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| | <StructureSection load='5kzj' size='340' side='right'caption='[[5kzj]], [[Resolution|resolution]] 2.20Å' scene=''> | | <StructureSection load='5kzj' size='340' side='right'caption='[[5kzj]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5kzj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pardp Pardp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KZJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KZJ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5kzj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_denitrificans_PD1222 Paracoccus denitrificans PD1222]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KZJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KZJ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4xrv|4xrv]]</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=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Pden_1597 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=318586 PARDP])</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=5kzj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kzj OCA], [https://pdbe.org/5kzj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kzj RCSB], [https://www.ebi.ac.uk/pdbsum/5kzj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kzj ProSAT]</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=5kzj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kzj OCA], [http://pdbe.org/5kzj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kzj RCSB], [http://www.ebi.ac.uk/pdbsum/5kzj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kzj ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/AZTC_PARDP AZTC_PARDP] Part of the ATP-binding cassette (ABC) transport system AztABCD involved in zinc import (PubMed:25787075, PubMed:26468286, PubMed:30353723, PubMed:32781785, PubMed:35128285). Binds zinc with high affinity and specificity and delivers it to the membrane permease for translocation into the cytoplasm (PubMed:25787075, PubMed:26468286, PubMed:30353723, PubMed:32781785, PubMed:35128285).<ref>PMID:25787075</ref> <ref>PMID:26468286</ref> <ref>PMID:30353723</ref> <ref>PMID:32781785</ref> <ref>PMID:35128285</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Pardp]] | + | [[Category: Paracoccus denitrificans PD1222]] |
| - | [[Category: Yukl, E]] | + | [[Category: Yukl E]] |
| - | [[Category: Deletion mutant]]
| + | |
| - | [[Category: Metal binding protein]]
| + | |
| - | [[Category: Periplasm]]
| + | |
| - | [[Category: Zinc binding protein]]
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| Structural highlights
Function
AZTC_PARDP Part of the ATP-binding cassette (ABC) transport system AztABCD involved in zinc import (PubMed:25787075, PubMed:26468286, PubMed:30353723, PubMed:32781785, PubMed:35128285). Binds zinc with high affinity and specificity and delivers it to the membrane permease for translocation into the cytoplasm (PubMed:25787075, PubMed:26468286, PubMed:30353723, PubMed:32781785, PubMed:35128285).[1] [2] [3] [4] [5]
Publication Abstract from PubMed
Bacteria can acquire the essential metal zinc from extremely zinc-limited environments by using ATP-binding cassette (ABC) transporters. These transporters are critical virulence factors relying on specific and high-affinity binding of zinc by a periplasmic solute-binding protein (SBP). As such, the mechanisms of zinc binding and release among bacterial SBPs are of considerable interest as antibacterial drug targets. Zinc SBPs are characterized by a flexible loop near the high-affinity zinc-binding site. The function of this structure is not always clear, and its flexibility has thus far prevented structural characterization by X-ray crystallography. Here, we present intact structures for the zinc-specific SBP AztC from the bacterium Paracoccus denitrificans in the zinc-bound and the apo states. A comparison of these structures revealed that zinc loss prompts significant structural rearrangements mediated by the formation of a sodium-binding site in the apo structure. We further show that the AztC flexible loop has no impact on zinc-binding affinity, stoichiometry, or protein structure, yet is essential for zinc transfer from the metallochaperone AztD. We also found that three His residues in the loop appear to temporarily coordinate zinc and then convey it to the high-affinity binding site. Consistent with this, mutation of any of these residues to Ala abrogated zinc transfer from AztD. Our structural and mechanistic findings conclusively identify a role for the AztC flexible loop in zinc acquisition from the metallochaperone AztD and yield critical insights into metal binding by AztC from both solution and AztD. These proteins are highly conserved in human pathogens, making this work potentially useful to the development of novel antibiotics.
Mechanisms of zinc binding to the solute binding protein AztC and transfer from the metallochaperone AztD.,Neupane DP, Avalos D, Fullam S, Roychowdhury H, Yukl ET J Biol Chem. 2017 Sep 7. pii: jbc.M117.804799. doi: 10.1074/jbc.M117.804799. PMID:28887302[6]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Handali M, Neupane DP, Roychowdhury H, Yukl ET. Transcriptional regulation, metal binding properties and structure of Pden1597, an unusual Zn transport protein from Paracoccus denitrificans. J Biol Chem. 2015 Mar 18. pii: jbc.M115.645853. PMID:25787075 doi:http://dx.doi.org/10.1074/jbc.M115.645853
- ↑ Handali M, Roychowdhury H, Neupane DP, Yukl ET. AztD, a Periplasmic Zinc Metallochaperone to an ATP-binding Cassette (ABC) Transporter System in Paracoccus denitrificans. J Biol Chem. 2015 Dec 11;290(50):29984-92. PMID:26468286 doi:10.1074/jbc.M115.684506
- ↑ Neupane DP, Kumar S, Yukl ET. Two ABC Transporters and a Periplasmic Metallochaperone Participate in Zinc Acquisition in Paracoccus denitrificans. Biochemistry. 2019 Jan 15;58(2):126-136. PMID:30353723 doi:10.1021/acs.biochem.8b00854
- ↑ Meni A, Yukl ET. Structural Features Mediating Zinc Binding and Transfer in the AztABCD Zinc Transporter System. Biomolecules. 2020 Aug 6;10(8):1156. PMID:32781785 doi:10.3390/biom10081156
- ↑ Serrano FA, Yukl ET. Contributions of Conformational Flexibility to High-Affinity Zinc Binding in the Solute Binding Protein AztC. ACS Omega. 2022 Jan 20;7(4):3768-3774. PMID:35128285 doi:10.1021/acsomega.1c06639
- ↑ Neupane DP, Avalos D, Fullam S, Roychowdhury H, Yukl ET. Mechanisms of zinc binding to the solute binding protein AztC and transfer from the metallochaperone AztD. J Biol Chem. 2017 Sep 7. pii: jbc.M117.804799. doi: 10.1074/jbc.M117.804799. PMID:28887302 doi:http://dx.doi.org/10.1074/jbc.M117.804799
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