAIC+ACID'>AZ1</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">LYSA, MJ1097 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</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=1tuf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tuf OCA], [https://pdbe.org/1tuf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tuf RCSB], [https://www.ebi.ac.uk/pdbsum/1tuf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tuf ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/1tuf TOPSAN]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopimelate_decarboxylase Diaminopimelate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.20 4.1.1.20] </span></td></tr>
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| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1tuf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tuf OCA], [http://pdbe.org/1tuf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tuf RCSB], [http://www.ebi.ac.uk/pdbsum/1tuf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1tuf ProSAT], [http://www.topsan.org/Proteins/NYSGXRC/1tuf TOPSAN]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DCDA_METJA DCDA_METJA]] Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine.<ref>PMID:12429091</ref> | + | [https://www.uniprot.org/uniprot/DCDA_METJA DCDA_METJA] Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine.<ref>PMID:12429091</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tu/1tuf_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tu/1tuf_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 43067]] | |
| - | [[Category: Diaminopimelate decarboxylase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bonanno, J B]] | + | [[Category: Methanocaldococcus jannaschii]] |
| - | [[Category: Burley, S K]] | + | [[Category: Bonanno JB]] |
| - | [[Category: He, G]] | + | [[Category: Burley SK]] |
| - | [[Category: Lencastre, H De]] | + | [[Category: De Lencastre H]] |
| - | [[Category: Structural genomic]] | + | [[Category: He G]] |
| - | [[Category: Pinho, M G]] | + | [[Category: Pinho MG]] |
| - | [[Category: Rajashankar, K]] | + | [[Category: Rajashankar K]] |
| - | [[Category: Ray, S R]] | + | [[Category: Ray SR]] |
| - | [[Category: Tomasz, A]] | + | [[Category: Tomasz A]] |
| - | [[Category: Antibiotic resistance]]
| + | |
| - | [[Category: Diamnopimilate decarboxylase]]
| + | |
| - | [[Category: Lyase]]
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| - | [[Category: Lysine biosynthesis]]
| + | |
| - | [[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]
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| - | [[Category: PSI, Protein structure initiative]]
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| - | [[Category: T135]]
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| Structural highlights
Function
DCDA_METJA Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine.[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
Cocrystal structures of Methanococcus jannaschii diaminopimelate decarboxylase (DAPDC) bound to a substrate analog, azelaic acid, and its L-lysine product have been determined at 2.6 A and 2.0 A, respectively. This PLP-dependent enzyme is responsible for the final step of L-lysine biosynthesis in bacteria and plays a role in beta-lactam antibiotic resistance in Staphylococcus aureus. Substrate specificity derives from recognition of the L-chiral center of diaminopimelate and a system of ionic "molecular rulers" that dictate substrate length. A coupled-enzyme assay system permitted measurement of kinetic parameters for recombinant DAPDCs and inhibition constants (K(i)) for azelaic acid (89 microM) and other substrate analogs. Implications for rational design of broad-spectrum antimicrobial agents targeted against DAPDCs of drug-resistant strains of bacterial pathogens, such as Staphylococcus aureus, are discussed.
Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor.,Ray SS, Bonanno JB, Rajashankar KR, Pinho MG, He G, De Lencastre H, Tomasz A, Burley SK Structure. 2002 Nov;10(11):1499-508. PMID:12429091[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ray SS, Bonanno JB, Rajashankar KR, Pinho MG, He G, De Lencastre H, Tomasz A, Burley SK. Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor. Structure. 2002 Nov;10(11):1499-508. PMID:12429091
- ↑ Ray SS, Bonanno JB, Rajashankar KR, Pinho MG, He G, De Lencastre H, Tomasz A, Burley SK. Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor. Structure. 2002 Nov;10(11):1499-508. PMID:12429091
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