7lce
From Proteopedia
(Difference between revisions)
| Line 1: | Line 1: | ||
==Structure of D-Glucosaminate-6-phosphate Ammonia-lyase== | ==Structure of D-Glucosaminate-6-phosphate Ammonia-lyase== | ||
| - | <StructureSection load='7lce' size='340' side='right'caption='[[7lce]]' scene=''> | + | <StructureSection load='7lce' size='340' side='right'caption='[[7lce]], [[Resolution|resolution]] 2.58Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LCE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LCE FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7lce]] is a 4 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=7LCE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LCE FirstGlance]. <br> |
| - | </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=7lce FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lce OCA], [https://pdbe.org/7lce PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lce RCSB], [https://www.ebi.ac.uk/pdbsum/7lce PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lce ProSAT]</span></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]] 2.58Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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'>[https://proteopedia.org/fgij/fg.htm?mol=7lce FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lce OCA], [https://pdbe.org/7lce PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lce RCSB], [https://www.ebi.ac.uk/pdbsum/7lce PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lce ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/DGAE_SALT1 DGAE_SALT1] Involved in the catabolism of D-glucosaminate. Catalyzes the conversion of D-glucosaminate 6-phosphate to yield keto-3-deoxygluconate 6-phosphate (KDGP).<ref>PMID:23836865</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | d-Glucosaminate-6-phosphate ammonia-lyase (DGL) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that produces 2-keto-3-deoxygluconate 6-phosphate (KDG-6-P) in the metabolism of d-glucosaminic acid by Salmonella enterica serovar typhimurium. We have determined the crystal structure of DGL by SAD phasing with selenomethionine to a resolution of 2.58 A. The sequence has very low identity with most other members of the aminotransferase (AT) superfamily. The structure forms an octameric assembly as a tetramer of dimers that has not been observed previously in the AT superfamily. PLP is covalently bound as a Schiff base to Lys-213 in the catalytic dimer at the interface of two monomers. The structure lacks the conserved arginine that binds the alpha-carboxylate of the substrate in most members of the AT superfamily. However, there is a cluster of arginines in the small domain that likely serves as a binding site for the phosphate of the substrate. The deamination reaction performed in D2O gives a KDG-6-P product stereospecifically deuterated at C3; thus, the mechanism must involve an enamine intermediate that is protonated by the enzyme before product release. Nuclear magnetic resonance (NMR) analysis demonstrates that the deuterium is located in the pro-R position in the product, showing that the elimination of water takes place with inversion of configuration at C3, which is unprecedented for a PLP-dependent dehydratase/deaminase. On the basis of the crystal structure and the NMR data, a reaction mechanism for DGL is proposed. | ||
| + | |||
| + | Structure and Mechanism of d-Glucosaminate-6-phosphate Ammonia-lyase: A Novel Octameric Assembly for a Pyridoxal 5'-Phosphate-Dependent Enzyme, and Unprecedented Stereochemical Inversion in the Elimination Reaction of a d-Amino Acid.,Phillips RS, Ting SC, Anderson K Biochemistry. 2021 May 25;60(20):1609-1618. doi: 10.1021/acs.biochem.1c00106., Epub 2021 May 5. PMID:33949189<ref>PMID:33949189</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7lce" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| + | [[Category: Salmonella enterica subsp. enterica serovar Typhimurium]] | ||
[[Category: Phillips RS]] | [[Category: Phillips RS]] | ||
Current revision
Structure of D-Glucosaminate-6-phosphate Ammonia-lyase
| |||||||||||
