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| | <StructureSection load='6n2h' size='340' side='right'caption='[[6n2h]], [[Resolution|resolution]] 1.72Å' scene=''> | | <StructureSection load='6n2h' size='340' side='right'caption='[[6n2h]], [[Resolution|resolution]] 1.72Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6n2h]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N2H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N2H FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6n2h]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N2H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6N2H FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</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]] 1.72Å</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=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</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='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=6n2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n2h OCA], [http://pdbe.org/6n2h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n2h RCSB], [http://www.ebi.ac.uk/pdbsum/6n2h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n2h 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=6n2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n2h OCA], [https://pdbe.org/6n2h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6n2h RCSB], [https://www.ebi.ac.uk/pdbsum/6n2h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6n2h ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/DOKDC_SALTY DOKDC_SALTY] Catalyzes the decarboxylation of D-ornithine and D-lysine (PubMed:29024617, PubMed:30699288). Ornithine is likely the physiological substrate (PubMed:29024617). Has no detectable diaminopimelate decarboxylase activity in vitro (PubMed:29024617).<ref>PMID:29024617</ref> <ref>PMID:30699288</ref> |
| | <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 6n2h" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6n2h" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Ornithine decarboxylase|Ornithine decarboxylase]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Hoover, T R]] | + | [[Category: Salmonella enterica subsp. enterica serovar Typhimurium]] |
| - | [[Category: Phillips, R S]] | + | [[Category: Hoover TR]] |
| - | [[Category: D-amino acid]] | + | [[Category: Phillips RS]] |
| - | [[Category: Decarboxylase]]
| + | |
| - | [[Category: Fold iii]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Pyridoxal-5'-phosphate]]
| + | |
| Structural highlights
Function
DOKDC_SALTY Catalyzes the decarboxylation of D-ornithine and D-lysine (PubMed:29024617, PubMed:30699288). Ornithine is likely the physiological substrate (PubMed:29024617). Has no detectable diaminopimelate decarboxylase activity in vitro (PubMed:29024617).[1] [2]
Publication Abstract from PubMed
A newly discovered Fold III pyridoxal 5'-phosphate (PLP)-dependent decarboxylase, d-ornithine/lysine decarboxylase (DOKDC), catalyzes decarboxylation of d-lysine and d-ornithine with inversion of stereochemistry. The X-ray crystal structure of DOKDC has been determined to 1.72 A. DOKDC has a low level of sequence identity (<30%) with meso-diaminopimelate decarboxylase (DAPDC) and l-lysine/ornithine decarboxylase (LODC), but its three-dimensional structure is very similar. The distal binding site of DAPDC contains a conserved arginine that forms an ion pair with the l-carboxylate end of DAP. In both LODC and DOKDC, this distal site is modified by replacement of the arginine with aspartate, changing the substrate specificity. l-Ornithine decarboxylase (ODC) and LODC have a conserved phenylalanine on the re-face of the PLP complex that has been found to play a key role in the decarboxylation mechanism. We have found that both DAPDC and DOKDC have tyrosine instead of phenylalanine at this position, which precludes the binding of l-amino acids. Because the PLP-binding lysine in ODC, LODC, DAPDC, and DOKDC is located on the re-face of the PLP, we propose that this is the acid group responsible for protonation of the product, thus resulting in the observed retention of configuration for decarboxylation of l-amino acids and inversion for decarboxylation of d-amino acids. The reactions of DAPDC and DOKDC are likely accelerated by positive electrostatics on the re-face by the lysine epsilon-ammonium ion and on the si-face by closure of the lid over the active site, resulting in desolvation and destabilization of the d-amino acid carboxylate.
Crystal Structure of d-Ornithine/d-Lysine Decarboxylase, a Stereoinverting Decarboxylase: Implications for Substrate Specificity and Stereospecificity of Fold III Decarboxylases.,Phillips RS, Poteh P, Krajcovic D, Miller KA, Hoover TR Biochemistry. 2019 Feb 26;58(8):1038-1042. doi: 10.1021/acs.biochem.8b01319. Epub, 2019 Feb 1. PMID:30699288[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Phillips RS, Poteh P, Miller KA, Hoover TR. STM2360 encodes a d-ornithine/d-lysine decarboxylase in Salmonella enterica serovar typhimurium. Arch Biochem Biophys. 2017 Nov 15;634:83-87. doi: 10.1016/j.abb.2017.09.010. Epub, 2017 Oct 9. PMID:29024617 doi:http://dx.doi.org/10.1016/j.abb.2017.09.010
- ↑ Phillips RS, Poteh P, Krajcovic D, Miller KA, Hoover TR. Crystal Structure of d-Ornithine/d-Lysine Decarboxylase, a Stereoinverting Decarboxylase: Implications for Substrate Specificity and Stereospecificity of Fold III Decarboxylases. Biochemistry. 2019 Feb 26;58(8):1038-1042. doi: 10.1021/acs.biochem.8b01319. Epub, 2019 Feb 1. PMID:30699288 doi:http://dx.doi.org/10.1021/acs.biochem.8b01319
- ↑ Phillips RS, Poteh P, Krajcovic D, Miller KA, Hoover TR. Crystal Structure of d-Ornithine/d-Lysine Decarboxylase, a Stereoinverting Decarboxylase: Implications for Substrate Specificity and Stereospecificity of Fold III Decarboxylases. Biochemistry. 2019 Feb 26;58(8):1038-1042. doi: 10.1021/acs.biochem.8b01319. Epub, 2019 Feb 1. PMID:30699288 doi:http://dx.doi.org/10.1021/acs.biochem.8b01319
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