5z5c: Difference between revisions
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==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=''> | |||
== 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> | |||
</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> | |||
<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='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'>[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> | |||
<div style="background-color:#fffaf0;"> | |||
== 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<ref>PMID:29343611</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 5z5c" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Cysteine synthase]] | |||
[[Category: Kezuka, Y]] | [[Category: Kezuka, Y]] | ||
[[Category: Nonaka, T]] | |||
[[Category: Yoshida, Y]] | [[Category: Yoshida, Y]] | ||
[[Category: | [[Category: Internal aldimine]] | ||
[[Category: Pyridoxal 5'-phosphate dependent enzyme]] | |||
[[Category: Transferase]] | |||
Revision as of 06:19, 15 February 2018
Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) from Fusobacterium nucleatum: lysine-dimethylated form
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