7c0y: Difference between revisions
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==Crystal structure of a dinucleotide-binding protein (Y246A) of ABC transporter endogenously bound to uridylyl-3'-5'-phospho-guanosine (Form I)== | |||
<StructureSection load='7c0y' size='340' side='right'caption='[[7c0y]], [[Resolution|resolution]] 1.70Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[7c0y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C0Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7C0Y FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO2:CARBON+DIOXIDE'>CO2</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FGO:[(1S,3R,3aR,6aS)-3-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-5,5-bis(oxidanyl)-1,3,3a,4,6,6a-hexahydrocyclopenta[c]furan-1-yl]methyl+[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-2-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl]+hydrogen+phosphate'>FGO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO3:PHOSPHITE+ION'>PO3</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=7c0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c0y OCA], [https://pdbe.org/7c0y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7c0y RCSB], [https://www.ebi.ac.uk/pdbsum/7c0y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7c0y ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q5SLB4_THET8 Q5SLB4_THET8] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Substrate (or solute)-binding proteins (SBPs) selectively bind the target ligands and deliver them to the ATP-binding cassette (ABC) transport system for their translocation. Irrespective of the different types of ligands, SBPs are structurally conserved. A wealth of structural details of SBPs bound to different types of ligands and the physiological basis of their import are available; however, the uptake mechanism of nucleotides is still deficient. In this study, we elucidated the structural details of an SBP endogenously bound to a novel ligand, a derivative of uridylyl-3'-5'-phospho-guanosine (U3G); thus, we named it a U3G-binding protein (U3GBP). To the best of our knowledge, this is the first report of U3G (and a dinucleotide) binding to the SBP of ABC transport system, and thus, U3GBP is classified as a first member of subcluster D-I SBPs. Thermodynamic data also suggest that U3GBP can bind phospholipid precursor sn-glycerophosphocholine (GPC) at a site other than the active site. Moreover, a combination of mutagenic and structural information reveals that the protein U3GBP follows the well-known 'Venus Fly-trap' mechanism for dinucleotide binding. DATABASES: Structural data are available in RCSB Protein Data Bank under the accession number(s) 7C0F, 7C0K, 7C0L, 7C0O, 7C0R, 7C0S, 7C0T, 7C0U, 7C0V, 7C0W, 7C0X, 7C0Y, 7C0Z, 7C14, 7C15, 7C16, 7C19, and 7C1B. | |||
Structural and thermodynamic insights into the novel dinucleotide-binding protein of ABC transporter unveils its moonlighting function.,Chandravanshi M, Samanta R, Kanaujia SP FEBS J. 2021 Feb 18. doi: 10.1111/febs.15774. PMID:33599038<ref>PMID:33599038</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 7c0y" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[ABC transporter 3D structures|ABC transporter 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Thermus thermophilus HB8]] | |||
[[Category: Chandravanshi M]] | |||
[[Category: Kanaujia SP]] | |||
[[Category: Samanta R]] | |||
Latest revision as of 18:48, 29 November 2023
Crystal structure of a dinucleotide-binding protein (Y246A) of ABC transporter endogenously bound to uridylyl-3'-5'-phospho-guanosine (Form I)Crystal structure of a dinucleotide-binding protein (Y246A) of ABC transporter endogenously bound to uridylyl-3'-5'-phospho-guanosine (Form I)
Structural highlights
FunctionPublication Abstract from PubMedSubstrate (or solute)-binding proteins (SBPs) selectively bind the target ligands and deliver them to the ATP-binding cassette (ABC) transport system for their translocation. Irrespective of the different types of ligands, SBPs are structurally conserved. A wealth of structural details of SBPs bound to different types of ligands and the physiological basis of their import are available; however, the uptake mechanism of nucleotides is still deficient. In this study, we elucidated the structural details of an SBP endogenously bound to a novel ligand, a derivative of uridylyl-3'-5'-phospho-guanosine (U3G); thus, we named it a U3G-binding protein (U3GBP). To the best of our knowledge, this is the first report of U3G (and a dinucleotide) binding to the SBP of ABC transport system, and thus, U3GBP is classified as a first member of subcluster D-I SBPs. Thermodynamic data also suggest that U3GBP can bind phospholipid precursor sn-glycerophosphocholine (GPC) at a site other than the active site. Moreover, a combination of mutagenic and structural information reveals that the protein U3GBP follows the well-known 'Venus Fly-trap' mechanism for dinucleotide binding. DATABASES: Structural data are available in RCSB Protein Data Bank under the accession number(s) 7C0F, 7C0K, 7C0L, 7C0O, 7C0R, 7C0S, 7C0T, 7C0U, 7C0V, 7C0W, 7C0X, 7C0Y, 7C0Z, 7C14, 7C15, 7C16, 7C19, and 7C1B. Structural and thermodynamic insights into the novel dinucleotide-binding protein of ABC transporter unveils its moonlighting function.,Chandravanshi M, Samanta R, Kanaujia SP FEBS J. 2021 Feb 18. doi: 10.1111/febs.15774. PMID:33599038[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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