This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
2z7b
From Proteopedia
(Difference between revisions)
| (6 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | [[Image:2z7b.png|left|200px]] | ||
| - | + | ==Crystal Structure of Mesorhizobium loti 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase== | |
| - | + | <StructureSection load='2z7b' size='340' side='right'caption='[[2z7b]], [[Resolution|resolution]] 1.90Å' scene=''> | |
| - | + | == Structural highlights == | |
| - | + | <table><tr><td colspan='2'>[[2z7b]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mesorhizobium_japonicum_MAFF_303099 Mesorhizobium japonicum MAFF 303099]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z7B FirstGlance]. <br> | |
| - | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> | |
| - | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=2z7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z7b OCA], [https://pdbe.org/2z7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z7b RCSB], [https://www.ebi.ac.uk/pdbsum/2z7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z7b ProSAT]</span></td></tr> |
| - | [[2z7b]] is a 1 chain structure with sequence from [ | + | </table> |
| - | + | == Function == | |
| - | == | + | [https://www.uniprot.org/uniprot/HMPD_RHILO HMPD_RHILO] Involved in the catabolism of pyridoxal 5-phosphate (Vitamin B6). Catalyzes the decarboxylation of 3-hydroxy-2-methylpyridine-4,5-dicarboxylate to yield 3-hydroxy-2-methylpyridine-5-carboxylate. The decarboxylation proceeds by an aldolase-like mechanism in which the binding of the substrate frees Glu-73 residue from its interaction with manganese ion replacing it by an interaction with the hydroxyl group from the substrate. Glu-73 residue then provides the proton for the keto-enol tautomerization. The decarboxylation reaction is analogous to the retroaldol reaction except that it does not need a base as the carboxylate is likely to be deprotonated under the reaction conditions.<ref>PMID:17973403</ref> |
| - | < | + | == Evolutionary Conservation == |
| - | [[ | + | [[Image:Consurf_key_small.gif|200px|right]] |
| - | [ | + | Check<jmol> |
| - | [[Category: | + | <jmolCheckbox> |
| - | [[Category: | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z7/2z7b_consurf.spt"</scriptWhenChecked> |
| - | [[Category: | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | [[Category: | + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | [[Category: | + | </jmolCheckbox> |
| - | [[Category: | + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2z7b ConSurf]. |
| + | <div style="clear:both"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Mesorhizobium japonicum MAFF 303099]] | ||
| + | [[Category: Begley TP]] | ||
| + | [[Category: Ealick SE]] | ||
| + | [[Category: McCulloch KM]] | ||
| + | [[Category: Mukherjee T]] | ||
Current revision
Crystal Structure of Mesorhizobium loti 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase
| |||||||||||
