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| | ==Crystal Structure of L-Threonine-O-3-Phosphate Decarboxylase from Salmonella enterica== | | ==Crystal Structure of L-Threonine-O-3-Phosphate Decarboxylase from Salmonella enterica== |
| - | <StructureSection load='1lkc' size='340' side='right' caption='[[1lkc]], [[Resolution|resolution]] 1.80Å' scene=''> | + | <StructureSection load='1lkc' size='340' side='right'caption='[[1lkc]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1lkc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_cholerae-suis"_smith_1894 "bacillus cholerae-suis" smith 1894]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1kus 1kus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LKC FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1lkc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica Salmonella enterica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LKC FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.8Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1kus|1kus]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cobD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=28901 "Bacillus cholerae-suis" Smith 1894])</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=1lkc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lkc OCA], [https://pdbe.org/1lkc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lkc RCSB], [https://www.ebi.ac.uk/pdbsum/1lkc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lkc ProSAT]</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=1lkc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lkc OCA], [http://pdbe.org/1lkc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lkc RCSB], [http://www.ebi.ac.uk/pdbsum/1lkc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lkc ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/COBD_SALTY COBD_SALTY]] Decarboxylates L-threonine-O-3-phosphate to yield (R)-1-amino-2-propanol O-2-phosphate, the precursor for the linkage between the nucleotide loop and the corrin ring in cobalamin.<ref>PMID:9446573</ref> | + | [https://www.uniprot.org/uniprot/COBD_SALTY COBD_SALTY] Decarboxylates L-threonine-O-3-phosphate to yield (R)-1-amino-2-propanol O-2-phosphate, the precursor for the linkage between the nucleotide loop and the corrin ring in cobalamin.<ref>PMID:9446573</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lk/1lkc_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lk/1lkc_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: Bacillus cholerae-suis smith 1894]] | + | [[Category: Large Structures]] |
| - | [[Category: Bauer, C B]] | + | [[Category: Salmonella enterica]] |
| - | [[Category: Brushaber, K R]] | + | [[Category: Bauer CB]] |
| - | [[Category: Cheong, C G]] | + | [[Category: Brushaber KR]] |
| - | [[Category: Escalante-Semerena, J C]] | + | [[Category: Cheong CG]] |
| - | [[Category: Rayment, I]] | + | [[Category: Escalante-Semerena JC]] |
| - | [[Category: 1-amino-2-propanol-phosphate]]
| + | [[Category: Rayment I]] |
| - | [[Category: Cobalamin]]
| + | |
| - | [[Category: Cobd]]
| + | |
| - | [[Category: Decarboxylase]]
| + | |
| - | [[Category: L-threonine-o-3-phosphate]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Plp]]
| + | |
| Structural highlights
Function
COBD_SALTY Decarboxylates L-threonine-O-3-phosphate to yield (R)-1-amino-2-propanol O-2-phosphate, the precursor for the linkage between the nucleotide loop and the corrin ring in cobalamin.[1]
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
The three-dimensional structure of the pyridoxal 5'-phosphate (PLP)-dependent L-threonine-O-3-phosphate decarboxylase (CobD) from Salmonella enterica is described here. This enzyme is responsible for synthesizing (R)-1-amino-2-propanol phosphate which is the precursor for the linkage between the nucleotide loop and the corrin ring in cobalamin. The molecule is a molecular dimer where each subunit consists of a large and small domain. Overall the protein is very similar to the members of the family of aspartate aminotransferases. Indeed, the arrangement of the ligands surrounding the cofactor and putative substrate binding site are remarkably close to that observed in histidinol phosphate aminotransferase, which suggests that this latter enzyme might have been its progenitor. The only significant differences in structure occur at the N-terminus, which is approximately 12 residues shorter in CobD and does not form the same type of interdomain interaction common to other aminotransferases. CobD is unusual since within the aspartate aminotransferase subfamily of PLP-dependent enzymes the chemical transformations are substantially conserved, where the only exceptions are 1-aminocyclopropane-1-carboxylate synthase and CobD. Although there are a large number of PLP-dependent amino acid decarboxylases, these are generally larger and structurally distinct from the members of the aspartate aminotransferase subfamily of enzymes. The structure of CobD suggests that the chemical fate of the external aldimine can be redirected by modifications at the N-terminus of the protein. This study provides insight into the evolutionary history of the cobalamin biosynthetic pathway and raises the question of why most PLP-dependent decarboxylases are considerably larger enzymes.
Three-dimensional structure of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica.,Cheong CG, Bauer CB, Brushaber KR, Escalante-Semerena JC, Rayment I Biochemistry. 2002 Apr 16;41(15):4798-808. PMID:11939774[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Brushaber KR, O'Toole GA, Escalante-Semerena JC. CobD, a novel enzyme with L-threonine-O-3-phosphate decarboxylase activity, is responsible for the synthesis of (R)-1-amino-2-propanol O-2-phosphate, a proposed new intermediate in cobalamin biosynthesis in Salmonella typhimurium LT2. J Biol Chem. 1998 Jan 30;273(5):2684-91. PMID:9446573
- ↑ Cheong CG, Bauer CB, Brushaber KR, Escalante-Semerena JC, Rayment I. Three-dimensional structure of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica. Biochemistry. 2002 Apr 16;41(15):4798-808. PMID:11939774
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