|
|
| Line 3: |
Line 3: |
| | <StructureSection load='5eio' size='340' side='right'caption='[[5eio]], [[Resolution|resolution]] 1.80Å' scene=''> | | <StructureSection load='5eio' size='340' side='right'caption='[[5eio]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5eio]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971] and [http://en.wikipedia.org/wiki/Thet2 Thet2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EIO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EIO FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5eio]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] and [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB27 Thermus thermophilus HB27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EIO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EIO FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.8Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5ein|5ein]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">argC2, argC, lysY, TT_C1542 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2]), orfF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</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=5eio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eio OCA], [https://pdbe.org/5eio PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5eio RCSB], [https://www.ebi.ac.uk/pdbsum/5eio PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5eio 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=5eio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eio OCA], [http://pdbe.org/5eio PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5eio RCSB], [http://www.ebi.ac.uk/pdbsum/5eio PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5eio ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/ARGC2_THET2 ARGC2_THET2]] Involved in both the arginine and lysine biosynthetic pathways. | + | [https://www.uniprot.org/uniprot/LYSY_THET2 LYSY_THET2] Catalyzes the NADPH-dependent reduction of [LysW]-aminoadipate 6-phosphate to yield [LysW]-aminoadipate 6-semialdehyde.[HAMAP-Rule:MF_02083]<ref>PMID:26966182</ref> <ref>PMID:19620981</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 24: |
Line 23: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Flavobacterium thermophilum yoshida and oshima 1971]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Thet2]] | + | [[Category: Thermus thermophilus]] |
| - | [[Category: Nishiyama, M]] | + | [[Category: Thermus thermophilus HB27]] |
| - | [[Category: Shimizu, T]] | + | [[Category: Nishiyama M]] |
| - | [[Category: Tomita, T]] | + | [[Category: Shimizu T]] |
| - | [[Category: Amino group-carrier-protein]] | + | [[Category: Tomita T]] |
| - | [[Category: Gapdh family]]
| + | |
| - | [[Category: Lysine biosynthesis]]
| + | |
| - | [[Category: Oxidoreductase-biosynthetic protein complex]]
| + | |
| Structural highlights
Function
LYSY_THET2 Catalyzes the NADPH-dependent reduction of [LysW]-aminoadipate 6-phosphate to yield [LysW]-aminoadipate 6-semialdehyde.[HAMAP-Rule:MF_02083][1] [2]
Publication Abstract from PubMed
Several bacteria and archaea utilize the amino group-carrier protein, LysW, for lysine biosynthesis, in which an isopeptide bond is formed between the C-terminal Glu of LysW and an amino group of alpha-aminoadipate (AAA). The resulting LysW-gamma-AAA is phosphorylated by LysZ to form LysW-gamma-AAA phosphate, which is subsequently reduced to LysW-gamma-aminoadipic semialdehyde (LysW-gamma-AASA) through a reaction catalyzed by LysY. In the present study, we determined the crystal structures of LysY from Thermus thermophilus HB27 (TtLysY) complexed with TtLysW-gamma-AASA and TtLysW-gamma-AAA, respectively. In both structures, the globular domain of TtLysW was recognized by positively-charged residues on helix alpha9 and the beta11-alpha10 loop of TtLysY through conformational changes. A mutational analysis confirmed that the interactions observed between TtLysY and TtLysW are important for the function of TtLysY. The extended LysW-recognition loop and conserved arginine residue were identified as signatures to discriminate LysY from ArgC, which is involved in arginine biosynthesis. Combined with the previously determined TtLysZ.TtLysW complex structure, TtLysW may simultaneously bind TtLysZ and TtLysY. These structural insights suggest the formation of a TtLysWZY ternary complex, in which the flexible C-terminal extension of TtLysW promotes the efficient transfer of the labile intermediate from the active site of TtLysZ to that of TtLysY during the sequential reactions catalyzed by TtLysZY.
Crystal structure of the LysY.LysW complex from Thermus thermophilus.,Shimizu T, Tomita T, Kuzuyama T, Nishiyama M J Biol Chem. 2016 Mar 9. pii: jbc.M115.707034. PMID:26966182[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Shimizu T, Tomita T, Kuzuyama T, Nishiyama M. Crystal structure of the LysY.LysW complex from Thermus thermophilus. J Biol Chem. 2016 Mar 9. pii: jbc.M115.707034. PMID:26966182 doi:http://dx.doi.org/10.1074/jbc.M115.707034
- ↑ Horie A, Tomita T, Saiki A, Kono H, Taka H, Mineki R, Fujimura T, Nishiyama C, Kuzuyama T, Nishiyama M. Discovery of proteinaceous N-modification in lysine biosynthesis of Thermus thermophilus. Nat Chem Biol. 2009 Sep;5(9):673-9. doi: 10.1038/nchembio.198. Epub 2009 Jul 20. PMID:19620981 doi:http://dx.doi.org/10.1038/nchembio.198
- ↑ Shimizu T, Tomita T, Kuzuyama T, Nishiyama M. Crystal structure of the LysY.LysW complex from Thermus thermophilus. J Biol Chem. 2016 Mar 9. pii: jbc.M115.707034. PMID:26966182 doi:http://dx.doi.org/10.1074/jbc.M115.707034
|
