|
|
| (2 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==Crystal Structure of ADP-AIR complex of purK: N5-carboxyaminoimidazole ribonucleotide synthetase== | | ==Crystal Structure of ADP-AIR complex of purK: N5-carboxyaminoimidazole ribonucleotide synthetase== |
| - | <StructureSection load='3r5h' size='340' side='right' caption='[[3r5h]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='3r5h' size='340' side='right'caption='[[3r5h]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3r5h]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacaa Bacaa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3R5H FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3r5h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_anthracis_str._A0248 Bacillus anthracis str. A0248]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R5H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R5H FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AIR:5-AMINOIMIDAZOLE+RIBONUCLEOTIDE'>AIR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.2Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BAA_0344, purK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=592021 BACAA])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AIR:5-AMINOIMIDAZOLE+RIBONUCLEOTIDE'>AIR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoribosylaminoimidazole_carboxylase Phosphoribosylaminoimidazole carboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.21 4.1.1.21] </span></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=3r5h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r5h OCA], [https://pdbe.org/3r5h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r5h RCSB], [https://www.ebi.ac.uk/pdbsum/3r5h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r5h 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=3r5h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r5h OCA], [http://pdbe.org/3r5h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3r5h RCSB], [http://www.ebi.ac.uk/pdbsum/3r5h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3r5h ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| Line 20: |
Line 19: |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Phosphoribosylaminoimidazole carboxylase|Phosphoribosylaminoimidazole carboxylase]] | + | *[[Phosphoribosylaminoimidazole carboxylase 3D structures|Phosphoribosylaminoimidazole carboxylase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacaa]] | + | [[Category: Bacillus anthracis str. A0248]] |
| - | [[Category: Phosphoribosylaminoimidazole carboxylase]] | + | [[Category: Large Structures]] |
| - | [[Category: Fung, L W]] | + | [[Category: Fung LW]] |
| - | [[Category: Johnson, M E]] | + | [[Category: Johnson ME]] |
| - | [[Category: Santarsiero, B D]] | + | [[Category: Santarsiero BD]] |
| - | [[Category: Tuntland, M L]] | + | [[Category: Tuntland ML]] |
| - | [[Category: Carboxylase]]
| + | |
| - | [[Category: Lyase]]
| + | |
| Structural highlights
Publication Abstract from PubMed
Structures of (N(5))-carboxyaminoimidazole ribonucleotide synthase (PurK) from Bacillus anthracis with various combinations of ATP, ADP, Mg(2+), bicarbonate and aminoimidazole ribonucleotide (AIR) in the active site are presented. The binding site of bicarbonate has only been speculated upon previously, but is shown here for the first time. The binding involves interactions with the conserved residues Arg272, His274 and Lys348. These structures provide insights into each ligand in the active site and allow a possible mechanism to be proposed for the reaction that converts bicarbonate and AIR, in the presence of ATP, to produce (N(5))-carboxyaminoimidazole ribonucleotide. The formation of a carboxyphosphate intermediate through ATP phosphoryl transfer is proposed, followed by carboxylation of AIR to give the product, facilitated by a cluster of conserved residues and an active-site water network.
Elucidation of the bicarbonate binding site and insights into the carboxylation mechanism of (N(5))-carboxyaminoimidazole ribonucleotide synthase (PurK) from Bacillus anthracis.,Tuntland ML, Santarsiero BD, Johnson ME, Fung LW Acta Crystallogr D Biol Crystallogr. 2014 Nov;70(Pt 11):3057-65. doi:, 10.1107/S1399004714021166. Epub 2014 Oct 29. PMID:25372694[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Tuntland ML, Santarsiero BD, Johnson ME, Fung LW. Elucidation of the bicarbonate binding site and insights into the carboxylation mechanism of (N(5))-carboxyaminoimidazole ribonucleotide synthase (PurK) from Bacillus anthracis. Acta Crystallogr D Biol Crystallogr. 2014 Nov;70(Pt 11):3057-65. doi:, 10.1107/S1399004714021166. Epub 2014 Oct 29. PMID:25372694 doi:http://dx.doi.org/10.1107/S1399004714021166
|
