This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
5z5c
From Proteopedia
(Difference between revisions)
m (Protected "5z5c" [edit=sysop:move=sysop]) |
|||
| Line 1: | Line 1: | ||
| - | '''Unreleased structure''' | ||
| - | + | ==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: Yoshida, Y]] | ||
[[Category: Nonaka, T]] | [[Category: Nonaka, T]] | ||
| + | [[Category: Yoshida, Y]] | ||
| + | [[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
| |||||||||||
