7dl9

From Proteopedia

(Difference between revisions)

Revision as of 09:13, 21 July 2021

Crystal structure of nucleoside transporter NupG

Structural highlights

7dl9 is a 2 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	nupG, b2964, JW2932 (ECOLI)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[NUPG_ECOLI] Broad-specificity transporter of purine and pyrimidine nucleosides. Driven by a proton motive force. Can transport uridine, adenosine, inosine, guanosine, thymidine and cytidine. Can also transport xanthosine, but with a very low affinity.^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

Nucleoside homeostasis, which is mediated by transporters and channels, is essential for all life on Earth. In Escherichia coli, NupG mediates the transport of nucleosides and was deemed to be the prototype of the nucleoside proton symporter (NHS) family as well as the major facilitator superfamily (MFS). To date, the substrate recognition and transport mechanisms of NHS transporters are still elusive. Here, we report two crystal structures of NupG (wild-type and D323A NupG) resolved at 3.0 A. Both structures reveal an identical inward-open conformation. Together with molecular docking and molecular dynamics simulations and in vitro uridine-binding assays, we found that the uridine binding site, which locates in the central cavity between N and C domains of NupG, is constituted by R136, T140, F143, Q225, N228, Q261, E264, Y318, and F322. Moreover, we found that D323 is very important for substrate binding via in vitro uridine-binding assays using D323 mutations, even though it does not have direct contact with uridine. Our structural and biochemical data therefore provide an important framework for the mechanistic understanding of nucleoside transporters of the NHS family.

Molecular basis for substrate recognition by the bacterial nucleoside transporter NupG.,Wang C, Xiao Q, Duan H, Li J, Zhang J, Wang Q, Guo L, Hu J, Sun B, Deng D J Biol Chem. 2021 Feb 25:100479. doi: 10.1016/j.jbc.2021.100479. PMID:33640454^[6]

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

References

↑ Norholm MH, Dandanell G. Specificity and topology of the Escherichia coli xanthosine permease, a representative of the NHS subfamily of the major facilitator superfamily. J Bacteriol. 2001 Aug;183(16):4900-4. doi: 10.1128/JB.183.16.4900-4904.2001. PMID:11466294 doi:http://dx.doi.org/10.1128/JB.183.16.4900-4904.2001
↑ Xie H, Patching SG, Gallagher MP, Litherland GJ, Brough AR, Venter H, Yao SY, Ng AM, Young JD, Herbert RB, Henderson PJ, Baldwin SA. Purification and properties of the Escherichia coli nucleoside transporter NupG, a paradigm for a major facilitator transporter sub-family. Mol Membr Biol. 2004 Sep-Oct;21(5):323-36. doi: 10.1080/09687860400003941. PMID:15513740 doi:http://dx.doi.org/10.1080/09687860400003941
↑ Patching SG, Baldwin SA, Baldwin AD, Young JD, Gallagher MP, Henderson PJ, Herbert RB. The nucleoside transport proteins, NupC and NupG, from Escherichia coli: specific structural motifs necessary for the binding of ligands. Org Biomol Chem. 2005 Feb 7;3(3):462-70. doi: 10.1039/b414739a. Epub 2005 Jan 10. PMID:15678184 doi:http://dx.doi.org/10.1039/b414739a
↑ Westh Hansen SE, Jensen N, Munch-Petersen A. Studies on the sequence and structure of the Escherichia coli K-12 nupG gene, encoding a nucleoside-transport system. Eur J Biochem. 1987 Oct 15;168(2):385-91. doi:, 10.1111/j.1432-1033.1987.tb13431.x. PMID:3311747 doi:http://dx.doi.org/10.1111/j.1432-1033.1987.tb13431.x
↑ Munch-Petersen A, Mygind B, Nicolaisen A, Pihl NJ. Nucleoside transport in cells and membrane vesicles from Escherichia coli K12. J Biol Chem. 1979 May 25;254(10):3730-7. PMID:374403
↑ Wang C, Xiao Q, Duan H, Li J, Zhang J, Wang Q, Guo L, Hu J, Sun B, Deng D. Molecular basis for substrate recognition by the bacterial nucleoside transporter NupG. J Biol Chem. 2021 Feb 25:100479. doi: 10.1016/j.jbc.2021.100479. PMID:33640454 doi:http://dx.doi.org/10.1016/j.jbc.2021.100479

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/7dl9"

@@ Line 1: / Line 1: @@
 ==Crystal structure of nucleoside transporter NupG==
-<StructureSection load='7dl9' size='340' side='right'caption='[[7dl9]]' scene=''>
+<StructureSection load='7dl9' size='340' side='right'caption='[[7dl9]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DL9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DL9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7dl9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DL9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DL9 FirstGlance]. <br>
-</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=7dl9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dl9 OCA], [https://pdbe.org/7dl9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dl9 RCSB], [https://www.ebi.ac.uk/pdbsum/7dl9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dl9 ProSAT]</span></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nupG, b2964, JW2932 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=7dl9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dl9 OCA], [https://pdbe.org/7dl9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dl9 RCSB], [https://www.ebi.ac.uk/pdbsum/7dl9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dl9 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[[https://www.uniprot.org/uniprot/NUPG_ECOLI NUPG_ECOLI]] Broad-specificity transporter of purine and pyrimidine nucleosides. Driven by a proton motive force. Can transport uridine, adenosine, inosine, guanosine, thymidine and cytidine. Can also transport xanthosine, but with a very low affinity.<ref>PMID:11466294</ref> <ref>PMID:15513740</ref> <ref>PMID:15678184</ref> <ref>PMID:3311747</ref> <ref>PMID:374403</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Nucleoside homeostasis, which is mediated by transporters and channels, is essential for all life on Earth. In Escherichia coli, NupG mediates the transport of nucleosides and was deemed to be the prototype of the nucleoside proton symporter (NHS) family as well as the major facilitator superfamily (MFS). To date, the substrate recognition and transport mechanisms of NHS transporters are still elusive. Here, we report two crystal structures of NupG (wild-type and D323A NupG) resolved at 3.0 A. Both structures reveal an identical inward-open conformation. Together with molecular docking and molecular dynamics simulations and in vitro uridine-binding assays, we found that the uridine binding site, which locates in the central cavity between N and C domains of NupG, is constituted by R136, T140, F143, Q225, N228, Q261, E264, Y318, and F322. Moreover, we found that D323 is very important for substrate binding via in vitro uridine-binding assays using D323 mutations, even though it does not have direct contact with uridine. Our structural and biochemical data therefore provide an important framework for the mechanistic understanding of nucleoside transporters of the NHS family.
+Molecular basis for substrate recognition by the bacterial nucleoside transporter NupG.,Wang C, Xiao Q, Duan H, Li J, Zhang J, Wang Q, Guo L, Hu J, Sun B, Deng D J Biol Chem. 2021 Feb 25:100479. doi: 10.1016/j.jbc.2021.100479. PMID:33640454<ref>PMID:33640454</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 7dl9" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
 __TOC__
 </StructureSection>
+[[Category: Ecoli]]
 [[Category: Large Structures]]
-[[Category: Deng D]]
+[[Category: Deng, D]]
-[[Category: Wang C]]
+[[Category: Wang, C]]
-[[Category: Xiao QJ]]
+[[Category: Xiao, Q J]]
+[[Category: Membrane protein]]
+[[Category: Mf]]
+[[Category: Nucleoside]]
+[[Category: Transport protein]]
+[[Category: Transporter]]

7dl9

From Proteopedia

Revision as of 09:13, 21 July 2021

Crystal structure of nucleoside transporter NupG

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox