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| | ==X-ray crystal structure of arginine decarboxylase complexed with Arginine from Vibrio vulnificus== | | ==X-ray crystal structure of arginine decarboxylase complexed with Arginine from Vibrio vulnificus== |
| - | <StructureSection load='3n2o' size='340' side='right' caption='[[3n2o]], [[Resolution|resolution]] 2.30Å' scene=''> | + | <StructureSection load='3n2o' size='340' side='right'caption='[[3n2o]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3n2o]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibvy Vibvy]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N2O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3N2O FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3n2o]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_vulnificus_YJ016 Vibrio vulnificus YJ016]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N2O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N2O FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AG2:AGMATINE'>AG2</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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]] 2.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3n29|3n29]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AG2:AGMATINE'>AG2</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ADC, speA, VV1986 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=196600 VIBVY])</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=3n2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n2o OCA], [https://pdbe.org/3n2o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3n2o RCSB], [https://www.ebi.ac.uk/pdbsum/3n2o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3n2o ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arginine_decarboxylase Arginine decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.19 4.1.1.19] </span></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=3n2o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n2o OCA], [http://pdbe.org/3n2o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3n2o RCSB], [http://www.ebi.ac.uk/pdbsum/3n2o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3n2o ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/SPEA_VIBVY SPEA_VIBVY]] Catalyzes the biosynthesis of agmatine from arginine (By similarity). | + | [https://www.uniprot.org/uniprot/SPEA_VIBVY SPEA_VIBVY] Catalyzes the biosynthesis of agmatine from arginine (By similarity). |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n2/3n2o_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n2/3n2o_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: Arginine decarboxylase]] | + | [[Category: Large Structures]] |
| - | [[Category: Vibvy]] | + | [[Category: Vibrio vulnificus YJ016]] |
| - | [[Category: Deng, X]] | + | [[Category: Deng X]] |
| - | [[Category: Goldsmith, E J]] | + | [[Category: Goldsmith EJ]] |
| - | [[Category: Lee, J]] | + | [[Category: Lee J]] |
| - | [[Category: Michael, A J]] | + | [[Category: Michael AJ]] |
| - | [[Category: Phillips, M A]] | + | [[Category: Phillips MA]] |
| - | [[Category: Tomchick, D R]] | + | [[Category: Tomchick DR]] |
| - | [[Category: Lyase]]
| + | |
| Structural highlights
Function
SPEA_VIBVY Catalyzes the biosynthesis of agmatine from arginine (By similarity).
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
Pyridoxal 5'-phosphate (PLP)-dependent basic amino acid decarboxylases from the beta/alpha-barrel-fold class (group IV) exist in most organisms and catalyze the decarboxylation of diverse substrates, essential for polyamine and lysine biosynthesis. Herein we describe the first x-ray structure determination of bacterial biosynthetic arginine decarboxylase (ADC) and carboxynorspermidine decarboxylase (CANSDC) to 2.3- and 2.0-A resolution, solved as product complexes with agmatine and norspermidine. Despite low overall sequence identity, the monomeric and dimeric structures are similar to other enzymes in the family, with the active sites formed between the beta/alpha-barrel domain of one subunit and the beta-barrel of the other. ADC contains both a unique interdomain insertion (4-helical bundle) and a C-terminal extension (3-helical bundle) and it packs as a tetramer in the asymmetric unit with the insertions forming part of the dimer and tetramer interfaces. Analytical ultracentrifugation studies confirmed that the ADC solution structure is a tetramer. Specificity for different basic amino acids appears to arise primarily from changes in the position of, and amino acid replacements in, a helix in the beta-barrel domain we refer to as the "specificity helix." Additionally, in CANSDC a key acidic residue that interacts with the distal amino group of other substrates is replaced by Leu(314), which interacts with the aliphatic portion of norspermidine. Neither product, agmatine in ADC nor norspermidine in CANSDC, form a Schiff base to pyridoxal 5'-phosphate, suggesting that the product complexes may promote product release by slowing the back reaction. These studies provide insight into the structural basis for the evolution of novel function within a common structural-fold.
Evolution of substrate specificity within a diverse family of beta/alpha-barrel-fold basic amino acid decarboxylases: X-ray structure determination of enzymes with specificity for L-arginine and carboxynorspermidine.,Deng X, Lee J, Michael AJ, Tomchick DR, Goldsmith EJ, Phillips MA J Biol Chem. 2010 Aug 13;285(33):25708-19. Epub 2010 Jun 8. PMID:20534592[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Deng X, Lee J, Michael AJ, Tomchick DR, Goldsmith EJ, Phillips MA. Evolution of substrate specificity within a diverse family of beta/alpha-barrel-fold basic amino acid decarboxylases: X-ray structure determination of enzymes with specificity for L-arginine and carboxynorspermidine. J Biol Chem. 2010 Aug 13;285(33):25708-19. Epub 2010 Jun 8. PMID:20534592 doi:10.1074/jbc.M110.121137
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