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| | ==Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) from Fusobacterium nucleatum: lysine-dimethylated form== | | ==Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) from Fusobacterium nucleatum: lysine-dimethylated form== |
| - | <StructureSection load='5z5c' size='340' side='right' caption='[[5z5c]], [[Resolution|resolution]] 2.07Å' scene=''> | + | <StructureSection load='5z5c' size='340' side='right'caption='[[5z5c]], [[Resolution|resolution]] 2.07Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5z5c]] is a 4 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5b54 5b54]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z5C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z5C FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5z5c]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Fusobacterium_nucleatum_subsp._nucleatum_ATCC_25586 Fusobacterium nucleatum subsp. nucleatum ATCC 25586]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z5C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z5C FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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]] 2.07Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cysteine_synthase Cysteine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.47 2.5.1.47] </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=5z5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z5c OCA], [https://pdbe.org/5z5c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z5c RCSB], [https://www.ebi.ac.uk/pdbsum/5z5c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z5c 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=5z5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z5c OCA], [http://pdbe.org/5z5c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z5c RCSB], [http://www.ebi.ac.uk/pdbsum/5z5c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z5c ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q8REP3_FUSNN Q8REP3_FUSNN] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Cysteine synthase]] | + | [[Category: Fusobacterium nucleatum subsp. nucleatum ATCC 25586]] |
| - | [[Category: Kezuka, Y]] | + | [[Category: Large Structures]] |
| - | [[Category: Nonaka, T]] | + | [[Category: Kezuka Y]] |
| - | [[Category: Yoshida, Y]]
| + | [[Category: Nonaka T]] |
| - | [[Category: Internal aldimine]] | + | [[Category: Yoshida Y]] |
| - | [[Category: Pyridoxal 5'-phosphate dependent enzyme]] | + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
Q8REP3_FUSNN
Publication Abstract from PubMed
Hydrogen sulfide (H2S) plays important roles in the pathogenesis of periodontitis. Oral pathogens typically produce H2S from L-cysteine in addition to pyruvate and NH4(+) However, fn1055 from Fusobacterium nucleatum subsp. nucleatum ATCC 25586 encodes a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the production of H2S and L-serine from L-cysteine and H2O, an unusual cysteine (hydroxyl) lyase reaction (beta-replacement reaction). To reveal the reaction mechanism, the crystal structure of substrate-free Fn1055 was determined. Based on this structure, a model of the L-cysteine-PLP Schiff base suggested that the thiol group forms hydrogen bonds with Asp(232) and Ser(74), and the substrate alpha-carboxylate interacts with Thr(73) and Gln(147) Asp(232) is a unique residue to Fn1055 and its substitution to asparagine (D232N) resulted in almost complete loss of beta-replacement activity. The D232N structure obtained in the presence of L-cysteine contained the alpha-aminoacrylate-PLP Schiff base in the active site, indicating that Asp(232) is essential for the addition of water to the alpha-aminoacrylate to produce the L-serine-PLP Schiff base. Rapid scan stopped-flow kinetic analyses showed an accumulation of the alpha-aminoacrylate intermediate during the reaction cycle, suggesting that water addition mediated by Asp(232) is the rate-limiting step. In contrast, mutants containing substitutions of other active-site residues (Ser(74), Thr(73), and Gln(147)) exhibited reduced beta-replacement activity by more than 100-fold. Finally, based on the structural and biochemical analyses, we propose a mechanism of the cysteine (hydroxyl) lyase reaction by Fn1055. This study leads to elucidation of the H2S-producing mechanism in F. nucleatum.
Structural insights into the catalytic mechanism of cysteine (hydroxyl) lyase from the hydrogen-sulfide producing oral pathogen, Fusobacterium nucleatum.,Kezuka Y, Ishida T, Yoshida Y, Nonaka T Biochem J. 2018 Jan 17. pii: BCJ20170838. doi: 10.1042/BCJ20170838. PMID:29343611[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kezuka Y, Ishida T, Yoshida Y, Nonaka T. Structural insights into the catalytic mechanism of cysteine (hydroxyl) lyase from the hydrogen-sulfide producing oral pathogen, Fusobacterium nucleatum. Biochem J. 2018 Jan 17. pii: BCJ20170838. doi: 10.1042/BCJ20170838. PMID:29343611 doi:http://dx.doi.org/10.1042/BCJ20170838
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