7r9x

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of a dehydrating condensation domain, AmbE-CmodAA, involved in nonribosomal peptide synthesis

Structural highlights

7r9x is a 2 chain structure with sequence from Pseudomonas aeruginosa PAO1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.14Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AMBE_PSEAE Involved in the biosynthesis of the antimetabolite L-2-amino-4-methoxy-trans-3-butenoic acid (AMB), a non-proteinogenic amino acid which is toxic for prokaryotes and eukaryotes (PubMed:20543073, PubMed:25814981). Adenylates L-glutamate and loads it onto its first peptidyl carrier domain via a thioester linkage to the phosphopanthetheine moiety (PubMed:25814981). The second peptidyl carrier domain is loaded with a L-alanine activated by AmbB (PubMed:25814981). After formation by AmbB of the L-Glu-L-Ala dipeptide at the first carrier domain of AmbE, the condensation domain of AmbE probably condenses this dipeptide with the L-Ala residue attached at the second carrier domain of AmbE to give the L-Ala-L-Glu-L-Ala tripeptide. The central amino acid, L-Glu, would then undergo a series of modifications to be converted into AMB while the two flanking L-Ala residues remain in place (PubMed:25814981). Finally, the L-Ala-AMB-L-Ala tripeptide is probably released by thioester cleavage via the thioester domain of AmbE (PubMed:25814981).^[1] ^[2]

Publication Abstract from PubMed

Dehydroamino acids are important structural motifs and biosynthetic intermediates for natural products. Many bioactive natural products of nonribosomal origin contain dehydroamino acids; however, the biosynthesis of dehydroamino acids in most nonribosomal peptides is not well understood. Here, we provide biochemical and bioinformatic evidence in support of the role of a unique class of condensation domains in dehydration (CmodAA). We also obtain the crystal structure of a CmodAA domain, which is part of the nonribosomal peptide synthetase AmbE in the biosynthesis of the antibiotic methoxyvinylglycine. Biochemical analysis reveals that AmbE-CmodAA modifies a peptide substrate that is attached to the donor carrier protein. Mutational studies of AmbE-CmodAA identify several key residues for activity, including four residues that are mostly conserved in the CmodAA subfamily. Alanine mutation of these conserved residues either significantly increases or decreases AmbE activity. AmbE exhibits a dimeric conformation, which is uncommon and could enable transfer of an intermediate between different protomers. Our discovery highlights a central dehydrating function for CmodAA domains that unifies dehydroamino acid biosynthesis in diverse nonribosomal peptide pathways. Our work also begins to shed light on the mechanism of CmodAA domains. Understanding CmodAA domain function may facilitate identification of new natural products that contain dehydroamino acids and enable engineering of dehydroamino acids into nonribosomal peptides.

Structure and Function of a Dehydrating Condensation Domain in Nonribosomal Peptide Biosynthesis.,Patteson JB, Fortinez CM, Putz AT, Rodriguez-Rivas J, Bryant LH 3rd, Adhikari K, Weigt M, Schmeing TM, Li B J Am Chem Soc. 2022 Jul 27. doi: 10.1021/jacs.1c13404. PMID:35895935^[3]

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

References

↑ Lee X, Fox A, Sufrin J, Henry H, Majcherczyk P, Haas D, Reimmann C. Identification of the biosynthetic gene cluster for the Pseudomonas aeruginosa antimetabolite L-2-amino-4-methoxy-trans-3-butenoic acid. J Bacteriol. 2010 Aug;192(16):4251-5. doi: 10.1128/JB.00492-10. Epub 2010 Jun 11. PMID:20543073 doi:http://dx.doi.org/10.1128/JB.00492-10
↑ Rojas Murcia N, Lee X, Waridel P, Maspoli A, Imker HJ, Chai T, Walsh CT, Reimmann C. The Pseudomonas aeruginosa antimetabolite L -2-amino-4-methoxy-trans-3-butenoic acid (AMB) is made from glutamate and two alanine residues via a thiotemplate-linked tripeptide precursor. Front Microbiol. 2015 Mar 12;6:170. doi: 10.3389/fmicb.2015.00170. eCollection, 2015. PMID:25814981 doi:http://dx.doi.org/10.3389/fmicb.2015.00170
↑ Patteson JB, Fortinez CM, Putz AT, Rodriguez-Rivas J, Bryant LH 3rd, Adhikari K, Weigt M, Schmeing TM, Li B. Structure and Function of a Dehydrating Condensation Domain in Nonribosomal Peptide Biosynthesis. J Am Chem Soc. 2022 Jul 27. doi: 10.1021/jacs.1c13404. PMID:35895935 doi:http://dx.doi.org/10.1021/jacs.1c13404

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/7r9x"

Categories: Large Structures | Pseudomonas aeruginosa PAO1 | Fortinez CM | Schmeing TM

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[7r9x]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7R9X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7R9X FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.14&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=7r9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7r9x OCA], [https://pdbe.org/7r9x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7r9x RCSB], [https://www.ebi.ac.uk/pdbsum/7r9x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7r9x ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/AMBE_PSEAE AMBE_PSEAE]] Involved in the biosynthesis of the antimetabolite L-2-amino-4-methoxy-trans-3-butenoic acid (AMB), a non-proteinogenic amino acid which is toxic for prokaryotes and eukaryotes (PubMed:20543073, PubMed:25814981). Adenylates L-glutamate and loads it onto its first peptidyl carrier domain via a thioester linkage to the phosphopanthetheine moiety (PubMed:25814981). The second peptidyl carrier domain is loaded with a L-alanine activated by AmbB (PubMed:25814981). After formation by AmbB of the L-Glu-L-Ala dipeptide at the first carrier domain of AmbE, the condensation domain of AmbE probably condenses this dipeptide with the L-Ala residue attached at the second carrier domain of AmbE to give the L-Ala-L-Glu-L-Ala tripeptide. The central amino acid, L-Glu, would then undergo a series of modifications to be converted into AMB while the two flanking L-Ala residues remain in place (PubMed:25814981). Finally, the L-Ala-AMB-L-Ala tripeptide is probably released by thioester cleavage via the thioester domain of AmbE (PubMed:25814981).<ref>PMID:20543073</ref> <ref>PMID:25814981</ref>
+[https://www.uniprot.org/uniprot/AMBE_PSEAE AMBE_PSEAE] Involved in the biosynthesis of the antimetabolite L-2-amino-4-methoxy-trans-3-butenoic acid (AMB), a non-proteinogenic amino acid which is toxic for prokaryotes and eukaryotes (PubMed:20543073, PubMed:25814981). Adenylates L-glutamate and loads it onto its first peptidyl carrier domain via a thioester linkage to the phosphopanthetheine moiety (PubMed:25814981). The second peptidyl carrier domain is loaded with a L-alanine activated by AmbB (PubMed:25814981). After formation by AmbB of the L-Glu-L-Ala dipeptide at the first carrier domain of AmbE, the condensation domain of AmbE probably condenses this dipeptide with the L-Ala residue attached at the second carrier domain of AmbE to give the L-Ala-L-Glu-L-Ala tripeptide. The central amino acid, L-Glu, would then undergo a series of modifications to be converted into AMB while the two flanking L-Ala residues remain in place (PubMed:25814981). Finally, the L-Ala-AMB-L-Ala tripeptide is probably released by thioester cleavage via the thioester domain of AmbE (PubMed:25814981).<ref>PMID:20543073</ref> <ref>PMID:25814981</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==

7r9x

From Proteopedia

Current revision

Crystal structure of a dehydrating condensation domain, AmbE-CmodAA, involved in nonribosomal peptide synthesis

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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