1oej: Difference between revisions

Revision as of 12:37, 13 December 2023

YodA from Escherichia coli crystallised with no added ions

Structural highlights

1oej is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.81Å
Ligands:	NI
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]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

We have determined the crystal structure of YodA, an Escherichia coli protein of unknown function. YodA had been identified under conditions of cadmium stress, and we confirm that it binds metals such as cadmium and zinc. We have also found nickel bound in one of the crystal forms. YodA is composed of two domains: a main lipocalin/calycin-like domain and a helical domain. The principal metal-binding site lies on one side of the calycin domain, thus making YodA the first metal-binding lipocalin known. Our experiments suggest that YodA expression may be part of a more general stress response. From sequence analogy with the C-terminal domain of a metal-binding receptor of a member of bacterial ATP-binding cassette transporters, we propose a three-dimensional model for this receptor and suggest that YodA may have a receptor-type partner in E. coli.

YodA from Escherichia coli is a metal-binding, lipocalin-like protein.,David G, Blondeau K, Schiltz M, Penel S, Lewit-Bentley A J Biol Chem. 2003 Oct 31;278(44):43728-35. Epub 2003 Aug 8. PMID:12909634^[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:https://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:https://dx.doi.org/10.1074/jbc.M109.001503
↑ David G, Blondeau K, Schiltz M, Penel S, Lewit-Bentley A. YodA from Escherichia coli is a metal-binding, lipocalin-like protein. J Biol Chem. 2003 Oct 31;278(44):43728-35. Epub 2003 Aug 8. PMID:12909634 doi:https://dx.doi.org/10.1074/jbc.M304484200

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] 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:https://dx.doi.org/10.1016/j.bbrc.2007.09.094

[2] 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:https://dx.doi.org/10.1074/jbc.M109.001503

[3] David G, Blondeau K, Schiltz M, Penel S, Lewit-Bentley A. YodA from Escherichia coli is a metal-binding, lipocalin-like protein. J Biol Chem. 2003 Oct 31;278(44):43728-35. Epub 2003 Aug 8. PMID:12909634 doi:https://dx.doi.org/10.1074/jbc.M304484200

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[2]

[3]

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[1oej]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OEJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OEJ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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]] 1.81&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1oee|1oee]], [[1oek|1oek]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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=1oej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oej OCA], [https://pdbe.org/1oej PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oej RCSB], [https://www.ebi.ac.uk/pdbsum/1oej PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oej 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>
+[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>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 35: / Line 35: @@
 [[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Blondeau, K]]
+[[Category: Blondeau K]]
-[[Category: David, G]]
+[[Category: David G]]
-[[Category: Lewit-Bentley, A]]
+[[Category: Lewit-Bentley A]]
-[[Category: Penel, S]]
+[[Category: Penel S]]
-[[Category: Renouard, M]]
+[[Category: Renouard M]]
-[[Category: Lipocalin]]
-[[Category: Stress protein]]
-[[Category: Stress protein-lipocalin complex]]
-[[Category: Stress protein/lipocalin]]
-[[Category: Yoda]]

1oej: Difference between revisions

Revision as of 12:37, 13 December 2023

YodA from Escherichia coli crystallised with no added ions

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

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