1c1d - Revision history

OCA at 06:40, 7 February 2024

OCA — Wed, 07 Feb 2024 06:40:19 GMT

←Older revision		Revision as of 06:40, 7 February 2024
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	<StructureSection load='1c1d' size='340' side='right'caption='[[1c1d]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='1c1d' size='340' side='right'caption='[[1c1d]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1c1d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Rhoso Rhoso~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1C1D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1c1d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_sp. Rhodococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1C1D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=PHE:PHENYLALANINE'>PHE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.25Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1c1x\|1c1x]]</div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=PHE:PHENYLALANINE'>PHE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=1c1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c1d OCA], [https://pdbe.org/1c1d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1c1d RCSB], [https://www.ebi.ac.uk/pdbsum/1c1d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1c1d 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=1c1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c1d OCA], [https://pdbe.org/1c1d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1c1d RCSB], [https://www.ebi.ac.uk/pdbsum/1c1d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1c1d ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DHPH_RHOSO DHPH_RHOSO] Catalyzes the reversible NAD(+)-dependent oxidative deamination of L-phenylalanine to phenylpyruvate.<ref>PMID:10924111</ref> <ref>PMID:8206922</ref>
	== 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=1c1d 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=1c1d ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Phenylalanine dehydrogenase catalyzes the reversible, pyridine nucleotide-dependent oxidative deamination of L-phenylalanine to form phenylpyruvate and ammonia. We have characterized the steady-state kinetic behavior of the enzyme from Rhodococcus sp. M4 and determined the X-ray crystal structures of the recombinant enzyme in the complexes, E.NADH.L-phenylalanine and E.NAD(+). L-3-phenyllactate, to 1.25 and 1.4 A resolution, respectively. Initial velocity, product inhibition, and dead-end inhibition studies indicate the kinetic mechanism is ordered, with NAD(+) binding prior to phenylalanine and the products' being released in the order of ammonia, phenylpyruvate, and NADH. The enzyme shows no activity with NADPH or other 2'-phosphorylated pyridine nucleotides but has broad activity with NADH analogues. Our initial structural analyses of the E.NAD(+).phenylpyruvate and E.NAD(+). 3-phenylpropionate complexes established that Lys78 and Asp118 function as the catalytic residues in the active site [Vanhooke et al. (1999) Biochemistry 38, 2326-2339]. We have studied the ionization behavior of these residues in steady-state turnover and use these findings in conjunction with the structural data described both here and in our first report to modify our previously proposed mechanism for the enzymatic reaction. The structural characterizations also illuminate the mechanism of the redox specificity that precludes alpha-amino acid dehydrogenases from functioning as alpha-hydroxy acid dehydrogenases.
-
-	Rhodococcus L-phenylalanine dehydrogenase: kinetics, mechanism, and structural basis for catalytic specificity.,Brunhuber NM, Thoden JB, Blanchard JS, Vanhooke JL Biochemistry. 2000 Aug 8;39(31):9174-87. PMID:10924111<ref>PMID:10924111</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1c1d" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 32:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Rhoso~~]]	+	[[Category: Rhodococcus sp]]
-	[[Category: Thoden~~, J B~~]]	+	[[Category: Thoden JB]]
-	[[Category: Vanhooke~~, J L]]~~	+	[[Category: Vanhooke JL]]
-	~~[[Category: Amino acid dehydrogenase]]~~	+
-	~~[[Category: Oxidative deamination mechanism]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 09:49, 15 September 2021

OCA — Wed, 15 Sep 2021 09:49:34 GMT

←Older revision		Revision as of 09:49, 15 September 2021
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	<StructureSection load='1c1d' size='340' side='right'caption='[[1c1d]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='1c1d' size='340' side='right'caption='[[1c1d]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1c1d]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Rhoso Rhoso]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C1D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1C1D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1c1d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhoso Rhoso]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1C1D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=PHE:PHENYLALANINE'>PHE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=PHE:PHENYLALANINE'>PHE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1c1x\|1c1x]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1c1x\|1c1x]]</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=1c1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c1d OCA], [~~http~~://pdbe.org/1c1d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1c1d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1c1d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1c1d 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=1c1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c1d OCA], [https://pdbe.org/1c1d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1c1d RCSB], [https://www.ebi.ac.uk/pdbsum/1c1d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1c1d ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 15:28, 11 December 2019

