7l7x
From Proteopedia
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==X-ray structure of the Pcryo_0638 aminotransferase from Psychrobacter cryohalolentis== | ==X-ray structure of the Pcryo_0638 aminotransferase from Psychrobacter cryohalolentis== | ||
| - | <StructureSection load='7l7x' size='340' side='right'caption='[[7l7x]]' scene=''> | + | <StructureSection load='7l7x' size='340' side='right'caption='[[7l7x]], [[Resolution|resolution]] 1.30Å' 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=7L7X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7L7X FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7l7x]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Psychrobacter_cryohalolentis_K5 Psychrobacter cryohalolentis K5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7L7X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7L7X 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=7l7x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l7x OCA], [https://pdbe.org/7l7x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l7x RCSB], [https://www.ebi.ac.uk/pdbsum/7l7x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l7x 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]] 1.3Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4RA:[(2R,3R,4R,5S,6R)-3-ACETAMIDO-6-METHYL-5-[(E)-[2-METHYL-3-OXIDANYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]-4-OXIDANYL-OXAN-2-YL]+[[(2R,3S,4R,5R)-5-[2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]+HYDROGEN+PHOSPHATE'>4RA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PMP:4-DEOXY-4-AMINOPYRIDOXAL-5-PHOSPHATE'>PMP</scene>, <scene name='pdbligand=TMA:TETRAMETHYLAMMONIUM+ION'>TMA</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=7l7x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l7x OCA], [https://pdbe.org/7l7x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l7x RCSB], [https://www.ebi.ac.uk/pdbsum/7l7x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l7x ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/Q1QD32_PSYCK Q1QD32_PSYCK] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Psychrobacter cryohalolentis strain K5(T) is a Gram-negative organism first isolated in 2006. It has a complex O-antigen that contains, in addition to l-rhamnose and d-galactose, two diacetamido- and a triacetamido-sugar. The biochemical pathways for the production of these unusual sugars are presently unknown. Utilizing the published genome sequence of the organism, we hypothesized that the genes 0612, 0638, and 0637 encode for a 4,6-dehydratase, an aminotransferase, and an N-acetyltransferase, respectively, which would be required for the biosynthesis of one of the diacetamido-sugars, 2,4-diacetamido-2,4,6-trideoxy-d-glucose, starting from UDP-N-acetylglucosamine. Here we present functional and structural data on the proteins encoded by the 0638 and 0637 genes. The kinetic properties of these enzymes were investigated by a discontinuous HPLC assay. An X-ray crystallographic structure of 0638, determined in its external aldimine form to 1.3 A resolution, demonstrated the manner in which the UDP ligand is positioned into the active site. It is strikingly different from that previously observed for PglE from Campylobacter jejuni, which functions on the same substrate. Four X-ray crystallographic structures were also determined for 0637 in various complexed states at resolutions between 1.3 and 1.55 A. Remarkably, a tetrahedral intermediate mimicking the presumed transition state was trapped in one of the complexes. The data presented herein confirm the hypothesized functions of these enzymes and provide new insight into an unusual sugar biosynthetic pathway in Gram-negative bacteria. We also describe an efficient method for acetyl-CoA synthesis that allowed us to overcome its prohibitive cost for this analysis. | ||
| + | |||
| + | Characterization of two enzymes from Psychrobacter cryohalolentis that are required for the biosynthesis of an unusual diacetamido-d-sugar.,Linehan MP, Thoden JB, Holden HM J Biol Chem. 2021 Jan-Jun;296:100463. doi: 10.1016/j.jbc.2021.100463. Epub 2021, Feb 25. PMID:33639157<ref>PMID:33639157</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7l7x" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| + | [[Category: Psychrobacter cryohalolentis K5]] | ||
[[Category: Holden HM]] | [[Category: Holden HM]] | ||
[[Category: Linehan MP]] | [[Category: Linehan MP]] | ||
[[Category: Thoden JB]] | [[Category: Thoden JB]] | ||
Current revision
X-ray structure of the Pcryo_0638 aminotransferase from Psychrobacter cryohalolentis
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