3ilo - Revision history

OCA at 13:09, 30 August 2023

2023-08-30T13:09:45Z

← Older revision		Revision as of 13:09, 30 August 2023
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	<StructureSection load='3ilo' size='340' side='right'caption='[[3ilo]], [[Resolution\|resolution]] 1.10Å' scene=''>		<StructureSection load='3ilo' size='340' side='right'caption='[[3ilo]], [[Resolution\|resolution]] 1.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3ilo]] is a 1 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=3ILO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ILO FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ilo]] is a 1 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=3ILO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ILO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PH2:2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE'>PH2</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]] 1.1Å</td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1q0n\|1q0n]], [[3ili\|3ili]], [[3ilj\|3ilj]], [[3ill\|3ill]]</div></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PH2:2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE'>PH2</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0142, foIK, folK, JW0138 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_diphosphokinase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.3 2.7.6.3] </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=3ilo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ilo OCA], [https://pdbe.org/3ilo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ilo RCSB], [https://www.ebi.ac.uk/pdbsum/3ilo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ilo 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=3ilo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ilo OCA], [https://pdbe.org/3ilo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ilo RCSB], [https://www.ebi.ac.uk/pdbsum/3ilo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ilo ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/HPPK_ECOLI HPPK_ECOLI]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=3ilo 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=3ilo ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	BACKGROUND: Folates are essential for life. Unlike mammals, most microorganisms must synthesize folates de novo. 6-Hydroxymethyl-7, 8-dihydropterin pyrophosphokinase (HPPK) catalyzes pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP), the first reaction in the folate pathway, and therefore is an ideal target for developing novel antimicrobial agents. HPPK from Escherichia coli is a 158-residue thermostable protein that provides a convenient model system for mechanistic studies. Crystal structures have been reported for HPPK without bound ligand, containing an HP analog, and complexed with an HP analog, two Mg(2+) ions, and ATP. RESULTS: We present the 1.25 A crystal structure of HPPK in complex with HP, two Mg(2+) ions, and AMPCPP (an ATP analog that inhibits the enzymatic reaction). This structure demonstrates that the enzyme seals the active center where the reaction occurs. The comparison with unligated HPPK reveals dramatic conformational changes of three flexible loops and many sidechains. The coordination of Mg(2+) ions has been defined and the roles of 26 residues have been derived. CONCLUSIONS: HPPK-HP-MgAMPCPP mimics most closely the natural ternary complex of HPPK and provides details of protein-substrate interactions. The coordination of the two Mg(2+) ions helps create the correct geometry for the one-step reaction of pyrophosphoryl transfer, for which we suggest an in-line single displacement mechanism with some associative character in the transition state. The rigidity of the adenine-binding pocket and hydrogen bonds are responsible for adenosine specificity. The nonconserved residues that interact with the substrate might be responsible for the species-dependent properties of an isozyme.

	Catalytic center assembly of HPPK as revealed by the crystal structure of a ternary complex at 1.25 A resolution.,Blaszczyk J, Shi G, Yan H, Ji X Structure. 2000 Oct 15;8(10):1049-58. PMID:11080626<ref>PMID:11080626</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 3ilo" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[HPPK 3D structures\|HPPK 3D structures]]		*[[HPPK 3D structures\|HPPK 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: 2-~~amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase]]~~		[[Category: Escherichia coli K-12]]
	~~[[Category: Ecoli~~]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Blaszczyk, J]]		[[Category: Blaszczyk J]]
	[[Category: Ji, X]]		[[Category: Ji X]]
	[[Category: Li, Y]]		[[Category: Li Y]]
	[[Category: Yan, H]]		[[Category: Yan H]]
	~~[[Category: Alpha beta]]~~
	~~[[Category: Atp-binding]]~~
	~~[[Category: Folate biosynthesis]]~~
	~~[[Category: Kinase]]~~
	~~[[Category: Nucleotide-binding]]~~
	~~[[Category: Transferase~~]]

OCA at 12:12, 13 October 2021

2021-10-13T12:12:25Z

← Older revision		Revision as of 12:12, 13 October 2021
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	==Crystal structure of E. coli HPPK(D97A) in complex with MgAMPCPP and 6-hydroxymethyl-7,8-dihydropterin==		==Crystal structure of E. coli HPPK(D97A) in complex with MgAMPCPP and 6-hydroxymethyl-7,8-dihydropterin==
	<StructureSection load='3ilo' size='340' side='right' caption='[[3ilo]], [[Resolution\|resolution]] 1.10Å' scene=''>		<StructureSection load='3ilo' size='340' side='right'caption='[[3ilo]], [[Resolution\|resolution]] 1.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3ilo]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ILO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3ILO FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ilo]] is a 1 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=3ILO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ILO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PH2:2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE'>PH2</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PH2:2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE'>PH2</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q0n\|1q0n]], [[3ili\|3ili]], [[3ilj\|3ilj]], [[3ill\|3ill]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1q0n\|1q0n]], [[3ili\|3ili]], [[3ilj\|3ilj]], [[3ill\|3ill]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0142, foIK, folK, JW0138 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0142, foIK, folK, JW0138 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_diphosphokinase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.3 2.7.6.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_diphosphokinase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.3 2.7.6.3] </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=3ilo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ilo OCA], [~~http~~://pdbe.org/3ilo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ilo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ilo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ilo 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=3ilo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ilo OCA], [https://pdbe.org/3ilo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ilo RCSB], [https://www.ebi.ac.uk/pdbsum/3ilo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ilo ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</div>		</div>
	<div class="pdbe-citations 3ilo" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3ilo" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[HPPK 3D structures\|HPPK 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase]]		[[Category: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase]]
	[[Category: Ecoli]]		[[Category: Ecoli]]
			[[Category: Large Structures]]
	[[Category: Blaszczyk, J]]		[[Category: Blaszczyk, J]]
	[[Category: Ji, X]]		[[Category: Ji, X]]