OCA — Wed, 11 Dec 2019 15:28:45 GMT

←Older revision		Revision as of 15:28, 11 December 2019
Line 3:		Line 3:
	<StructureSection load='1c1d' size='340' side='right'caption='[[1c1d]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='1c1d' size='340' side='right'caption='[[1c1d]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1c1d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1C1D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1c1d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhoso Rhoso]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1C1D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=PHE:PHENYLALANINE'>PHE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=PHE:PHENYLALANINE'>PHE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1c1x\|1c1x]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1c1x\|1c1x]]</td></tr>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Rhoso]]
	[[Category: Thoden, J B]]		[[Category: Thoden, J B]]
	[[Category: Vanhooke, J L]]		[[Category: Vanhooke, J L]]

OCA at 07:37, 29 May 2019

OCA — Wed, 29 May 2019 07:37:40 GMT

←Older revision		Revision as of 07:37, 29 May 2019
Line 1:		Line 1:

	==L-PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NADH AND L-PHENYLALANINE==		==L-PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NADH AND L-PHENYLALANINE==
-	<StructureSection load='1c1d' size='340' side='right' caption='[[1c1d]], [[Resolution\|resolution]] 1.25Å' scene=''>	+	<StructureSection load='1c1d' size='340' side='right'caption='[[1c1d]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1c1d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1C1D FirstGlance]. <br>		<table><tr><td colspan='2'>[[1c1d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1C1D FirstGlance]. <br>
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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/c1/1c1d_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c1/1c1d_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 31:		Line 31:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Thoden, J B]]		[[Category: Thoden, J B]]
	[[Category: Vanhooke, J L]]		[[Category: Vanhooke, J L]]

OCA at 11:19, 24 August 2017

OCA — Thu, 24 Aug 2017 11:19:10 GMT

←Older revision		Revision as of 11:19, 24 August 2017
Line 1:		Line 1:
		+
	==L-PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NADH AND L-PHENYLALANINE==		==L-PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NADH AND L-PHENYLALANINE==
	<StructureSection load='1c1d' size='340' side='right' caption='[[1c1d]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='1c1d' size='340' side='right' caption='[[1c1d]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1c1d]] is a 2 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Rhoso Rhoso]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1C1D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1c1d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1C1D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=PHE:PHENYLALANINE'>PHE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=PHE:PHENYLALANINE'>PHE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1c1x\|1c1x]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1c1x\|1c1x]]</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=1c1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c1d OCA], [http://pdbe.org/1c1d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1c1d RCSB], [http://www.ebi.ac.uk/pdbsum/1c1d 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=1c1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c1d OCA], [http://pdbe.org/1c1d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1c1d RCSB], [http://www.ebi.ac.uk/pdbsum/1c1d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1c1d ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 15:		Line 16:
	<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=1c1d ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 30:		Line 31:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Rhoso]]
	[[Category: Thoden, J B]]		[[Category: Thoden, J B]]
	[[Category: Vanhooke, J L]]		[[Category: Vanhooke, J L]]

OCA at 01:53, 12 September 2015

OCA — Sat, 12 Sep 2015 01:53:08 GMT

←Older revision		Revision as of 01:53, 12 September 2015
Line 2:		Line 2:
	<StructureSection load='1c1d' size='340' side='right' caption='[[1c1d]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='1c1d' size='340' side='right' caption='[[1c1d]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1c1d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rhodococcus_sp. Rhodococcus sp.~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1C1D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1c1d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhoso Rhoso]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1C1D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=PHE:PHENYLALANINE'>PHE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=PHE:PHENYLALANINE'>PHE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1c1x\|1c1x]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1c1x\|1c1x]]</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=1c1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c1d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1c1d RCSB], [http://www.ebi.ac.uk/pdbsum/1c1d 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=1c1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c1d OCA], [http://pdbe.org/1c1d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1c1d RCSB], [http://www.ebi.ac.uk/pdbsum/1c1d PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 25:		Line 25:
	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 1c1d" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Rhodococcus sp~~]]	+	[[Category: Rhoso]]
	[[Category: Thoden, J B]]		[[Category: Thoden, J B]]
	[[Category: Vanhooke, J L]]		[[Category: Vanhooke, J L]]

