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| | <StructureSection load='6ldr' size='340' side='right'caption='[[6ldr]], [[Resolution|resolution]] 1.79Å' scene=''> | | <StructureSection load='6ldr' size='340' side='right'caption='[[6ldr]], [[Resolution|resolution]] 1.79Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6ldr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Metja Metja]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LDR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LDR FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6ldr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii_DSM_2661 Methanocaldococcus jannaschii DSM 2661]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LDR FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.79Å</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6jy1|6jy1]]</div></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=6ldr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ldr OCA], [https://pdbe.org/6ldr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ldr RCSB], [https://www.ebi.ac.uk/pdbsum/6ldr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ldr ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mfnA, MJ0050 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243232 METJA])</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=6ldr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ldr OCA], [http://pdbe.org/6ldr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ldr RCSB], [http://www.ebi.ac.uk/pdbsum/6ldr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ldr ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/MFNA_METJA MFNA_METJA]] Specifically catalyzes the decarboxylation of L-tyrosine to produce tyramine.<ref>PMID:15715981</ref> | + | [https://www.uniprot.org/uniprot/MFNA_METJA MFNA_METJA] Specifically catalyzes the decarboxylation of L-tyrosine to produce tyramine.<ref>PMID:15715981</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Metja]] | + | [[Category: Methanocaldococcus jannaschii DSM 2661]] |
| - | [[Category: Gayathri, S C]] | + | [[Category: Gayathri SC]] |
| - | [[Category: Manoj, N]] | + | [[Category: Manoj N]] |
| - | [[Category: Catalytic domain]]
| + | |
| - | [[Category: Group ii decarboxylase]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Lys mutant]]
| + | |
| - | [[Category: Plp dependent decarboxylase]]
| + | |
| - | [[Category: Protein conformation]]
| + | |
| - | [[Category: Pyridoxal 5-phosphate]]
| + | |
| - | [[Category: Structure-activity relationship]]
| + | |
| Structural highlights
6ldr is a 1 chain structure with sequence from Methanocaldococcus jannaschii DSM 2661. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.79Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
MFNA_METJA Specifically catalyzes the decarboxylation of L-tyrosine to produce tyramine.[1]
Publication Abstract from PubMed
Formation of the internal aldimine (LLP) is the first regulatory step that activates pyridoxal 5'-phosphate (PLP) dependent enzymes. The process involves a nucleophilic attack on PLP by an active site Lys residue, followed by proton transfers resulting in a carbinolamine (CBA) intermediate that undergoes dehydration to form the aldimine. Despite a general understanding of the pathway, the structural basis of the mechanistic roles of specific residues in each of these steps is unclear. Here we determined the crystal structure of the LLP form (holo-form) of a Group II PLP-dependent decarboxylase from Methanocaldococcus jannaschii (MjDC) at 1.7A resolution. By comparing the crystal structure of MjDC in the LLP form with that of the pyridoxal-P (non-covalently bound aldehyde) form, we demonstrate structural evidence for a water-mediated mechanism of LLP formation. A conserved extended hydrogen-bonding network around PLP coupled to the pyridinyl nitrogen influences activation and catalysis by affecting the electronic configuration of PLP. Furthermore, the two cofactor bound forms revealed open and closed conformations of the catalytic loop (CL) in the absence of a ligand, supporting a hypothesis for a regulatory link between LLP formation and CL dynamics. The evidence suggests that activation of Group II decarboxylases involves a complex interplay of interactions between the electronic states of PLP, the active site micro-environment and CL dynamics.
Structural insights into the mechanism of internal aldimine formation and catalytic loop dynamics in an archaeal Group II decarboxylase.,Chellam Gayathri S, Manoj N J Struct Biol. 2019 Nov 1;208(2):137-151. doi: 10.1016/j.jsb.2019.08.009. Epub, 2019 Aug 21. PMID:31445086[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kezmarsky ND, Xu H, Graham DE, White RH. Identification and characterization of a L-tyrosine decarboxylase in Methanocaldococcus jannaschii. Biochim Biophys Acta. 2005 Mar 11;1722(2):175-82. Epub 2005 Jan 22. PMID:15715981 doi:http://dx.doi.org/S0304-4165(04)00312-5
- ↑ Chellam Gayathri S, Manoj N. Structural insights into the mechanism of internal aldimine formation and catalytic loop dynamics in an archaeal Group II decarboxylase. J Struct Biol. 2019 Nov 1;208(2):137-151. doi: 10.1016/j.jsb.2019.08.009. Epub, 2019 Aug 21. PMID:31445086 doi:http://dx.doi.org/10.1016/j.jsb.2019.08.009
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