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| | <StructureSection load='5x8g' size='340' side='right'caption='[[5x8g]], [[Resolution|resolution]] 1.90Å' scene=''> | | <StructureSection load='5x8g' size='340' side='right'caption='[[5x8g]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5x8g]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X8G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X8G FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5x8g]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X8G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X8G FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=S0N:O-SUCCINYLBENZOYL-N-COENZYME+A'>S0N</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]] 1.9Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">menE, BSU30790 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=S0N:O-SUCCINYLBENZOYL-N-COENZYME+A'>S0N</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/o-succinylbenzoate--CoA_ligase o-succinylbenzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.26 6.2.1.26] </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=5x8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x8g OCA], [https://pdbe.org/5x8g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x8g RCSB], [https://www.ebi.ac.uk/pdbsum/5x8g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x8g 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=5x8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x8g OCA], [http://pdbe.org/5x8g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x8g RCSB], [http://www.ebi.ac.uk/pdbsum/5x8g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x8g ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/MENE_BACSU MENE_BACSU]] Converts 2-succinylbenzoate (OSB) to 2-succinylbenzoyl-CoA (OSB-CoA).[HAMAP-Rule:MF_00731] | + | [https://www.uniprot.org/uniprot/MENE_BACSU MENE_BACSU] Converts 2-succinylbenzoate (OSB) to 2-succinylbenzoyl-CoA (OSB-CoA).[HAMAP-Rule:MF_00731] |
| | <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: Bacsu]] | + | [[Category: Bacillus subtilis subsp. subtilis str. 168]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: O-succinylbenzoate--CoA ligase]]
| + | [[Category: Chen Y]] |
| - | [[Category: Chen, Y]] | + | [[Category: Guo Z]] |
| - | [[Category: Guo, Z]] | + | |
| - | [[Category: Acyl-coa synthetase]]
| + | |
| - | [[Category: Adenylate-forming enzyme]]
| + | |
| - | [[Category: Adp binding subsite]]
| + | |
| - | [[Category: Coa]]
| + | |
| - | [[Category: Domain alternation]]
| + | |
| - | [[Category: Inter-domain linker]]
| + | |
| - | [[Category: Large conformational change]]
| + | |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: Pantetheine tunnel]]
| + | |
| - | [[Category: Thioester conformation]]
| + | |
| Structural highlights
5x8g is a 4 chain structure with sequence from Bacillus subtilis subsp. subtilis str. 168. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.9Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
MENE_BACSU Converts 2-succinylbenzoate (OSB) to 2-succinylbenzoyl-CoA (OSB-CoA).[HAMAP-Rule:MF_00731]
Publication Abstract from PubMed
o-Succinylbenzoyl-CoA (OSB-CoA) synthetase (MenE) is an essential enzyme in bacterial vitamin K biosynthesis and an important target in the development of new antibiotics. It is a member of the adenylating enzymes (ANL) family, which reconfigure their active site in two different active conformations, one for the adenylation half-reaction and the other for a thioesterification half-reaction, in a domain-alternation catalytic mechanism. Although several aspects of the adenylating mechanism in MenE have recently been uncovered, its thioesterification conformation remains elusive. Here, using a catalytically competent Bacillus subtilis mutant protein complexed with an OSB-CoA analogue, we determined MenE high-resolution structures to 1.76 and 1.90 A resolution in a thioester-forming conformation. By comparison with the adenylation conformation, we found that MenE's C-domain rotates around the Ser-384 hinge by 139.5 degrees during domain-alternation catalysis. The structures also revealed a thioesterification active site specifically conserved among MenE orthologues and a substrate-binding mode distinct from those of many other acyl/aryl-CoA synthetases. Of note, using site-directed mutagenesis, we identified several residues that specifically contribute to the thioesterification half-reaction without affecting the adenylation half-reaction. Moreover, we observed a substantial movement of the activated succinyl group in the thioesterification half-reaction. These findings provide new insights into the domain-alternation catalysis of a bacterial enzyme essential for vitamin K biosynthesis and of its adenylating homologues in the ANL enzyme family.
Crystal structure of the thioesterification conformation of Bacillus subtilis o-succinylbenzoyl-CoA synthetase reveals a distinct substrate-binding mode.,Chen Y, Li TL, Lin X, Li X, Li XD, Guo Z J Biol Chem. 2017 Jul 21;292(29):12296-12310. doi: 10.1074/jbc.M117.790410. Epub , 2017 May 30. PMID:28559280[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Chen Y, Li TL, Lin X, Li X, Li XD, Guo Z. Crystal structure of the thioesterification conformation of Bacillus subtilis o-succinylbenzoyl-CoA synthetase reveals a distinct substrate-binding mode. J Biol Chem. 2017 Jul 21;292(29):12296-12310. doi: 10.1074/jbc.M117.790410. Epub , 2017 May 30. PMID:28559280 doi:http://dx.doi.org/10.1074/jbc.M117.790410
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