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4dg9

From Proteopedia

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Current revision (14:34, 14 March 2024) (edit) (undo)
 
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<StructureSection load='4dg9' size='340' side='right'caption='[[4dg9]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
<StructureSection load='4dg9' size='340' side='right'caption='[[4dg9]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4dg9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DG9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DG9 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4dg9]] is a 1 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=4DG9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DG9 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DG9:5-({[(2R,3R)-3-AMINO-2-{[2-({N-[(2R)-2-HYDROXY-3,3-DIMETHYL-4-{[OXIDO(OXO)PHOSPHONIO]OXY}BUTANOYL]-BETA-ALANYL}AMINO)ETHYL]SULFANYL}-4-METHYLPENTYL]SULFONYL}AMINO)-5-DEOXYADENOSINE'>DG9</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.55&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4dg8|4dg8]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DG9:5-({[(2R,3R)-3-AMINO-2-{[2-({N-[(2R)-2-HYDROXY-3,3-DIMETHYL-4-{[OXIDO(OXO)PHOSPHONIO]OXY}BUTANOYL]-BETA-ALANYL}AMINO)ETHYL]SULFANYL}-4-METHYLPENTYL]SULFONYL}AMINO)-5-DEOXYADENOSINE'>DG9</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PA1221 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4dg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dg9 OCA], [https://pdbe.org/4dg9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dg9 RCSB], [https://www.ebi.ac.uk/pdbsum/4dg9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dg9 ProSAT]</span></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=4dg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dg9 OCA], [https://pdbe.org/4dg9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dg9 RCSB], [https://www.ebi.ac.uk/pdbsum/4dg9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dg9 ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q9I4B7_PSEAE Q9I4B7_PSEAE]
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Many bacteria use large modular enzymes for the synthesis of polyketide and peptide natural products. These multidomain enzymes contain integrated carrier domains that deliver bound substrates to multiple catalytic domains, requiring coordination of these chemical steps. Nonribosomal peptide synthetases (NRPSs) load amino acids onto carrier domains through the activity of an upstream adenylation domain. Our lab recently determined the structure of an engineered two-domain NRPS containing fused adenylation and carrier domains. This structure adopted a domain-swapped dimer that illustrated the interface between these two domains. To continue our investigation, we now examine PA1221, a natural two-domain protein from Pseudomonas aeruginosa. We have determined the amino acid specificity of this new enzyme and used domain specific mutations to demonstrate that loading the downstream carrier domain within a single protein molecule occurs more quickly than loading of a nonfused carrier domain intermolecularly. Finally, we have determined crystal structures of both apo- and holo-PA1221 proteins, the latter using a valine-adenosine vinylsulfonamide inhibitor that traps the adenylation domain-carrier domain interaction. The protein adopts an interface similar to that seen with the prior adenylation domain-carrier protein construct. A comparison of these structures with previous structures of multidomain NRPSs suggests that a large conformational change within the NRPS adenylation domains guides the carrier domain into the active site for thioester formation.
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Structure of PA1221, a Nonribosomal Peptide Synthetase Containing Adenylation and Peptidyl Carrier Protein Domains.,Mitchell CA, Shi C, Aldrich CC, Gulick AM Biochemistry. 2012 Apr 17;51(15):3252-63. Epub 2012 Apr 3. PMID:22452656<ref>PMID:22452656</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 4dg9" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Pseae]]
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[[Category: Pseudomonas aeruginosa PAO1]]
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[[Category: Aldrich, C C]]
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[[Category: Aldrich CC]]
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[[Category: Gulick, A M]]
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[[Category: Gulick AM]]
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[[Category: Mitchell, C A]]
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[[Category: Mitchell CA]]
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[[Category: Shi, C]]
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[[Category: Shi C]]
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[[Category: Adenylation domain]]
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[[Category: Anl superfamily]]
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[[Category: Ligase-inhibitor complex]]
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[[Category: Non-ribosomal peptide synthetase]]
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[[Category: Nrp]]
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[[Category: Pantetheine]]
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[[Category: Peptidyl carrier protein]]
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[[Category: Valine adenylation]]
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[[Category: Vinylsulfonamide]]
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Current revision

Structure of holo-PA1221, an NRPS protein containing adenylation and PCP domains bound to vinylsulfonamide inhibitor

PDB ID 4dg9

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