1gxt - Revision history

OCA at 11:25, 27 March 2024

OCA — Wed, 27 Mar 2024 11:25:28 GMT

←Older revision		Revision as of 11:25, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='1gxt' size='340' side='right'caption='[[1gxt]], [[Resolution\|resolution]] 1.27Å' scene=''>		<StructureSection load='1gxt' size='340' side='right'caption='[[1gxt]], [[Resolution\|resolution]] 1.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1gxt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GXT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GXT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1gxt]] 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=1GXT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GXT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 1.27Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1gxu\|1gxu]]</div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=1gxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gxt OCA], [https://pdbe.org/1gxt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gxt RCSB], [https://www.ebi.ac.uk/pdbsum/1gxt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gxt 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=1gxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gxt OCA], [https://pdbe.org/1gxt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gxt RCSB], [https://www.ebi.ac.uk/pdbsum/1gxt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gxt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/HYPF_ECOLI HYPF_ECOLI]] Along with HypE, it catalyzes the synthesis of the CN ligands of the active site iron of [NiFe]-hydrogenases using carbamoylphosphate as a substrate. It functions as a carbamoyl transferase using carbamoylphosphate as a substrate and transferring the carboxamido moiety in an ATP-dependent reaction to the thiolate of the C-terminal cysteine of HypE yielding a protein-S-carboxamide.<ref>PMID:8661925</ref> <ref>PMID:12377778</ref> <ref>PMID:15291820</ref> <ref>PMID:15504408</ref>	+	[https://www.uniprot.org/uniprot/HYPF_ECOLI HYPF_ECOLI] Along with HypE, it catalyzes the synthesis of the CN ligands of the active site iron of [NiFe]-hydrogenases using carbamoylphosphate as a substrate. It functions as a carbamoyl transferase using carbamoylphosphate as a substrate and transferring the carboxamido moiety in an ATP-dependent reaction to the thiolate of the C-terminal cysteine of HypE yielding a protein-S-carboxamide.<ref>PMID:8661925</ref> <ref>PMID:12377778</ref> <ref>PMID:15291820</ref> <ref>PMID:15504408</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1gxt ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1gxt ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	[NiFe]-hydrogenases require a set of complementary and regulatory proteins for correct folding and maturation processes. One of the essential regulatory proteins, HypF (82kDa) contains a N-terminal acylphosphatase (ACT)-like domain, a sequence motif shared with enzymes catalyzing O-carbamoylation, and two zinc finger motifs similar to those found in the DnaJ chaperone. The HypF acylphosphatase domain is thought to support the conversion of carbamoylphosphate into CO and CN(-), promoting coordination of these ligands to the hydrogenase metal cluster. It has been shown recently that the HypF N-terminal domain can aggregate in vitro to yield fibrils matching those formed by proteins linked to amyloid diseases. The 1.27A resolution HypF acylphosphatase domain crystal structure (residues 1-91; R-factor 13.1%) shows a domain fold of betaalphabetabetaalphabeta topology, as observed in mammalian acylphosphatases specifically catalyzing the hydrolysis of the carboxyl-phosphate bonds in acylphosphates. The HypF N-terminal domain can be assigned to the ferredoxin structural superfamily, to which RNA-binding domains of small nuclear ribonucleoproteins and some metallochaperone proteins belong. Additionally, the HypF N-terminal domain displays an intriguing structural relationship to the recently discovered ACT domains. The structures of different HypF acylphosphatase domain complexes show a phosphate binding cradle comparable to the P-loop observed in unrelated phosphatase families. On the basis of the catalytic mechanism proposed for acylphosphatases, whereby residues Arg23 and Asn41 would support substrate orientation and the nucleophilic attack of a water molecule on the phosphate group, fine structural features of the HypF N-terminal domain putative active site region may account for the lack of acylphosphatase activity observed for the expressed domain. The crystallographic analyses here reported were undertaken to shed light on the molecular bases of inactivity, folding, misfolding and aggregation of the HypF N-terminal acylphosphatase domain.
-
-	Crystal structure and anion binding in the prokaryotic hydrogenase maturation factor HypF acylphosphatase-like domain.,Rosano C, Zuccotti S, Bucciantini M, Stefani M, Ramponi G, Bolognesi M J Mol Biol. 2002 Aug 30;321(5):785-96. PMID:12206761<ref>PMID:12206761</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1gxt" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bolognesi, M]]	+	[[Category: Bolognesi M]]
-	[[Category: Bucciantini, M]]	+	[[Category: Bucciantini M]]
-	[[Category: Ramponi, G]]	+	[[Category: Ramponi G]]
-	[[Category: Rosano, C]]	+	[[Category: Rosano C]]
-	[[Category: Stefani, M]]	+	[[Category: Stefani M]]
-	[[Category: Zuccotti, S]]	+	[[Category: Zuccotti S]]
-	~~[[Category: Acylphosphatase]]~~	+
-	~~[[Category: Fibril formation]]~~	+
-	~~[[Category: Hydrogenase maturation]]~~	+
-	~~[[Category: Phosphatase]]~~	+
-	~~[[Category: Zinc-finger~~]]	+

OCA at 05:47, 28 April 2021

OCA — Wed, 28 Apr 2021 05:47:57 GMT

←Older revision		Revision as of 05:47, 28 April 2021
Line 3:		Line 3:
	<StructureSection load='1gxt' size='340' side='right'caption='[[1gxt]], [[Resolution\|resolution]] 1.27Å' scene=''>		<StructureSection load='1gxt' size='340' side='right'caption='[[1gxt]], [[Resolution\|resolution]] 1.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1gxt]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GXT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1GXT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1gxt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GXT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GXT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gxu\|1gxu]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1gxu\|1gxu]]</div></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=1gxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gxt OCA], [~~http~~://pdbe.org/1gxt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1gxt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1gxt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1gxt 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=1gxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gxt OCA], [https://pdbe.org/1gxt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gxt RCSB], [https://www.ebi.ac.uk/pdbsum/1gxt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gxt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/HYPF_ECOLI HYPF_ECOLI]] Along with HypE, it catalyzes the synthesis of the CN ligands of the active site iron of [NiFe]-hydrogenases using carbamoylphosphate as a substrate. It functions as a carbamoyl transferase using carbamoylphosphate as a substrate and transferring the carboxamido moiety in an ATP-dependent reaction to the thiolate of the C-terminal cysteine of HypE yielding a protein-S-carboxamide.<ref>PMID:8661925</ref> <ref>PMID:12377778</ref> <ref>PMID:15291820</ref> <ref>PMID:15504408</ref>	+	[[https://www.uniprot.org/uniprot/HYPF_ECOLI HYPF_ECOLI]] Along with HypE, it catalyzes the synthesis of the CN ligands of the active site iron of [NiFe]-hydrogenases using carbamoylphosphate as a substrate. It functions as a carbamoyl transferase using carbamoylphosphate as a substrate and transferring the carboxamido moiety in an ATP-dependent reaction to the thiolate of the C-terminal cysteine of HypE yielding a protein-S-carboxamide.<ref>PMID:8661925</ref> <ref>PMID:12377778</ref> <ref>PMID:15291820</ref> <ref>PMID:15504408</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[HypA-HypB-HypC-HypD-HypE-HypF\|HypA-HypB-HypC-HypD-HypE-HypF]]	+	*[[HypA%2C HypB%2C HypC%2C HypD%2C HypE and HypF 3D structures\|HypA%2C HypB%2C HypC%2C HypD%2C HypE and HypF 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:41, 24 July 2019

OCA — Wed, 24 Jul 2019 06:41:42 GMT

←Older revision		Revision as of 06:41, 24 July 2019
Line 1:		Line 1:

	==Hydrogenase Maturation Protein HypF "acylphosphatase-like" N-terminal domain (HypF-ACP) in complex with Sulfate==		==Hydrogenase Maturation Protein HypF "acylphosphatase-like" N-terminal domain (HypF-ACP) in complex with Sulfate==
-	<StructureSection load='1gxt' size='340' side='right' caption='[[1gxt]], [[Resolution\|resolution]] 1.27Å' scene=''>	+	<StructureSection load='1gxt' size='340' side='right'caption='[[1gxt]], [[Resolution\|resolution]] 1.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1gxt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GXT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GXT FirstGlance]. <br>		<table><tr><td colspan='2'>[[1gxt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GXT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GXT FirstGlance]. <br>
Line 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1gxt" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1gxt" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[HypA-HypB-HypC-HypD-HypE-HypF\|HypA-HypB-HypC-HypD-HypE-HypF]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Bolognesi, M]]		[[Category: Bolognesi, M]]
	[[Category: Bucciantini, M]]		[[Category: Bucciantini, M]]

OCA at 06:46, 3 January 2018

OCA — Wed, 03 Jan 2018 06:46:28 GMT

←Older revision		Revision as of 06:46, 3 January 2018
Line 1:		Line 1:
-	==~~HYDROGENASE MATURATION PROTEIN HYPF~~ "~~ACYLPHOSPHATASE~~-~~LIKE~~" N-~~TERMINAL DOMAIN~~ (~~HYPF~~-ACP) ~~IN COMPLEX WITH SULFATE~~==	+
		+	==Hydrogenase Maturation Protein HypF "acylphosphatase-like" N-terminal domain (HypF-ACP) in complex with Sulfate==
	<StructureSection load='1gxt' size='340' side='right' caption='[[1gxt]], [[Resolution\|resolution]] 1.27Å' scene=''>		<StructureSection load='1gxt' size='340' side='right' caption='[[1gxt]], [[Resolution\|resolution]] 1.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gxu\|1gxu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gxu\|1gxu]]</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=1gxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gxt OCA], [http://pdbe.org/1gxt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gxt RCSB], [http://www.ebi.ac.uk/pdbsum/1gxt 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=1gxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gxt OCA], [http://pdbe.org/1gxt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gxt RCSB], [http://www.ebi.ac.uk/pdbsum/1gxt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1gxt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gx/1gxt_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gx/1gxt_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1gxt" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1gxt" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[HypA-HypB-HypC-HypD-HypE-HypF\|HypA-HypB-HypC-HypD-HypE-HypF]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 01:44, 9 February 2016

OCA — Tue, 09 Feb 2016 01:44:42 GMT

←Older revision		Revision as of 01:44, 9 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1gxt ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 17:23, 10 September 2015

OCA — Thu, 10 Sep 2015 17:23:58 GMT

←Older revision		Revision as of 17:23, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1gxt' size='340' side='right' caption='[[1gxt]], [[Resolution\|resolution]] 1.27Å' scene=''>		<StructureSection load='1gxt' size='340' side='right' caption='[[1gxt]], [[Resolution\|resolution]] 1.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1gxt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GXT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GXT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1gxt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GXT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GXT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gxu\|1gxu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gxu\|1gxu]]</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=1gxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gxt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gxt RCSB], [http://www.ebi.ac.uk/pdbsum/1gxt 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=1gxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gxt OCA], [http://pdbe.org/1gxt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gxt RCSB], [http://www.ebi.ac.uk/pdbsum/1gxt PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	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 1gxt" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[HypA-HypB-HypC-HypD-HypE-HypF\|HypA-HypB-HypC-HypD-HypE-HypF]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Bolognesi, M]]		[[Category: Bolognesi, M]]
	[[Category: Bucciantini, M]]		[[Category: Bucciantini, M]]

OCA at 03:34, 25 December 2014

OCA — Thu, 25 Dec 2014 03:34:09 GMT

←Older revision		Revision as of 03:34, 25 December 2014
Line 7:		Line 7:
	<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=1gxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gxt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gxt RCSB], [http://www.ebi.ac.uk/pdbsum/1gxt 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=1gxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gxt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gxt RCSB], [http://www.ebi.ac.uk/pdbsum/1gxt PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HYPF_ECOLI HYPF_ECOLI]] Along with HypE, it catalyzes the synthesis of the CN ligands of the active site iron of [NiFe]-hydrogenases using carbamoylphosphate as a substrate. It functions as a carbamoyl transferase using carbamoylphosphate as a substrate and transferring the carboxamido moiety in an ATP-dependent reaction to the thiolate of the C-terminal cysteine of HypE yielding a protein-S-carboxamide.<ref>PMID:8661925</ref> <ref>PMID:12377778</ref> <ref>PMID:15291820</ref> <ref>PMID:15504408</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 19:51, 22 December 2014

OCA — Mon, 22 Dec 2014 19:51:15 GMT

←Older revision		Revision as of 19:51, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1gxt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GXT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GXT FirstGlance]. <br>		<table><tr><td colspan='2'>[[1gxt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GXT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GXT FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gxu\|1gxu]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gxu\|1gxu]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1gxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gxt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gxt RCSB], [http://www.ebi.ac.uk/pdbsum/1gxt 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=1gxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gxt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gxt RCSB], [http://www.ebi.ac.uk/pdbsum/1gxt PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Bolognesi, M.]]	+	[[Category: Bolognesi, M]]
-	[[Category: Bucciantini, M.]]	+	[[Category: Bucciantini, M]]
-	[[Category: Ramponi, G.]]	+	[[Category: Ramponi, G]]
-	[[Category: Rosano, C.]]	+	[[Category: Rosano, C]]
-	[[Category: Stefani, M.]]	+	[[Category: Stefani, M]]
-	[[Category: Zuccotti, S.]]	+	[[Category: Zuccotti, S]]
	[[Category: Acylphosphatase]]		[[Category: Acylphosphatase]]
	[[Category: Fibril formation]]		[[Category: Fibril formation]]

OCA at 09:43, 28 September 2014

OCA — Sun, 28 Sep 2014 09:43:36 GMT

←Older revision		Revision as of 09:43, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1gxt.~~png~~\|~~left~~\|200px]]	+	==HYDROGENASE MATURATION PROTEIN HYPF "ACYLPHOSPHATASE-LIKE" N-TERMINAL DOMAIN (HYPF-ACP) IN COMPLEX WITH SULFATE==
		+	<StructureSection load='1gxt' size='340' side='right' caption='[[1gxt]], [[Resolution\|resolution]] 1.27Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1gxt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GXT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GXT FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1gxu\|1gxu]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1gxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gxt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gxt RCSB], [http://www.ebi.ac.uk/pdbsum/1gxt PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gx/1gxt_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	[NiFe]-hydrogenases require a set of complementary and regulatory proteins for correct folding and maturation processes. One of the essential regulatory proteins, HypF (82kDa) contains a N-terminal acylphosphatase (ACT)-like domain, a sequence motif shared with enzymes catalyzing O-carbamoylation, and two zinc finger motifs similar to those found in the DnaJ chaperone. The HypF acylphosphatase domain is thought to support the conversion of carbamoylphosphate into CO and CN(-), promoting coordination of these ligands to the hydrogenase metal cluster. It has been shown recently that the HypF N-terminal domain can aggregate in vitro to yield fibrils matching those formed by proteins linked to amyloid diseases. The 1.27A resolution HypF acylphosphatase domain crystal structure (residues 1-91; R-factor 13.1%) shows a domain fold of betaalphabetabetaalphabeta topology, as observed in mammalian acylphosphatases specifically catalyzing the hydrolysis of the carboxyl-phosphate bonds in acylphosphates. The HypF N-terminal domain can be assigned to the ferredoxin structural superfamily, to which RNA-binding domains of small nuclear ribonucleoproteins and some metallochaperone proteins belong. Additionally, the HypF N-terminal domain displays an intriguing structural relationship to the recently discovered ACT domains. The structures of different HypF acylphosphatase domain complexes show a phosphate binding cradle comparable to the P-loop observed in unrelated phosphatase families. On the basis of the catalytic mechanism proposed for acylphosphatases, whereby residues Arg23 and Asn41 would support substrate orientation and the nucleophilic attack of a water molecule on the phosphate group, fine structural features of the HypF N-terminal domain putative active site region may account for the lack of acylphosphatase activity observed for the expressed domain. The crystallographic analyses here reported were undertaken to shed light on the molecular bases of inactivity, folding, misfolding and aggregation of the HypF N-terminal acylphosphatase domain.

-	~~{{STRUCTURE_1gxt\| PDB=1gxt \| SCENE= }}~~	+	Crystal structure and anion binding in the prokaryotic hydrogenase maturation factor HypF acylphosphatase-like domain.,Rosano C, Zuccotti S, Bucciantini M, Stefani M, Ramponi G, Bolognesi M J Mol Biol. 2002 Aug 30;321(5):785-96. PMID:12206761<ref>PMID:12206761</ref>

-	~~===HYDROGENASE MATURATION PROTEIN HYPF "ACYLPHOSPHATASE-LIKE" N-TERMINAL DOMAIN (HYPF-ACP) IN COMPLEX WITH SULFATE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12206761}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1gxt]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1GXT OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012206761<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Bolognesi, M.]]		[[Category: Bolognesi, M.]]

OCA: Protected "1gxt" [edit=sysop:move=sysop]

OCA — Wed, 21 Nov 2012 16:16:22 GMT

Protected "1gxt" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:16, 21 November 2012