4m5c - Revision history

OCA at 08:55, 20 March 2024

OCA — Wed, 20 Mar 2024 08:55:57 GMT

←Older revision		Revision as of 08:55, 20 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4m5c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Caldanaerobacter_subterraneus_subsp._tengcongensis_MB4 Caldanaerobacter subterraneus subsp. tengcongensis MB4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M5C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4M5C FirstGlance]. <br>		<table><tr><td colspan='2'>[[4m5c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Caldanaerobacter_subterraneus_subsp._tengcongensis_MB4 Caldanaerobacter subterraneus subsp. tengcongensis MB4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M5C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4M5C FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=HEZ:HEXANE-1,6-DIOL'>HEZ</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]] 2.5Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=HEZ:HEXANE-1,6-DIOL'>HEZ</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=4m5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m5c OCA], [https://pdbe.org/4m5c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4m5c RCSB], [https://www.ebi.ac.uk/pdbsum/4m5c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4m5c ProSAT]</span></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=4m5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m5c OCA], [https://pdbe.org/4m5c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4m5c RCSB], [https://www.ebi.ac.uk/pdbsum/4m5c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4m5c ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q8R9C0_CALS4 Q8R9C0_CALS4]		[https://www.uniprot.org/uniprot/Q8R9C0_CALS4 Q8R9C0_CALS4]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The energy-coupling factor (ECF) transporters are multi-subunit protein complexes that mediate uptake of transition-metal ions and vitamins in about 50% of the prokaryotes, including bacteria and archaea. Biological and structural studies have been focused on ECF transporters for vitamins, but the molecular mechanism by which ECF systems transport metal ions from the environment remains unknown. Here we report the first crystal structure of a NikM, TtNikM2, the substrate-binding component (S component) of an ECF-type nickel transporter from Thermoanaerobacter tengcongensis. In contrast to the structures of the vitamin-specific S proteins with six transmembrane segments (TSs), TtNikM2 possesses an additional TS at its N-terminal region, resulting in an extracellular N-terminus. The highly conserved N-terminal loop inserts into the center of TtNikM2 and occludes a region corresponding to the substrate-binding sites of the vitamin-specific S components. Nickel binds to NikM via its coordination to four nitrogen atoms, which are derived from Met1, His2 and His67 residues. These nitrogen atoms form an approximately square-planar geometry, similar to that of the metal ion-binding sites in the amino-terminal Cu(2+)- and Ni(2+)-binding (ATCUN) motif. Replacements of residues in NikM contributing to nickel coordination compromised the Ni-transport activity. Furthermore, systematic quantum chemical investigation indicated that this geometry enables NikM to also selectively recognize Co(2+). Indeed, the structure of TtNikM2 containing a bound Co(2+) ion has almost no conformational change compared to the structure that contains a nickel ion. Together, our data reveal an evolutionarily conserved mechanism underlying the metal selectivity of EcfS proteins, and provide insights into the ion-translocation process mediated by ECF transporters.
-
-	Planar substrate-binding site dictates the specificity of ECF-type nickel/cobalt transporters.,Yu Y, Zhou M, Kirsch F, Xu C, Zhang L, Wang Y, Jiang Z, Wang N, Li J, Eitinger T, Yang M Cell Res. 2014 Mar;24(3):267-77. doi: 10.1038/cr.2013.172. Epub 2013 Dec 24. PMID:24366337<ref>PMID:24366337</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4m5c" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:57, 21 December 2022

OCA — Wed, 21 Dec 2022 10:57:06 GMT

←Older revision		Revision as of 10:57, 21 December 2022
Line 1:		Line 1:

	==Crystal Structure of an Truncated Transition metal Transporter==		==Crystal Structure of an Truncated Transition metal Transporter==
-	<StructureSection load='4m5c' size='340' side='right' caption='[[4m5c]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='4m5c' size='340' side='right'caption='[[4m5c]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4m5c]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Caldanaerobacter_subterraneus_subsp.~~_tengcongensis~~ Caldanaerobacter subterraneus subsp. tengcongensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M5C OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4M5C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4m5c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Caldanaerobacter_subterraneus_subsp._tengcongensis_MB4 Caldanaerobacter subterraneus subsp. tengcongensis MB4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M5C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4M5C FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=HEZ:HEXANE-1,6-DIOL'>HEZ</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=HEZ:HEXANE-1,6-DIOL'>HEZ</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4m58\|4m58]], [[4m5b\|4m5b]]</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=4m5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m5c OCA], [https://pdbe.org/4m5c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4m5c RCSB], [https://www.ebi.ac.uk/pdbsum/4m5c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4m5c ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CbiM2, TTE1695 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273068 Caldanaerobacter subterraneus subsp. tengcongensis])</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=4m5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m5c OCA], [~~http~~://pdbe.org/4m5c PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4m5c RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4m5c PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4m5c ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8R9C0_CALS4 Q8R9C0_CALS4]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Caldanaerobacter subterraneus subsp. tengcongensis]]	+	[[Category: Caldanaerobacter subterraneus subsp. tengcongensis MB4]]
-	[[Category: ~~Gu, J K~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Yu, Y~~]]	+	[[Category: Gu JK]]
-	[[Category: ~~Zhou, M Z~~]]	+	[[Category: Yu Y]]
-	[[Category: ~~Cobalt]]~~	+	[[Category: Zhou MZ]]
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Transporter~~]]	+

OCA at 08:15, 11 August 2016

OCA — Thu, 11 Aug 2016 08:15:54 GMT

←Older revision		Revision as of 08:15, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of an Truncated Transition metal Transporter==		==Crystal Structure of an Truncated Transition metal Transporter==
	<StructureSection load='4m5c' size='340' side='right' caption='[[4m5c]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='4m5c' size='340' side='right' caption='[[4m5c]], [[Resolution\|resolution]] 2.50Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4m58\|4m58]], [[4m5b\|4m5b]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4m58\|4m58]], [[4m5b\|4m5b]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CbiM2, TTE1695 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273068 Caldanaerobacter subterraneus subsp. tengcongensis])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CbiM2, TTE1695 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273068 Caldanaerobacter subterraneus subsp. tengcongensis])</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=4m5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m5c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4m5c RCSB], [http://www.ebi.ac.uk/pdbsum/4m5c PDBsum]</span></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=4m5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m5c OCA], [http://pdbe.org/4m5c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4m5c RCSB], [http://www.ebi.ac.uk/pdbsum/4m5c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4m5c ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4m5c" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:16, 5 January 2015

OCA — Mon, 05 Jan 2015 09:16:53 GMT

←Older revision		Revision as of 09:16, 5 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4m5c\| PDB=4m5c \| SCENE= }}~~	+	==Crystal Structure of an Truncated Transition metal Transporter==
-	===Crystal Structure of an Truncated Transition metal Transporter===	+	<StructureSection load='4m5c' size='340' side='right' caption='[[4m5c]], [[Resolution\|resolution]] 2.50Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24366337}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4m5c]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Caldanaerobacter_subterraneus_subsp._tengcongensis Caldanaerobacter subterraneus subsp. tengcongensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M5C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4M5C FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=HEZ:HEXANE-1,6-DIOL'>HEZ</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4m58\|4m58]], [[4m5b\|4m5b]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CbiM2, TTE1695 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273068 Caldanaerobacter subterraneus subsp. tengcongensis])</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=4m5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4m5c OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4m5c RCSB], [http://www.ebi.ac.uk/pdbsum/4m5c PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The energy-coupling factor (ECF) transporters are multi-subunit protein complexes that mediate uptake of transition-metal ions and vitamins in about 50% of the prokaryotes, including bacteria and archaea. Biological and structural studies have been focused on ECF transporters for vitamins, but the molecular mechanism by which ECF systems transport metal ions from the environment remains unknown. Here we report the first crystal structure of a NikM, TtNikM2, the substrate-binding component (S component) of an ECF-type nickel transporter from Thermoanaerobacter tengcongensis. In contrast to the structures of the vitamin-specific S proteins with six transmembrane segments (TSs), TtNikM2 possesses an additional TS at its N-terminal region, resulting in an extracellular N-terminus. The highly conserved N-terminal loop inserts into the center of TtNikM2 and occludes a region corresponding to the substrate-binding sites of the vitamin-specific S components. Nickel binds to NikM via its coordination to four nitrogen atoms, which are derived from Met1, His2 and His67 residues. These nitrogen atoms form an approximately square-planar geometry, similar to that of the metal ion-binding sites in the amino-terminal Cu(2+)- and Ni(2+)-binding (ATCUN) motif. Replacements of residues in NikM contributing to nickel coordination compromised the Ni-transport activity. Furthermore, systematic quantum chemical investigation indicated that this geometry enables NikM to also selectively recognize Co(2+). Indeed, the structure of TtNikM2 containing a bound Co(2+) ion has almost no conformational change compared to the structure that contains a nickel ion. Together, our data reveal an evolutionarily conserved mechanism underlying the metal selectivity of EcfS proteins, and provide insights into the ion-translocation process mediated by ECF transporters.

-	~~==About this Structure==~~	+	Planar substrate-binding site dictates the specificity of ECF-type nickel/cobalt transporters.,Yu Y, Zhou M, Kirsch F, Xu C, Zhang L, Wang Y, Jiang Z, Wang N, Li J, Eitinger T, Yang M Cell Res. 2014 Mar;24(3):267-77. doi: 10.1038/cr.2013.172. Epub 2013 Dec 24. PMID:24366337<ref>PMID:24366337</ref>
-	~~[[4m5c]] is a 1 chain structure~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.~~il/oca-bin/ocashort?id=4M5C OCA]~~.	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024366337</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Gu, J K.]]	+	== References ==
-	[[Category: Yu, Y.]]	+	<references/>
-	[[Category: Zhou, M Z.]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Caldanaerobacter subterraneus subsp. tengcongensis]]
		+	[[Category: Gu, J K]]
		+	[[Category: Yu, Y]]
		+	[[Category: Zhou, M Z]]
	[[Category: Cobalt]]		[[Category: Cobalt]]
	[[Category: Membrane protein]]		[[Category: Membrane protein]]
	[[Category: Transporter]]		[[Category: Transporter]]

OCA at 09:25, 26 March 2014

OCA — Wed, 26 Mar 2014 09:25:48 GMT

←Older revision		Revision as of 09:25, 26 March 2014
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4m5c\| PDB=4m5c \| SCENE= }}
		+	===Crystal Structure of an Truncated Transition metal Transporter===
		+	{{ABSTRACT_PUBMED_24366337}}

-	~~The entry~~ 4m5c is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[4m5c]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4M5C OCA].

-	~~Authors~~: Yu, Y., Zhou, M.Z.~~, Gu, J.K.~~	+	==Reference==
-		+	<ref group="xtra">PMID:024366337</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Crystal Structure of an Truncated Transition metal~~ Transporter	+	[[Category: Gu, J K.]]
		+	[[Category: Yu, Y.]]
		+	[[Category: Zhou, M Z.]]
		+	[[Category: Cobalt]]
		+	[[Category: Membrane protein]]
		+	[[Category: Transporter]]

OCA at 04:47, 12 September 2013

OCA — Thu, 12 Sep 2013 04:47:43 GMT

←Older revision		Revision as of 04:47, 12 September 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4m5c is ON HOLD	+	The entry 4m5c is ON HOLD until Paper Publication

	Authors: Yu, Y., Zhou, M.Z., Gu, J.K.		Authors: Yu, Y., Zhou, M.Z., Gu, J.K.

	Description: Crystal Structure of an Truncated Transition metal Transporter		Description: Crystal Structure of an Truncated Transition metal Transporter

OCA: Protected "4m5c" [edit=sysop:move=sysop]

OCA — Wed, 14 Aug 2013 07:27:19 GMT

Protected "4m5c" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:27, 14 August 2013

OCA: New page: '''Unreleased structure''' The entry 4m5c is ON HOLD Authors: Yu, Y., Zhou, M.Z., Gu, J.K. Description: Crystal Structure of an Truncated Transition metal Transporter

OCA — Wed, 14 Aug 2013 07:27:17 GMT

New page: '''Unreleased structure''' The entry 4m5c is ON HOLD Authors: Yu, Y., Zhou, M.Z., Gu, J.K. Description: Crystal Structure of an Truncated Transition metal Transporter

New page

'''Unreleased structure'''

The entry 4m5c is ON HOLD

Authors: Yu, Y., Zhou, M.Z., Gu, J.K.

Description: Crystal Structure of an Truncated Transition metal Transporter