3ite

From Proteopedia

(Difference between revisions)

Current revision

The third adenylation domain of the fungal SidN non-ribosomal peptide synthetase

Structural highlights

3ite is a 2 chain structure with sequence from Epichloe festucae var. lolii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SIDN_EPIFI Nonribosomal peptide synthase required for the biosynthetis of epichloenin A, an extracellular siderophore that plays a crucial role in endophyte-grass symbioses (PubMed:19923209, PubMed:23658520). SidN assembles epichloenin A by activating and incorporating three trans-anhydromevalonylhydroxyornithine (trans-AMHO), 1 glutamine and 4 glycine moieties (PubMed:23658520). Trans-AMHO is produced from L-ornithine via 2 steps involving a L-ornithine N(5)-monooxygenase and an AHMO-N(5)-transacylase that have still to be identified (PubMed:19923209). The third adenylation domain (A3) of sidN incorporates the hydroxamate groups of the siderophore which forms an octahedral iron complex (PubMed:19923209). The other component amino acids are assembled by sidN adenylation domains A1 and A2 (PubMed:19923209, PubMed:23658520).^[1] ^[2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Nonribosomal peptide synthetases (NRPSs) are large, multidomain proteins that are involved in the biosynthesis of an array of secondary metabolites. We report the structure of the third adenylation domain from the siderophore-synthesizing NRPS, SidN, from the endophytic fungus Neotyphodium lolii. This is the first structure of a eukaryotic NRPS domain, and it reveals a large binding pocket required to accommodate the unusual amino acid substrate, N(delta)-cis-anhydromevalonyl-N(delta)-hydroxy-L-ornithine (cis-AMHO). The specific activation of cis-AMHO was confirmed biochemically, and an AMHO moiety was unambiguously identified as a component of the fungal siderophore using mass spectroscopy. The protein structure shows that the substrate binding pocket is defined by 17 amino acid residues, in contrast to both prokaryotic adenylation domains and to previous predictions based on modeling. Existing substrate prediction methods for NRPS adenylation domains fail for domains from eukaryotes due to the divergence of their signature sequences from those of prokaryotes. Thus, this new structure will provide a basis for improving prediction methods for eukaryotic NRPS enzymes that play important and diverse roles in the biology of fungi.

Structure of a eukaryotic nonribosomal peptide synthetase adenylation domain that activates a large hydroxamate amino acid in siderophore biosynthesis.,Lee TV, Johnson LJ, Johnson RD, Koulman A, Lane GA, Lott JS, Arcus VL J Biol Chem. 2010 Jan 22;285(4):2415-27. Epub 2009 Nov 18. PMID:19923209^[3]

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

References

↑ Lee TV, Johnson LJ, Johnson RD, Koulman A, Lane GA, Lott JS, Arcus VL. Structure of a eukaryotic nonribosomal peptide synthetase adenylation domain that activates a large hydroxamate amino acid in siderophore biosynthesis. J Biol Chem. 2010 Jan 22;285(4):2415-27. Epub 2009 Nov 18. PMID:19923209 doi:10.1074/jbc.M109.071324
↑ Johnson LJ, Koulman A, Christensen M, Lane GA, Fraser K, Forester N, Johnson RD, Bryan GT, Rasmussen S. An extracellular siderophore is required to maintain the mutualistic interaction of Epichloë festucae with Lolium perenne. PLoS Pathog. 2013;9(5):e1003332. PMID:23658520 doi:10.1371/journal.ppat.1003332
↑ Lee TV, Johnson LJ, Johnson RD, Koulman A, Lane GA, Lott JS, Arcus VL. Structure of a eukaryotic nonribosomal peptide synthetase adenylation domain that activates a large hydroxamate amino acid in siderophore biosynthesis. J Biol Chem. 2010 Jan 22;285(4):2415-27. Epub 2009 Nov 18. PMID:19923209 doi:10.1074/jbc.M109.071324

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3ite"

@@ Line 3: / Line 3: @@
 <StructureSection load='3ite' size='340' side='right'caption='[[3ite]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ite]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acremonium_lolii Acremonium lolii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ITE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ITE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ite]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Epichloe_festucae_var._lolii Epichloe festucae var. lolii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ITE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ITE FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">sidN ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=73839 Acremonium lolii])</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=3ite FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ite OCA], [https://pdbe.org/3ite PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ite RCSB], [https://www.ebi.ac.uk/pdbsum/3ite PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ite ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/SIDN_EPIFI SIDN_EPIFI] Nonribosomal peptide synthase required for the biosynthetis of epichloenin A, an extracellular siderophore that plays a crucial role in endophyte-grass symbioses (PubMed:19923209, PubMed:23658520). SidN assembles epichloenin A by activating and incorporating three trans-anhydromevalonylhydroxyornithine (trans-AMHO), 1 glutamine and 4 glycine moieties (PubMed:23658520). Trans-AMHO is produced from L-ornithine via 2 steps involving a L-ornithine N(5)-monooxygenase and an AHMO-N(5)-transacylase that have still to be identified (PubMed:19923209). The third adenylation domain (A3) of sidN incorporates the hydroxamate groups of the siderophore which forms an octahedral iron complex (PubMed:19923209). The other component amino acids are assembled by sidN adenylation domains A1 and A2 (PubMed:19923209, PubMed:23658520).<ref>PMID:19923209</ref> <ref>PMID:23658520</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 14: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/it/3ite_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 32: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Acremonium lolii]]
+[[Category: Epichloe festucae var. lolii]]
 [[Category: Large Structures]]
-[[Category: Arcus, V L]]
+[[Category: Arcus VL]]
-[[Category: Johnson, L J]]
+[[Category: Johnson LJ]]
-[[Category: Johnson, R D]]
+[[Category: Johnson RD]]
-[[Category: Lee, T V]]
+[[Category: Lee TV]]
-[[Category: Lott, J S]]
+[[Category: Lott JS]]
-[[Category: Endophyte]]
-[[Category: Fungal]]
-[[Category: Ligase]]
-[[Category: Non-ribosomal peptide synthesis]]
-[[Category: Nrp]]
-[[Category: Siderophore synthetase]]
-[[Category: Sidna3]]

3ite

From Proteopedia

Current revision

The third adenylation domain of the fungal SidN non-ribosomal peptide synthetase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox