5edl: Difference between revisions

Latest revision as of 06:22, 5 July 2023

Crystal structure of an S-component of ECF transporter

Structural highlights

5edl is a 1 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.95Å
Ligands:	MPG, VIB
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

YKOE_BACSU Part of the ABC transporter complex YkoCDEF that could transport hydroxymethylpyrimidine (HMP) and/or thiamine. Could also transport other HMP-containing products. Probably responsible for the translocation of the substrate across the membrane (Probable).^[1] ^[2]

Publication Abstract from PubMed

Energy coupling factor (ECF) transporters are responsible for the uptake of essential scarce nutrients in prokaryotes. This ATP-binding cassette transporter family comprises two subgroups that share a common architecture forming a tripartite membrane protein complex consisting of a translocation component and ATP hydrolyzing module and a substrate-capture (S) component. Here, we present the crystal structure of YkoE from Bacillus subtilis, the S component of the previously uncharacterized group I ECF transporter YkoEDC. Structural and biochemical analyses revealed the constituent residues of the thiamine-binding pocket as well as an unexpected mode of vitamin recognition. In addition, our experimental and bioinformatics data demonstrate major differences between YkoE and group II ECF transporters and indicate how group I vitamin transporter S components have diverged from other group I and group II ECF transporters.

Crystal Structure of a Group I Energy Coupling Factor Vitamin Transporter S Component in Complex with Its Cognate Substrate.,Josts I, Almeida Hernandez Y, Andreeva A, Tidow H Cell Chem Biol. 2016 Jul 21;23(7):827-36. doi: 10.1016/j.chembiol.2016.06.008. PMID:27447050^[3]

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

References

↑ Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms. J Biol Chem. 2002 Dec 13;277(50):48949-59. Epub 2002 Oct 9. PMID:12376536 doi:https://dx.doi.org/10.1074/jbc.M208965200
↑ Schyns G, Potot S, Geng Y, Barbosa TM, Henriques A, Perkins JB. Isolation and characterization of new thiamine-deregulated mutants of Bacillus subtilis. J Bacteriol. 2005 Dec;187(23):8127-36. PMID:16291685 doi:https://dx.doi.org/187/23/8127
↑ Josts I, Almeida Hernandez Y, Andreeva A, Tidow H. Crystal Structure of a Group I Energy Coupling Factor Vitamin Transporter S Component in Complex with Its Cognate Substrate. Cell Chem Biol. 2016 Jul 21;23(7):827-36. doi: 10.1016/j.chembiol.2016.06.008. PMID:27447050 doi:https://dx.doi.org/10.1016/j.chembiol.2016.06.008

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OCA

[1] Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms. J Biol Chem. 2002 Dec 13;277(50):48949-59. Epub 2002 Oct 9. PMID:12376536 doi:https://dx.doi.org/10.1074/jbc.M208965200

[2] Schyns G, Potot S, Geng Y, Barbosa TM, Henriques A, Perkins JB. Isolation and characterization of new thiamine-deregulated mutants of Bacillus subtilis. J Bacteriol. 2005 Dec;187(23):8127-36. PMID:16291685 doi:https://dx.doi.org/187/23/8127

[3] Josts I, Almeida Hernandez Y, Andreeva A, Tidow H. Crystal Structure of a Group I Energy Coupling Factor Vitamin Transporter S Component in Complex with Its Cognate Substrate. Cell Chem Biol. 2016 Jul 21;23(7):827-36. doi: 10.1016/j.chembiol.2016.06.008. PMID:27447050 doi:https://dx.doi.org/10.1016/j.chembiol.2016.06.008

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5edl is ON HOLD  until Paper Publication
+==Crystal structure of an S-component of ECF transporter==
+<StructureSection load='5edl' size='340' side='right'caption='[[5edl]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5edl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EDL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EDL 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]] 1.95&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPG:[(Z)-OCTADEC-9-ENYL]+(2R)-2,3-BIS(OXIDANYL)PROPANOATE'>MPG</scene>, <scene name='pdbligand=VIB:3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM'>VIB</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=5edl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5edl OCA], [https://pdbe.org/5edl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5edl RCSB], [https://www.ebi.ac.uk/pdbsum/5edl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5edl ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/YKOE_BACSU YKOE_BACSU] Part of the ABC transporter complex YkoCDEF that could transport hydroxymethylpyrimidine (HMP) and/or thiamine. Could also transport other HMP-containing products. Probably responsible for the translocation of the substrate across the membrane (Probable).<ref>PMID:12376536</ref> <ref>PMID:16291685</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Energy coupling factor (ECF) transporters are responsible for the uptake of essential scarce nutrients in prokaryotes. This ATP-binding cassette transporter family comprises two subgroups that share a common architecture forming a tripartite membrane protein complex consisting of a translocation component and ATP hydrolyzing module and a substrate-capture (S) component. Here, we present the crystal structure of YkoE from Bacillus subtilis, the S component of the previously uncharacterized group I ECF transporter YkoEDC. Structural and biochemical analyses revealed the constituent residues of the thiamine-binding pocket as well as an unexpected mode of vitamin recognition. In addition, our experimental and bioinformatics data demonstrate major differences between YkoE and group II ECF transporters and indicate how group I vitamin transporter S components have diverged from other group I and group II ECF transporters.
-Authors: Josts, I., Tidow, H.
+Crystal Structure of a Group I Energy Coupling Factor Vitamin Transporter S Component in Complex with Its Cognate Substrate.,Josts I, Almeida Hernandez Y, Andreeva A, Tidow H Cell Chem Biol. 2016 Jul 21;23(7):827-36. doi: 10.1016/j.chembiol.2016.06.008. PMID:27447050<ref>PMID:27447050</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Josts, I]]
+<div class="pdbe-citations 5edl" style="background-color:#fffaf0;"></div>
-[[Category: Tidow, H]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Bacillus subtilis]]
+[[Category: Large Structures]]
+[[Category: Josts I]]
+[[Category: Tidow H]]

5edl: Difference between revisions

Latest revision as of 06:22, 5 July 2023

Crystal structure of an S-component of ECF transporter

Structural highlights

Function

Publication Abstract from PubMed

References

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