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5kbw

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Crystal structure of TmRibU, the riboflavin-binding S subunit from the Thermotoga maritima ECF transporter

Structural highlights

5kbw is a 2 chain structure with sequence from Thermotoga maritima MSB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.6093Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RIBU_THEMA Substrate-binding (S) component of an energy-coupling factor (ECF) ABC-transporter complex. Mediates riboflavin uptake, may also transport FMN and roseoflavin. Probably a riboflavin-binding protein that interacts with the energy-coupling factor (ECF) ABC-transporter complex. Unlike classic ABC transporters this ECF transporter provides the energy necessary to transport a number of different substrates. The substrates themselves are bound by transmembrane, not extracytoplasmic soluble proteins (Probable). Expression of the complex plus RibU in E.coli allows riboflavin uptake; uptake does not occur in the absence of RibU or the EcfA1A2T complex.^[1]

Publication Abstract from PubMed

ECF transporters are a family of active membrane transporters for essential micronutrients, such as vitamins and trace metals. Found exclusively in archaea and bacteria, these transporters are composed of four subunits: an integral membrane substrate-binding subunit (EcfS), a transmembrane coupling subunit (EcfT), and two ATP-binding cassette ATPases (EcfA and EcfA'). We have characterized the structural basis of substrate binding by the EcfS subunit for riboflavin from Thermotoga maritima, TmRibU. TmRibU binds riboflavin with high affinity, and the protein-substrate complex is exceptionally stable in solution. The crystal structure of riboflavin-bound TmRibU reveals an electronegative binding pocket at the extracellular surface in which the substrate is completely buried. Analysis of the intermolecular contacts indicates that nearly every available substrate hydrogen bond is satisfied. A conserved aromatic residue at the extracellular end of TM5, Tyr130, caps the binding site to generate a substrate-bound, occluded state, and non-conservative mutation of Tyr130 reduces the stability of this conformation. Using a novel fluorescence binding assay, we find that an aromatic residue at this position is essential for high-affinity substrate binding. Comparison with other S subunit structures suggests that TM5 and Loop5-6 contain a dynamic, conserved motif that plays a key role in gating substrate entry and release by S subunits of ECF transporters.

An Aromatic Cap Seals the Substrate Binding Site in an ECF-Type S Subunit for Riboflavin.,Karpowich NK, Song J, Wang DN J Mol Biol. 2016 Jun 13. pii: S0022-2836(16)30211-X. doi:, 10.1016/j.jmb.2016.06.003. PMID:27312125^[2]

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

References

↑ Karpowich NK, Wang DN. Assembly and mechanism of a group II ECF transporter. Proc Natl Acad Sci U S A. 2013 Feb 12;110(7):2534-9. doi:, 10.1073/pnas.1217361110. Epub 2013 Jan 28. PMID:23359690 doi:http://dx.doi.org/10.1073/pnas.1217361110
↑ Karpowich NK, Song J, Wang DN. An Aromatic Cap Seals the Substrate Binding Site in an ECF-Type S Subunit for Riboflavin. J Mol Biol. 2016 Jun 13. pii: S0022-2836(16)30211-X. doi:, 10.1016/j.jmb.2016.06.003. PMID:27312125 doi:http://dx.doi.org/10.1016/j.jmb.2016.06.003

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5kbw"

Categories: Large Structures | Thermotoga maritima MSB8 | Karpowich NK | Song JM | Wang DN

@@ Line 1: / Line 1: @@
 ==Crystal structure of TmRibU, the riboflavin-binding S subunit from the Thermotoga maritima ECF transporter==
-<StructureSection load='5kbw' size='340' side='right' caption='[[5kbw]], [[Resolution|resolution]] 2.61&Aring;' scene=''>
+<StructureSection load='5kbw' size='340' side='right'caption='[[5kbw]], [[Resolution|resolution]] 2.61&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5kbw]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KBW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KBW FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5kbw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KBW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KBW FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RBF:RIBOFLAVIN'>RBF</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]] 2.6093&#8491;</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=5kbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kbw OCA], [http://pdbe.org/5kbw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kbw RCSB], [http://www.ebi.ac.uk/pdbsum/5kbw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kbw ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=RBF:RIBOFLAVIN'>RBF</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=5kbw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kbw OCA], [https://pdbe.org/5kbw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kbw RCSB], [https://www.ebi.ac.uk/pdbsum/5kbw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kbw ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RIBU_THEMA RIBU_THEMA]] Substrate-binding (S) component of an energy-coupling factor (ECF) ABC-transporter complex. Mediates riboflavin uptake, may also transport FMN and roseoflavin. Probably a riboflavin-binding protein that interacts with the energy-coupling factor (ECF) ABC-transporter complex. Unlike classic ABC transporters this ECF transporter provides the energy necessary to transport a number of different substrates. The substrates themselves are bound by transmembrane, not extracytoplasmic soluble proteins (Probable). Expression of the complex plus RibU in E.coli allows riboflavin uptake; uptake does not occur in the absence of RibU or the EcfA1A2T complex.<ref>PMID:23359690</ref>
+[https://www.uniprot.org/uniprot/RIBU_THEMA RIBU_THEMA] Substrate-binding (S) component of an energy-coupling factor (ECF) ABC-transporter complex. Mediates riboflavin uptake, may also transport FMN and roseoflavin. Probably a riboflavin-binding protein that interacts with the energy-coupling factor (ECF) ABC-transporter complex. Unlike classic ABC transporters this ECF transporter provides the energy necessary to transport a number of different substrates. The substrates themselves are bound by transmembrane, not extracytoplasmic soluble proteins (Probable). Expression of the complex plus RibU in E.coli allows riboflavin uptake; uptake does not occur in the absence of RibU or the EcfA1A2T complex.<ref>PMID:23359690</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Karpowich, N K]]
+[[Category: Large Structures]]
-[[Category: Song, J M]]
+[[Category: Thermotoga maritima MSB8]]
-[[Category: Wang, D N]]
+[[Category: Karpowich NK]]
-[[Category: Ecf transporter]]
+[[Category: Song JM]]
-[[Category: Integral membrane protein]]
+[[Category: Wang DN]]
-[[Category: Membrane protein]]
-[[Category: Membrane transport]]
-[[Category: Transport protein]]
-[[Category: Vitamin]]

5kbw

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Current revision

Crystal structure of TmRibU, the riboflavin-binding S subunit from the Thermotoga maritima ECF transporter

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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