3caw
From Proteopedia
(Difference between revisions)
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==Crystal structure of o-succinylbenzoate synthase from Bdellovibrio bacteriovorus liganded with Mg== | ==Crystal structure of o-succinylbenzoate synthase from Bdellovibrio bacteriovorus liganded with Mg== | ||
| - | <StructureSection load='3caw' size='340' side='right'caption='[[3caw]]' scene=''> | + | <StructureSection load='3caw' size='340' side='right'caption='[[3caw]], [[Resolution|resolution]] 1.87Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CAW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CAW FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3caw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bdellovibrio_bacteriovorus_HD100 Bdellovibrio bacteriovorus HD100]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CAW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CAW FirstGlance]. <br> |
| - | </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=3caw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3caw OCA], [https://pdbe.org/3caw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3caw RCSB], [https://www.ebi.ac.uk/pdbsum/3caw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3caw ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/3caw TOPSAN]</span></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]] 1.87Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=3caw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3caw OCA], [https://pdbe.org/3caw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3caw RCSB], [https://www.ebi.ac.uk/pdbsum/3caw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3caw ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/3caw TOPSAN]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/MENC_BDEBA MENC_BDEBA] Converts 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) to 2-succinylbenzoate (OSB) (PubMed:24872444). Does not show N-succinylamino acid racemase (NSAR) activity with N-succinyl-L-phenylglycine as substrate (PubMed:24872444).<ref>PMID:24872444</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The rate of protein evolution is determined by a combination of selective pressure on protein function and biophysical constraints on protein folding and structure. Determining the relative contributions of these properties is an unsolved problem in molecular evolution with broad implications for protein engineering and function prediction. As a case study, we examined the structural divergence of the rapidly evolving o-succinylbenzoate synthase (OSBS) family, which catalyzes a step in menaquinone synthesis in diverse microorganisms and plants. On average, the OSBS family is much more divergent than other protein families from the same set of species, with the most divergent family members sharing <15% sequence identity. Comparing 11 representative structures revealed that loss of quaternary structure and large deletions or insertions are associated with the family's rapid evolution. Neither of these properties has been investigated in previous studies to identify factors that affect the rate of protein evolution. Intriguingly, one subfamily retained a multimeric quaternary structure and has small insertions and deletions compared with related enzymes that catalyze diverse reactions. Many proteins in this subfamily catalyze both OSBS and N-succinylamino acid racemization (NSAR). Retention of ancestral structural characteristics in the NSAR/OSBS subfamily suggests that the rate of protein evolution is not proportional to the capacity to evolve new protein functions. Instead, structural features that are conserved among proteins with diverse functions might contribute to the evolution of new functions. | ||
| + | |||
| + | Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family.,Odokonyero D, Sakai A, Patskovsky Y, Malashkevich VN, Fedorov AA, Bonanno JB, Fedorov EV, Toro R, Agarwal R, Wang C, Ozerova ND, Yew WS, Sauder JM, Swaminathan S, Burley SK, Almo SC, Glasner ME Proc Natl Acad Sci U S A. 2014 May 28. pii: 201318703. PMID:24872444<ref>PMID:24872444</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 3caw" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Bdellovibrio bacteriovorus HD100]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Almo SC]] | [[Category: Almo SC]] | ||
Revision as of 18:09, 1 November 2023
Crystal structure of o-succinylbenzoate synthase from Bdellovibrio bacteriovorus liganded with Mg
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