4bbj: Difference between revisions

Latest revision as of 10:40, 6 November 2024

Copper-transporting PIB-ATPase in complex with beryllium fluoride representing the E2P state

Structural highlights

4bbj is a 1 chain structure with sequence from Legionella pneumophila subsp. pneumophila. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.75Å
Ligands:	BFD, CE1, MG, NAD, PC
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

COPA_LEGPH Couples the hydrolysis of ATP with the export of copper.^[1] ^[2] ^[3]

Publication Abstract from PubMed

Heavy metals in cells are typically regulated by PIB-type ATPases. The first structure of the class, a Cu+-ATPase from Legionella pneumophila (LpCopA), outlined a copper transport pathway across the membrane, which was inferred to be occluded. Here we show by molecular dynamics simulations that extracellular water solvated the transmembrane (TM) domain, results indicative of a Cu+-release pathway. Furthermore, a new LpCopA crystal structure determined at 2.8-A resolution, trapped in the preceding E2P state, delineated the same passage, and site-directed-mutagenesis activity assays support a functional role for the conduit. The structural similarities between the TM domains of the two conformations suggest that Cu+-ATPases couple dephosphorylation and ion extrusion differently than do the well-characterized PII-type ATPases. The ion pathway explains why certain Menkes' and Wilson's disease mutations impair protein function and points to a site for inhibitors targeting pathogens.

Copper-transporting P-type ATPases use a unique ion-release pathway.,Andersson M, Mattle D, Sitsel O, Klymchuk T, Nielsen AM, Moller LB, White SH, Nissen P, Gourdon P Nat Struct Mol Biol. 2013 Dec 8. doi: 10.1038/nsmb.2721. PMID:24317491^[4]

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

References

↑ Andersson M, Mattle D, Sitsel O, Klymchuk T, Nielsen AM, Moller LB, White SH, Nissen P, Gourdon P. Copper-transporting P-type ATPases use a unique ion-release pathway. Nat Struct Mol Biol. 2013 Dec 8. doi: 10.1038/nsmb.2721. PMID:24317491 doi:https://dx.doi.org/10.1038/nsmb.2721
↑ Placenti MA, Roman EA, González Flecha FL, González-Lebrero RM. Functional characterization of Legionella pneumophila Cu(+) transport ATPase. The activation by Cu(+) and ATP. Biochim Biophys Acta Biomembr. 2022 Feb 1;1864(2):183822. PMID:34826402 doi:10.1016/j.bbamem.2021.183822
↑ Gourdon P, Liu XY, Skjorringe T, Morth JP, Moller LB, Pedersen BP, Nissen P. Crystal structure of a copper-transporting PIB-type ATPase. Nature. 2011 Jun 29;475(7354):59-64. doi: 10.1038/nature10191. PMID:21716286 doi:10.1038/nature10191
↑ Andersson M, Mattle D, Sitsel O, Klymchuk T, Nielsen AM, Moller LB, White SH, Nissen P, Gourdon P. Copper-transporting P-type ATPases use a unique ion-release pathway. Nat Struct Mol Biol. 2013 Dec 8. doi: 10.1038/nsmb.2721. PMID:24317491 doi:https://dx.doi.org/10.1038/nsmb.2721

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Andersson M, Mattle D, Sitsel O, Klymchuk T, Nielsen AM, Moller LB, White SH, Nissen P, Gourdon P. Copper-transporting P-type ATPases use a unique ion-release pathway. Nat Struct Mol Biol. 2013 Dec 8. doi: 10.1038/nsmb.2721. PMID:24317491 doi:https://dx.doi.org/10.1038/nsmb.2721

[2] Placenti MA, Roman EA, González Flecha FL, González-Lebrero RM. Functional characterization of Legionella pneumophila Cu(+) transport ATPase. The activation by Cu(+) and ATP. Biochim Biophys Acta Biomembr. 2022 Feb 1;1864(2):183822. PMID:34826402 doi:10.1016/j.bbamem.2021.183822

[3] Gourdon P, Liu XY, Skjorringe T, Morth JP, Moller LB, Pedersen BP, Nissen P. Crystal structure of a copper-transporting PIB-type ATPase. Nature. 2011 Jun 29;475(7354):59-64. doi: 10.1038/nature10191. PMID:21716286 doi:10.1038/nature10191

[4] Andersson M, Mattle D, Sitsel O, Klymchuk T, Nielsen AM, Moller LB, White SH, Nissen P, Gourdon P. Copper-transporting P-type ATPases use a unique ion-release pathway. Nat Struct Mol Biol. 2013 Dec 8. doi: 10.1038/nsmb.2721. PMID:24317491 doi:https://dx.doi.org/10.1038/nsmb.2721

[1]

[2]

[3]

[4]

@@ Line 3: / Line 3: @@
 <StructureSection load='4bbj' size='340' side='right'caption='[[4bbj]], [[Resolution|resolution]] 2.75&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4bbj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Legionella_pneumophila_subsp._pneumophila Legionella pneumophila subsp. pneumophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BBJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4BBJ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4bbj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Legionella_pneumophila_subsp._pneumophila Legionella pneumophila subsp. pneumophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BBJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BBJ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CE1:O-DODECANYL+OCTAETHYLENE+GLYCOL'>CE1</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PC:PHOSPHOCHOLINE'>PC</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]] 2.75&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BFD:ASPARTATE+BERYLLIUM+TRIFLUORIDE'>BFD</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BFD:ASPARTATE+BERYLLIUM+TRIFLUORIDE'>BFD</scene>, <scene name='pdbligand=CE1:O-DODECANYL+OCTAETHYLENE+GLYCOL'>CE1</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PC:PHOSPHOCHOLINE'>PC</scene></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=4bbj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bbj OCA], [http://pdbe.org/4bbj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4bbj RCSB], [http://www.ebi.ac.uk/pdbsum/4bbj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4bbj 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=4bbj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bbj OCA], [https://pdbe.org/4bbj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4bbj RCSB], [https://www.ebi.ac.uk/pdbsum/4bbj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4bbj ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/COPA_LEGPH COPA_LEGPH] Couples the hydrolysis of ATP with the export of copper.<ref>PMID:24317491</ref> <ref>PMID:34826402</ref> <ref>PMID:21716286</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 21: @@
 ==See Also==
-*[[ATPase|ATPase]]
+*[[ATPase 3D structures|ATPase 3D structures]]
 == References ==
 <references/>
@@ Line 26: / Line 28: @@
 [[Category: Large Structures]]
 [[Category: Legionella pneumophila subsp. pneumophila]]
-[[Category: Gourdon, P]]
+[[Category: Gourdon P]]
-[[Category: Mattle, D]]
+[[Category: Mattle D]]
-[[Category: Nissen, P]]
+[[Category: Nissen P]]
-[[Category: Cation transport protein]]
-[[Category: Cell membrane]]
-[[Category: Hepatolenticular degeneration]]
-[[Category: Hydrolase]]
-[[Category: Membrane protein]]
-[[Category: Menkes disease]]
-[[Category: Sarcoplasmic reticulum calcium-transporting atpase]]
-[[Category: Structure-activity relationship]]
-[[Category: Wilson disease]]

4bbj: Difference between revisions

Latest revision as of 10:40, 6 November 2024

Copper-transporting PIB-ATPase in complex with beryllium fluoride representing the E2P state

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools