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| | ==Crystal Structure of Pasteurella multocida N-Acetyl-D-Neuraminic acid lyase trapped with pyruvate covalently bound through a Schiff base to Lys164== | | ==Crystal Structure of Pasteurella multocida N-Acetyl-D-Neuraminic acid lyase trapped with pyruvate covalently bound through a Schiff base to Lys164== |
| - | <StructureSection load='4imd' size='340' side='right' caption='[[4imd]], [[Resolution|resolution]] 2.10Å' scene=''> | + | <StructureSection load='4imd' size='340' side='right'caption='[[4imd]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4imd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pasteurella_multocida_subsp._gallicida_p1059 Pasteurella multocida subsp. gallicida p1059]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IMD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IMD FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4imd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pasteurella_multocida_subsp._gallicida_P1059 Pasteurella multocida subsp. gallicida P1059]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IMD 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=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]] 2.1Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KPI:(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC+ACID'>KPI</scene></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=KPI:(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC+ACID'>KPI</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4imc|4imc]], [[4ime|4ime]], [[4imf|4imf]], [[4img|4img]]</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=4imd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4imd OCA], [https://pdbe.org/4imd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4imd RCSB], [https://www.ebi.ac.uk/pdbsum/4imd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4imd ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nanA, PM1715 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1169409 Pasteurella multocida subsp. gallicida P1059])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acetylneuraminate_lyase N-acetylneuraminate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.3 4.1.3.3] </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=4imd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4imd OCA], [http://pdbe.org/4imd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4imd RCSB], [http://www.ebi.ac.uk/pdbsum/4imd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4imd ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/NANA_PASMU NANA_PASMU]] Catalyzes the cleavage of N-acetylneuraminic acid (sialic acid) to form pyruvate and N-acetylmannosamine via a Schiff base intermediate (By similarity). | + | [https://www.uniprot.org/uniprot/NANA_PASMU NANA_PASMU] Catalyzes the cleavage of N-acetylneuraminic acid (sialic acid) to form pyruvate and N-acetylmannosamine via a Schiff base intermediate (By similarity). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 4imd" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4imd" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[N-acetylneuraminate lyase 3D structures|N-acetylneuraminate lyase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: N-acetylneuraminate lyase]] | + | [[Category: Large Structures]] |
| - | [[Category: Pasteurella multocida subsp. gallicida p1059]] | + | [[Category: Pasteurella multocida subsp. gallicida P1059]] |
| - | [[Category: Fisher, A J]] | + | [[Category: Fisher AJ]] |
| - | [[Category: Huynh, N]] | + | [[Category: Huynh N]] |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Schiff base]]
| + | |
| - | [[Category: Tim barrel]]
| + | |
| Structural highlights
Function
NANA_PASMU Catalyzes the cleavage of N-acetylneuraminic acid (sialic acid) to form pyruvate and N-acetylmannosamine via a Schiff base intermediate (By similarity).
Publication Abstract from PubMed
<i>N</i>-Acetylneuraminate lyases (NALs) or sialic acid aldolases catalyze the reversible aldol cleavage of <i>N</i>-acetylneuraminic acid (Neu5Ac, the most common form of sialic acid) to form pyruvate and <i>N</i>-acetyl-D-mannosamine (ManNAc). Although equilibrium favors sialic acid cleavage, these enzymes can be used for high-yield chemoenzymatic synthesis of structurally diverse sialic acids in the presence of excess pyruvate. Engineering these enzymes to synthesize structurally modified natural sialic acids and their non-natural derivatives holds promise in creating novel therapeutic agents. Atomic resolution structures of these enzymes will greatly assist in guiding mutagenic and modeling studies to engineer enzymes with altered substrate specificity. We report here the crystal structures of wild-type <i>Pasteurella multocida N</I>-acetylneuraminate lyase and its K164A mutant. Like other bacterial lyases, it assembles into a homotetramer with each monomer folding into a classic (beta/alpha)<sub>8</sub> TIM barrel. Two wild-type structures were determined; in the absence of substrates, and trapped in a Schiff base intermediate between Lys164 and pyruvate, respectively. Three structures of the K164A variant were determined: one in the absence of substrates and two binary complexes with <i>N</i>-acetylneuraminic acid (Neu5Ac) and <i>N</i>-glycolylneuraminic acid (Neu5Gc), respectively. Both sialic acids bind to the active site in the open-chain ketone form of the monosaccharide. The structures reveal that every hydroxyl group of the linear sugars makes hydrogen bond interactions with the enzyme and the residues that determine specificity were identified. Additionally, the structures lend some clues in explaining the natural discrimination of sialic acid substrates between the <i>P. multocida</i> and <i>E. coli</i> NALs.
Structural basis for substrate specificity and mechanism of <i>N</i>-acetyl-D-neuraminic acid lyase from <i>Pasteurella multocida.</i>,Huynh N, Aye A, Li Y, Yu H, Cao H, Tiwari VK, Shin DW, Chen X, Fisher AJ Biochemistry. 2013 Oct 23. PMID:24152047[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Huynh N, Aye A, Li Y, Yu H, Cao H, Tiwari VK, Shin DW, Chen X, Fisher AJ. Structural basis for substrate specificity and mechanism of N-acetyl-D-neuraminic acid lyase from Pasteurella multocida. Biochemistry. 2013 Oct 23. PMID:24152047 doi:http://dx.doi.org/10.1021/bi4011754
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