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7tgm

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Crystal structure of HSC-AMS bound DesD, the desferrioxamine synthetase from the Streptomyces griseoflavus ferrimycin biosynthetic pathway

Structural highlights

7tgm is a 5 chain structure with sequence from Streptomyces griseoflavus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

Siderophores are conditionally essential metabolites used by microbes for environmental iron sequestration. Most Streptomyces strains produce hydroxamate-based desferrioxamine (DFO) siderophores composed of repeating units of N(1)-hydroxy-cadaverine (or N(1)-hydroxy-putrescine) and succinate. The DFO biosynthetic operon, desABCD, is highly conserved in Streptomyces; however, expression of desABCD alone does not account for the vast structural diversity within this natural product class. Here, we report the in vitro reconstitution and biochemical characterization of four DesD orthologs from Streptomyces strains that produce unique DFO siderophores. Under in vitro conditions, all four DesD orthologs displayed similar saturation steady-state kinetics (vmax = 0.9-2.5 muMmin(-1)) and produced the macrocyclic trimer desferrioxamine E (DFOE) as the favored product, suggesting a conserved role for DesD in the biosynthesis of DFO siderophores. We further synthesized a structural mimic of HSC-acyl adenylate, the HSC-acyl sulfamoyl adenosine analog (HSC-AMS), and obtained crystal structures of DesD in the ATP-bound, AMP/PPi-bound, and HSC-AMS/Pi-bound forms. We found HSC-AMS inhibited DesD orthologs (IC50 values = 48-53 muM) leading to accumulation of linear trimeric desferrioxamine G (DFOG) and di-HSC at the expense of macrocyclic DFOE. Addition of exogenous PPi enhanced DesD inhibition by HSC-AMS, presumably via stabilization of the DesD/HSC-AMS complex, similar to the proposed mode of adenylate stabilization where PPi remains buried in the active site. In conclusion, our data suggest that acyl-AMS derivatives may have utility as chemical probes and bi-substrate inhibitors to reveal valuable mechanistic and structural insight for this unique family of adenylating enzymes.

An acyl-adenylate mimic reveals the structural basis for substrate recognition by the iterative siderophore synthetase DesD.,Yang J, Banas VS, Patel KD, Rivera GSM, Mydy LS, Gulick AM, Wencewicz TA J Biol Chem. 2022 Jun 21:102166. doi: 10.1016/j.jbc.2022.102166. PMID:35750210^[1]

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

References

↑ Yang J, Banas VS, Patel KD, Rivera GSM, Mydy LS, Gulick AM, Wencewicz TA. An acyl-adenylate mimic reveals the structural basis for substrate recognition by the iterative siderophore synthetase DesD. J Biol Chem. 2022 Jun 21:102166. doi: 10.1016/j.jbc.2022.102166. PMID:35750210 doi:http://dx.doi.org/10.1016/j.jbc.2022.102166

1 Structural highlights
2 Publication Abstract from PubMed
3 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

Categories: Large Structures | Streptomyces griseoflavus | Gulick AM | Patel KD

@@ Line 3: / Line 3: @@
 <StructureSection load='7tgm' size='340' side='right'caption='[[7tgm]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7tgm]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TGM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TGM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7tgm]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_griseoflavus Streptomyces griseoflavus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TGM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TGM FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=I3U:4-[(5-aminopentyl)(hydroxy)amino]-4-oxobutanoic+acid'>I3U</scene>, <scene name='pdbligand=LMS:[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDRO-2-FURANYL]METHYL+SULFAMATE'>LMS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=I3U:4-[(5-aminopentyl)(hydroxy)amino]-4-oxobutanoic+acid'>I3U</scene>, <scene name='pdbligand=LMS:[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDRO-2-FURANYL]METHYL+SULFAMATE'>LMS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7tgm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7tgm OCA], [https://pdbe.org/7tgm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7tgm RCSB], [https://www.ebi.ac.uk/pdbsum/7tgm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7tgm ProSAT]</span></td></tr>
 </table>
@@ Line 21: / Line 22: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Gulick, A M]]
+[[Category: Streptomyces griseoflavus]]
-[[Category: Patel, K D]]
+[[Category: Gulick AM]]
-[[Category: Adenylate-forming enzyme]]
+[[Category: Patel KD]]
-[[Category: Amide ligase]]
-[[Category: Inhibitor]]
-[[Category: Iterative synthetase]]
-[[Category: Ligase]]
-[[Category: Ligase-inhibitor complex]]

7tgm

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Current revision

Crystal structure of HSC-AMS bound DesD, the desferrioxamine synthetase from the Streptomyces griseoflavus ferrimycin biosynthetic pathway

Structural highlights

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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