6mtg: Difference between revisions

Latest revision as of 06:38, 11 October 2023

A Single Reactive Noncanonical Amino Acid is Able to Dramatically Stabilize Protein Structure

Structural highlights

6mtg is a 2 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.85Å
Ligands:	CSD, FMT, GOL, PEG
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

METAS_ECOLI Transfers a succinyl group from succinyl-CoA to L-homoserine, forming succinyl-L-homoserine (PubMed:10572016, PubMed:17442255, PubMed:17302437, PubMed:28581482). Utilizes a ping-pong kinetic mechanism in which the succinyl group of succinyl-CoA is initially transferred to the enzyme to form a succinyl-enzyme intermediate before subsequent transfer to homoserine to form the final product, O-succinylhomoserine (PubMed:10572016, PubMed:17442255, PubMed:17302437). Cannot use acetyl-CoA (PubMed:10572016).^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

A p-isothiocyanate phenylalanine mutant of the homodimeric protein homoserine o-succinyltransferase (MetA) was isolated in a temperature dependent selection from a library of metA mutants containing noncanonical amino acids. This mutant protein has a dramatic increase of 24 degrees C in thermal stability compared to the wild type protein. Peptide mapping experiments revealed that the isothiocyanate group forms a thiourea cross-link to the N terminal proline of the other monomer, despite the two positions being >30 A apart in the X-ray crystal structure of the wild type protein. These results show that an expanded set of building blocks beyond the canonical 20 amino acids can lead to significant changes in the properties of proteins.

A Single Reactive Noncanonical Amino Acid Is Able to Dramatically Stabilize Protein Structure.,Li JC, Nastertorabi F, Xuan W, Han GW, Stevens RC, Schultz PG ACS Chem Biol. 2019 Jun 4. doi: 10.1021/acschembio.9b00002. PMID:31181898^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Born TL, Blanchard JS. Enzyme-catalyzed acylation of homoserine: mechanistic characterization of the Escherichia coli metA-encoded homoserine transsuccinylase. Biochemistry. 1999 Oct 26;38(43):14416-23. doi: 10.1021/bi991710o. PMID:10572016 doi:https://dx.doi.org/10.1021/bi991710o
↑ Ziegler K, Noble SM, Mutumanje E, Bishop B, Huddler DP, Born TL. Identification of catalytic cysteine, histidine, and lysine residues in Escherichia coli homoserine transsuccinylase. Biochemistry. 2007 Mar 13;46(10):2674-83. doi: 10.1021/bi0620252. Epub 2007 Feb, 16. PMID:17302437 doi:https://dx.doi.org/10.1021/bi0620252
↑ Coe DM, Viola RE. Assessing the roles of essential functional groups in the mechanism of homoserine succinyltransferase. Arch Biochem Biophys. 2007 May 15;461(2):211-8. doi: 10.1016/j.abb.2007.03.004., Epub 2007 Apr 2. PMID:17442255 doi:https://dx.doi.org/10.1016/j.abb.2007.03.004
↑ Bastard K, Perret A, Mariage A, Bessonnet T, Pinet-Turpault A, Petit JL, Darii E, Bazire P, Vergne-Vaxelaire C, Brewee C, Debard A, Pellouin V, Besnard-Gonnet M, Artiguenave F, Medigue C, Vallenet D, Danchin A, Zaparucha A, Weissenbach J, Salanoubat M, de Berardinis V. Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis. Nat Chem Biol. 2017 Aug;13(8):858-866. doi: 10.1038/nchembio.2397. Epub 2017 Jun , 5. PMID:28581482 doi:https://dx.doi.org/10.1038/nchembio.2397
↑ Li JC, Nastertorabi F, Xuan W, Han GW, Stevens RC, Schultz PG. A Single Reactive Noncanonical Amino Acid Is Able to Dramatically Stabilize Protein Structure. ACS Chem Biol. 2019 Jun 4. doi: 10.1021/acschembio.9b00002. PMID:31181898 doi:https://dx.doi.org/10.1021/acschembio.9b00002

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OCA

[1] Born TL, Blanchard JS. Enzyme-catalyzed acylation of homoserine: mechanistic characterization of the Escherichia coli metA-encoded homoserine transsuccinylase. Biochemistry. 1999 Oct 26;38(43):14416-23. doi: 10.1021/bi991710o. PMID:10572016 doi:https://dx.doi.org/10.1021/bi991710o

[2] Ziegler K, Noble SM, Mutumanje E, Bishop B, Huddler DP, Born TL. Identification of catalytic cysteine, histidine, and lysine residues in Escherichia coli homoserine transsuccinylase. Biochemistry. 2007 Mar 13;46(10):2674-83. doi: 10.1021/bi0620252. Epub 2007 Feb, 16. PMID:17302437 doi:https://dx.doi.org/10.1021/bi0620252

[3] Coe DM, Viola RE. Assessing the roles of essential functional groups in the mechanism of homoserine succinyltransferase. Arch Biochem Biophys. 2007 May 15;461(2):211-8. doi: 10.1016/j.abb.2007.03.004., Epub 2007 Apr 2. PMID:17442255 doi:https://dx.doi.org/10.1016/j.abb.2007.03.004

[4] Bastard K, Perret A, Mariage A, Bessonnet T, Pinet-Turpault A, Petit JL, Darii E, Bazire P, Vergne-Vaxelaire C, Brewee C, Debard A, Pellouin V, Besnard-Gonnet M, Artiguenave F, Medigue C, Vallenet D, Danchin A, Zaparucha A, Weissenbach J, Salanoubat M, de Berardinis V. Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis. Nat Chem Biol. 2017 Aug;13(8):858-866. doi: 10.1038/nchembio.2397. Epub 2017 Jun , 5. PMID:28581482 doi:https://dx.doi.org/10.1038/nchembio.2397

[5] Li JC, Nastertorabi F, Xuan W, Han GW, Stevens RC, Schultz PG. A Single Reactive Noncanonical Amino Acid Is Able to Dramatically Stabilize Protein Structure. ACS Chem Biol. 2019 Jun 4. doi: 10.1021/acschembio.9b00002. PMID:31181898 doi:https://dx.doi.org/10.1021/acschembio.9b00002

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[2]

[3]

[4]

[5]

@@ Line 3: / Line 3: @@
 <StructureSection load='6mtg' size='340' side='right'caption='[[6mtg]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6mtg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MTG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MTG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6mtg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MTG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MTG FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.85&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">metAS, metA, b4013, JW3973 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=6mtg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mtg OCA], [https://pdbe.org/6mtg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mtg RCSB], [https://www.ebi.ac.uk/pdbsum/6mtg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mtg ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Homoserine_O-succinyltransferase Homoserine O-succinyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.46 2.3.1.46] </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=6mtg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mtg OCA], [http://pdbe.org/6mtg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mtg RCSB], [http://www.ebi.ac.uk/pdbsum/6mtg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mtg ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/METAS_ECOLI METAS_ECOLI]] Transfers a succinyl group from succinyl-CoA to L-homoserine, forming succinyl-L-homoserine (PubMed:10572016, PubMed:17442255, PubMed:17302437, PubMed:28581482). Utilizes a ping-pong kinetic mechanism in which the succinyl group of succinyl-CoA is initially transferred to the enzyme to form a succinyl-enzyme intermediate before subsequent transfer to homoserine to form the final product, O-succinylhomoserine (PubMed:10572016, PubMed:17442255, PubMed:17302437). Cannot use acetyl-CoA (PubMed:10572016).<ref>PMID:10572016</ref> <ref>PMID:17302437</ref> <ref>PMID:17442255</ref> <ref>PMID:28581482</ref>
+[https://www.uniprot.org/uniprot/METAS_ECOLI METAS_ECOLI] Transfers a succinyl group from succinyl-CoA to L-homoserine, forming succinyl-L-homoserine (PubMed:10572016, PubMed:17442255, PubMed:17302437, PubMed:28581482). Utilizes a ping-pong kinetic mechanism in which the succinyl group of succinyl-CoA is initially transferred to the enzyme to form a succinyl-enzyme intermediate before subsequent transfer to homoserine to form the final product, O-succinylhomoserine (PubMed:10572016, PubMed:17442255, PubMed:17302437). Cannot use acetyl-CoA (PubMed:10572016).<ref>PMID:10572016</ref> <ref>PMID:17302437</ref> <ref>PMID:17442255</ref> <ref>PMID:28581482</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
+[[Category: Escherichia coli K-12]]
-[[Category: Homoserine O-succinyltransferase]]
 [[Category: Large Structures]]
-[[Category: Han, G W]]
+[[Category: Han GW]]
-[[Category: Li, J C]]
+[[Category: Li JC]]
-[[Category: Nasertorabi, F]]
+[[Category: Nasertorabi F]]
-[[Category: Schultz, P G]]
+[[Category: Schultz PG]]
-[[Category: Stevens, R C]]
+[[Category: Stevens RC]]
-[[Category: Xuan, W]]
+[[Category: Xuan W]]
-[[Category: Crosslink]]
-[[Category: Isothiocyanate]]
-[[Category: Noncanonical amino acid]]
-[[Category: Stabilization]]
-[[Category: Thiourea]]
-[[Category: Transferase]]

6mtg: Difference between revisions

Latest revision as of 06:38, 11 October 2023

A Single Reactive Noncanonical Amino Acid is Able to Dramatically Stabilize Protein Structure

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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