5yxc

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Zinc binding protein ZinT in complex with citrate from E. coli

Structural highlights

5yxc is a 2 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.763Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ZINT_ECOLI May function as a periplasmic zinc chaperone or mediate direct transport of zinc from the periplasm to the cytoplasm under zinc-limited conditions. Binds zinc with high affinity, and can also bind cadmium, mercury or nickel. Preferentially binds Zn(2+) over Cd(2+). Contains one high affinity metal binding site, and can bind additional metal ions at other sites.^[1] ^[2]

Publication Abstract from PubMed

The ZnuABC ATP-binding cassette transporter found in gram-negative bacteria has been implicated in ensuring adequate zinc import into Zn(II)-poor environments. ZinT is an essential component of ZnuABC and contributes to metal transport by transferring metals to ZnuA, which delivers them to ZnuB in periplasmic zinc recruitment. Although several structures of E. coli ZinT have been reported, its zinc-binding sites and oligomeric state have not been clearly identified. Here, we report the crystal structure of E. coli ZinT at 1.76A resolution. This structure contains one zinc ion in its calycin-like domain, and this ion is coordinated by three highly conserved histidine residues (His167, His176 and His178). Moreover, three oxygen atoms (O1, O6 and O7) from the citrate molecule interact with zinc, giving the zinc ion stable octahedral coordination. Our EcZinT structure shows the fewest zinc ions bound of all reported EcZinT structures. Crystallographic packing and size exclusion chromatography suggest that EcZinT prefers to form monomers in solution. Our results provide insights into the molecular function of ZinT.

Crystal structure of E. coli ZinT with one zinc-binding mode and complexed with citrate.,Chen J, Wang L, Shang F, Dong Y, Ha NC, Nam KH, Quan C, Xu Y Biochem Biophys Res Commun. 2018 Jun 2;500(2):139-144. doi:, 10.1016/j.bbrc.2018.03.192. Epub 2018 Apr 13. PMID:29596824^[3]

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

References

↑ Kershaw CJ, Brown NL, Hobman JL. Zinc dependence of zinT (yodA) mutants and binding of zinc, cadmium and mercury by ZinT. Biochem Biophys Res Commun. 2007 Dec 7;364(1):66-71. Epub 2007 Oct 2. PMID:17931600 doi:http://dx.doi.org/10.1016/j.bbrc.2007.09.094
↑ Graham AI, Hunt S, Stokes SL, Bramall N, Bunch J, Cox AG, McLeod CW, Poole RK. Severe zinc depletion of Escherichia coli: roles for high affinity zinc binding by ZinT, zinc transport and zinc-independent proteins. J Biol Chem. 2009 Jul 3;284(27):18377-89. doi: 10.1074/jbc.M109.001503. Epub 2009, Apr 19. PMID:19377097 doi:http://dx.doi.org/10.1074/jbc.M109.001503
↑ Chen J, Wang L, Shang F, Dong Y, Ha NC, Nam KH, Quan C, Xu Y. Crystal structure of E. coli ZinT with one zinc-binding mode and complexed with citrate. Biochem Biophys Res Commun. 2018 Jun 2;500(2):139-144. doi:, 10.1016/j.bbrc.2018.03.192. Epub 2018 Apr 13. PMID:29596824 doi:http://dx.doi.org/10.1016/j.bbrc.2018.03.192

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/5yxc"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5yxc is ON HOLD
+==Crystal structure of Zinc binding protein ZinT in complex with citrate from E. coli==
+<StructureSection load='5yxc' size='340' side='right'caption='[[5yxc]], [[Resolution|resolution]] 1.76&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5yxc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YXC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YXC 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]] 1.763&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5yxc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yxc OCA], [https://pdbe.org/5yxc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yxc RCSB], [https://www.ebi.ac.uk/pdbsum/5yxc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yxc ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ZINT_ECOLI ZINT_ECOLI] May function as a periplasmic zinc chaperone or mediate direct transport of zinc from the periplasm to the cytoplasm under zinc-limited conditions. Binds zinc with high affinity, and can also bind cadmium, mercury or nickel. Preferentially binds Zn(2+) over Cd(2+). Contains one high affinity metal binding site, and can bind additional metal ions at other sites.<ref>PMID:17931600</ref> <ref>PMID:19377097</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The ZnuABC ATP-binding cassette transporter found in gram-negative bacteria has been implicated in ensuring adequate zinc import into Zn(II)-poor environments. ZinT is an essential component of ZnuABC and contributes to metal transport by transferring metals to ZnuA, which delivers them to ZnuB in periplasmic zinc recruitment. Although several structures of E. coli ZinT have been reported, its zinc-binding sites and oligomeric state have not been clearly identified. Here, we report the crystal structure of E. coli ZinT at 1.76A resolution. This structure contains one zinc ion in its calycin-like domain, and this ion is coordinated by three highly conserved histidine residues (His167, His176 and His178). Moreover, three oxygen atoms (O1, O6 and O7) from the citrate molecule interact with zinc, giving the zinc ion stable octahedral coordination. Our EcZinT structure shows the fewest zinc ions bound of all reported EcZinT structures. Crystallographic packing and size exclusion chromatography suggest that EcZinT prefers to form monomers in solution. Our results provide insights into the molecular function of ZinT.
-Authors: Chen, J., Wang, L., Shang, F., Xu, Y.
+Crystal structure of E. coli ZinT with one zinc-binding mode and complexed with citrate.,Chen J, Wang L, Shang F, Dong Y, Ha NC, Nam KH, Quan C, Xu Y Biochem Biophys Res Commun. 2018 Jun 2;500(2):139-144. doi:, 10.1016/j.bbrc.2018.03.192. Epub 2018 Apr 13. PMID:29596824<ref>PMID:29596824</ref>
-Description: Crystal structure of Zinc binding protein ZinT complex with citrate from E. coli
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Shang, F]]
+<div class="pdbe-citations 5yxc" style="background-color:#fffaf0;"></div>
-[[Category: Chen, J]]
+== References ==
-[[Category: Wang, L]]
+<references/>
-[[Category: Xu, Y]]
+__TOC__
+</StructureSection>
+[[Category: Escherichia coli K-12]]
+[[Category: Large Structures]]
+[[Category: Chen J]]
+[[Category: Shang F]]
+[[Category: Wang L]]
+[[Category: Xu Y]]

5yxc

From Proteopedia

Current revision

Crystal structure of Zinc binding protein ZinT in complex with citrate from E. coli

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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