OCA at 19:21, 24 January 2018

2018-01-24T19:21:45Z

← Older revision		Revision as of 19:21, 24 January 2018
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/il/3ilo_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/il/3ilo_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>

OCA at 08:08, 1 November 2017

2017-11-01T08:08:46Z

← Older revision		Revision as of 08:08, 1 November 2017
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	</div>		</div>
	<div class="pdbe-citations 3ilo" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3ilo" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[6-hydroxymethyl-7%2C8-dihydropterin pyrophosphokinase\|6-hydroxymethyl-7%2C8-dihydropterin pyrophosphokinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:06, 4 August 2016

2016-08-04T16:06:20Z

← Older revision		Revision as of 16:06, 4 August 2016
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	==Crystal structure of E. coli HPPK(D97A) in complex with MgAMPCPP and 6-hydroxymethyl-7,8-dihydropterin==		==Crystal structure of E. coli HPPK(D97A) in complex with MgAMPCPP and 6-hydroxymethyl-7,8-dihydropterin==
	<StructureSection load='3ilo' size='340' side='right' caption='[[3ilo]], [[Resolution\|resolution]] 1.10Å' scene=''>		<StructureSection load='3ilo' size='340' side='right' caption='[[3ilo]], [[Resolution\|resolution]] 1.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3ilo]] 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=3ILO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ILO FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ilo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ILO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ILO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PH2:2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE'>PH2</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PH2:2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE'>PH2</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q0n\|1q0n]], [[3ili\|3ili]], [[3ilj\|3ilj]], [[3ill\|3ill]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q0n\|1q0n]], [[3ili\|3ili]], [[3ilj\|3ilj]], [[3ill\|3ill]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0142, foIK, folK, JW0138 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~562 Escherichia coli~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0142, foIK, folK, JW0138 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_diphosphokinase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.3 2.7.6.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_diphosphokinase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.3 2.7.6.3] </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=3ilo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ilo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ilo RCSB], [http://www.ebi.ac.uk/pdbsum/3ilo 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=3ilo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ilo OCA], [http://pdbe.org/3ilo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ilo RCSB], [http://www.ebi.ac.uk/pdbsum/3ilo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ilo ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	<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=3ilo ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 28:
	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 3ilo" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	</StructureSection>		</StructureSection>
	[[Category: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase]]		[[Category: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase]]
	[[Category: ~~Escherichia coli~~]]		[[Category: Ecoli]]
	[[Category: Blaszczyk, J]]		[[Category: Blaszczyk, J]]
	[[Category: Ji, X]]		[[Category: Ji, X]]

OCA at 06:38, 18 December 2014

2014-12-18T06:38:03Z

← Older revision		Revision as of 06:38, 18 December 2014
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	~~{{STRUCTURE_3ilo\| PDB=3ilo \| SCENE= }}~~		==Crystal structure of E. coli HPPK(D97A) in complex with MgAMPCPP and 6-hydroxymethyl-7,8-dihydropterin==
	===Crystal structure of E. coli HPPK(D97A) in complex with MgAMPCPP and 6-hydroxymethyl-7,8-dihydropterin===		<StructureSection load='3ilo' size='340' side='right' caption='[[3ilo]], [[Resolution\|resolution]] 1.10Å' scene=''>
	~~{{ABSTRACT_PUBMED_11080626}}~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[3ilo]] 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=3ILO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ILO FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PH2:2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE'>PH2</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q0n\|1q0n]], [[3ili\|3ili]], [[3ilj\|3ilj]], [[3ill\|3ill]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b0142, foIK, folK, JW0138 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
			<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_diphosphokinase 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.6.3 2.7.6.3] </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=3ilo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ilo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ilo RCSB], [http://www.ebi.ac.uk/pdbsum/3ilo 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/il/3ilo_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 ==
			BACKGROUND: Folates are essential for life. Unlike mammals, most microorganisms must synthesize folates de novo. 6-Hydroxymethyl-7, 8-dihydropterin pyrophosphokinase (HPPK) catalyzes pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP), the first reaction in the folate pathway, and therefore is an ideal target for developing novel antimicrobial agents. HPPK from Escherichia coli is a 158-residue thermostable protein that provides a convenient model system for mechanistic studies. Crystal structures have been reported for HPPK without bound ligand, containing an HP analog, and complexed with an HP analog, two Mg(2+) ions, and ATP. RESULTS: We present the 1.25 A crystal structure of HPPK in complex with HP, two Mg(2+) ions, and AMPCPP (an ATP analog that inhibits the enzymatic reaction). This structure demonstrates that the enzyme seals the active center where the reaction occurs. The comparison with unligated HPPK reveals dramatic conformational changes of three flexible loops and many sidechains. The coordination of Mg(2+) ions has been defined and the roles of 26 residues have been derived. CONCLUSIONS: HPPK-HP-MgAMPCPP mimics most closely the natural ternary complex of HPPK and provides details of protein-substrate interactions. The coordination of the two Mg(2+) ions helps create the correct geometry for the one-step reaction of pyrophosphoryl transfer, for which we suggest an in-line single displacement mechanism with some associative character in the transition state. The rigidity of the adenine-binding pocket and hydrogen bonds are responsible for adenosine specificity. The nonconserved residues that interact with the substrate might be responsible for the species-dependent properties of an isozyme.

	~~==About this Structure==~~		Catalytic center assembly of HPPK as revealed by the crystal structure of a ternary complex at 1.25 A resolution.,Blaszczyk J, Shi G, Yan H, Ji X Structure. 2000 Oct 15;8(10):1049-58. PMID:11080626<ref>PMID:11080626</ref>
	~~[[3ilo]] 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=3ILO OCA].~~

	==~~Reference~~==		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	~~<ref group~~=~~"xtra">PMID:011080626~~</~~ref~~><~~references group="xtra"~~/>		</div>

			==See Also==
			*[[6-hydroxymethyl-7%2C8-dihydropterin pyrophosphokinase\|6-hydroxymethyl-7%2C8-dihydropterin pyrophosphokinase]]
			== References ==
			<references/>
			__TOC__
			</StructureSection>
	[[Category: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase]]		[[Category: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Blaszczyk, J.]]		[[Category: Blaszczyk, J]]
	[[Category: Ji, X.]]		[[Category: Ji, X]]
	[[Category: Li, Y.]]		[[Category: Li, Y]]
	[[Category: Yan, H.]]		[[Category: Yan, H]]
	[[Category: Alpha beta]]		[[Category: Alpha beta]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]

OCA: Protected "3ilo" [edit=sysop:move=sysop]

2013-03-13T11:10:13Z

Protected "3ilo" [edit=sysop:move=sysop]

← Older revision	Revision as of 11:10, 13 March 2013
(No difference)

OCA at 11:10, 13 March 2013

2013-03-13T11:10:07Z

← Older revision		Revision as of 11:10, 13 March 2013
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	~~{{Seed}}~~
	~~[[Image:3ilo.jpg\|left\|200px]]~~

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_3ilo", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_3ilo\| PDB=3ilo \| SCENE= }}		{{STRUCTURE_3ilo\| PDB=3ilo \| SCENE= }}

	===Crystal structure of E. coli HPPK(D97A) in complex with MgAMPCPP and 6-hydroxymethyl-7,8-dihydropterin===		===Crystal structure of E. coli HPPK(D97A) in complex with MgAMPCPP and 6-hydroxymethyl-7,8-dihydropterin===
			{{ABSTRACT_PUBMED_11080626}}

	==About this Structure==		==About this Structure==
	~~3ILO~~ 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=3ILO OCA].		[[3ilo]] 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=3ILO OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~11080626~~</ref><references group="xtra"/>		<ref group="xtra">PMID:011080626</ref><references group="xtra"/>
	[[Category: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase]]		[[Category: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
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	[[Category: Nucleotide-binding]]		[[Category: Nucleotide-binding]]
	[[Category: Transferase]]		[[Category: Transferase]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 11 23:54:39 2010''~~

OCA at 19:47, 11 August 2010

2010-08-11T19:47:22Z

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-'''Unreleased structure'''
+{{Seed}}
-The entry 3ilo is ON HOLD  until Paper Publication
+<!--
-Authors: Blaszczyk, J., Li, Y., Yan, H., Ji, X.
+===Crystal structure of E. coli HPPK(D97A) in complex with MgAMPCPP and 6-hydroxymethyl-7,8-dihydropterin===
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Sep  3 15:21:33 2009''
+==About this Structure==

OCA at 12:21, 3 September 2009

2009-09-03T12:21:33Z

← Older revision		Revision as of 12:21, 3 September 2009
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 3ilo is ON HOLD		The entry 3ilo is ON HOLD until Paper Publication

	Authors: Blaszczyk, J., Li, Y., Yan, H., Ji, X.		Authors: Blaszczyk, J., Li, Y., Yan, H., Ji, X.
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	Description: Crystal structure of E. coli HPPK(D97A) in complex with MgAMPCPP and 6-hydroxymethyl-7,8-dihydropterin		Description: Crystal structure of E. coli HPPK(D97A) in complex with MgAMPCPP and 6-hydroxymethyl-7,8-dihydropterin

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Aug 19 12~~:37:07 2009''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Sep 3 15:21:33 2009''