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1sjb
From Proteopedia
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==X-ray structure of o-succinylbenzoate synthase complexed with o-succinylbenzoic acid== | ==X-ray structure of o-succinylbenzoate synthase complexed with o-succinylbenzoic acid== | ||
| - | <StructureSection load='1sjb' size='340' side='right' caption='[[1sjb]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='1sjb' size='340' side='right'caption='[[1sjb]], [[Resolution|resolution]] 2.20Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[1sjb]] is a 4 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[1sjb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Amycolatopsis_sp. Amycolatopsis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SJB FirstGlance]. <br> |
| - | </td></tr><tr id=' | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> |
| - | <tr id=' | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OSB:2-SUCCINYLBENZOATE'>OSB</scene></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=1sjb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sjb OCA], [https://pdbe.org/1sjb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sjb RCSB], [https://www.ebi.ac.uk/pdbsum/1sjb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sjb ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | |
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/NSAR_AMYSP NSAR_AMYSP] Acts as a N-succinylamino acid racemase (NSAR) that catalyzes the racemization of N-succinyl-phenylglycine and N-succinyl-methionine (PubMed:14705949, PubMed:24955846). Can catalyze the racemization of a broad range of N-acylamino acids, including N-acetyl-D/L-methionine, N-propionyl-D/L-methionine, N-butyryl-D/L-methionine and N-chloroacetyl-L-valine (PubMed:7766084, PubMed:10194342, PubMed:14705949, PubMed:23130969). Also converts 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) to 2-succinylbenzoate (OSB) (PubMed:10194342, PubMed:14705949, PubMed:24955846). Catalyzes both N-succinylamino acid racemization and OSB synthesis at equivalent rates (PubMed:14705949, PubMed:24955846). NSAR is probably the biological function of this enzyme (Probable).<ref>PMID:10194342</ref> <ref>PMID:14705949</ref> <ref>PMID:23130969</ref> <ref>PMID:24955846</ref> <ref>PMID:7766084</ref> <ref>PMID:16740275</ref> <ref>PMID:24955846</ref> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sj/1sjb_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sj/1sjb_consurf.spt"</scriptWhenChecked> |
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </jmolCheckbox> | ||
| - | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/ | + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1sjb ConSurf]. |
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | Divergent evolution of enzyme function is commonly explained by a gene duplication event followed by mutational changes that allow the protein encoded by the copy to acquire a new function. An alternate hypothesis is that this process is facilitated when the progenitor enzyme acquires a second function while maintaining the original activity. This phenomenon has been suggested to occur in the o-succinylbenzoate synthase (OSBS) from a species of Amycolatopsis that catalyzes not only the physiological syn-dehydration reaction of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate but also an accidental racemization of N-acylamino acids [Palmer, D. R., Garrett, J. B., Sharma, V., Meganathan, R., Babbitt, P. C., and Gerlt, J. A. (1999) Biochemistry 38, 4252-4258]. To understand the molecular basis of this promiscuity, three-dimensional structures of liganded complexes of this enzyme have been determined, including the product of the OSBS reaction and three N-acylamino acid substrates for the N-acylamino acid racemase (NAAAR) reaction, N-acetylmethionine, N-succinylmethionine, and N-succinylphenylglycine, to 2.2, 2.3, 2.1, and 1.9 A resolution, respectively. These structures show how the active-site cavity can accommodate both the hydrophobic substrate for the OSBS reaction and the substrates for the accidental NAAAR reaction. As expected, the N-acylamino acid is sandwiched between lysines 163 and 263, which function as the catalytic bases for the abstraction of the alpha-proton in the (R)- and (S)-racemization reactions, respectively [Taylor Ringia, E. A., Garrett, J. B, Thoden, J. B., Holden, H. M., Rayment, I., and Gerlt, J. A. (2004) Biochemistry 42, 224-229]. Importantly, the protein forms specific favorable interactions with the hydrophobic amino acid side chain, alpha-carbon, carboxylate, and the polar components of the N-acyl linkage. Accommodation of the components of the N-acyl linkage appears to be the reason that this enzyme is capable of a racemization reaction on these substrates, whereas the orthologous OSBS from Escherichia coli lacks this functionality. | ||
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| - | Evolution of enzymatic activity in the enolase superfamily: structural studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis.,Thoden JB, Taylor Ringia EA, Garrett JB, Gerlt JA, Holden HM, Rayment I Biochemistry. 2004 May 18;43(19):5716-27. PMID:15134446<ref>PMID:15134446</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 1sjb" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Amycolatopsis sp]] | [[Category: Amycolatopsis sp]] | ||
| - | [[Category: Garrett | + | [[Category: Large Structures]] |
| - | [[Category: Gerlt | + | [[Category: Garrett JB]] |
| - | [[Category: Holden | + | [[Category: Gerlt JA]] |
| - | [[Category: Rayment | + | [[Category: Holden HM]] |
| - | [[Category: Taylor-Ringia | + | [[Category: Rayment I]] |
| - | [[Category: Thoden | + | [[Category: Taylor-Ringia EA]] |
| - | + | [[Category: Thoden JB]] | |
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Current revision
X-ray structure of o-succinylbenzoate synthase complexed with o-succinylbenzoic acid
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