OCA at 11:15, 22 December 2014

OCA — Mon, 22 Dec 2014 11:15:37 GMT

←Older revision		Revision as of 11:15, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1c1d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodococcus_sp. Rhodococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1C1D FirstGlance]. <br>		<table><tr><td colspan='2'>[[1c1d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodococcus_sp. Rhodococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1C1D FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=PHE:PHENYLALANINE'>PHE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=PHE:PHENYLALANINE'>PHE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1c1x\|1c1x]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1c1x\|1c1x]]</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=1c1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c1d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1c1d RCSB], [http://www.ebi.ac.uk/pdbsum/1c1d 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=1c1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c1d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1c1d RCSB], [http://www.ebi.ac.uk/pdbsum/1c1d 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 29:		Line 29:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Rhodococcus sp.]]	+	[[Category: Rhodococcus sp]]
-	[[Category: Thoden, J B.]]	+	[[Category: Thoden, J B]]
-	[[Category: Vanhooke, J L.]]	+	[[Category: Vanhooke, J L]]
	[[Category: Amino acid dehydrogenase]]		[[Category: Amino acid dehydrogenase]]
	[[Category: Oxidative deamination mechanism]]		[[Category: Oxidative deamination mechanism]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 05:36, 3 October 2014

OCA — Fri, 03 Oct 2014 05:36:43 GMT

←Older revision		Revision as of 05:36, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1c1d\| PDB=1c1d \| SCENE= }}~~	+	==L-PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NADH AND L-PHENYLALANINE==
-	===L-PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NADH AND L-PHENYLALANINE===	+	<StructureSection load='1c1d' size='340' side='right' caption='[[1c1d]], [[Resolution\|resolution]] 1.25Å' scene=''>
-	~~{{ABSTRACT_PUBMED_10924111}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1c1d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodococcus_sp. Rhodococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1C1D FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=PHE:PHENYLALANINE'>PHE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1c1x\|1c1x]]</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=1c1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c1d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1c1d RCSB], [http://www.ebi.ac.uk/pdbsum/1c1d 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/c1/1c1d_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 ==
		+	Phenylalanine dehydrogenase catalyzes the reversible, pyridine nucleotide-dependent oxidative deamination of L-phenylalanine to form phenylpyruvate and ammonia. We have characterized the steady-state kinetic behavior of the enzyme from Rhodococcus sp. M4 and determined the X-ray crystal structures of the recombinant enzyme in the complexes, E.NADH.L-phenylalanine and E.NAD(+). L-3-phenyllactate, to 1.25 and 1.4 A resolution, respectively. Initial velocity, product inhibition, and dead-end inhibition studies indicate the kinetic mechanism is ordered, with NAD(+) binding prior to phenylalanine and the products' being released in the order of ammonia, phenylpyruvate, and NADH. The enzyme shows no activity with NADPH or other 2'-phosphorylated pyridine nucleotides but has broad activity with NADH analogues. Our initial structural analyses of the E.NAD(+).phenylpyruvate and E.NAD(+). 3-phenylpropionate complexes established that Lys78 and Asp118 function as the catalytic residues in the active site [Vanhooke et al. (1999) Biochemistry 38, 2326-2339]. We have studied the ionization behavior of these residues in steady-state turnover and use these findings in conjunction with the structural data described both here and in our first report to modify our previously proposed mechanism for the enzymatic reaction. The structural characterizations also illuminate the mechanism of the redox specificity that precludes alpha-amino acid dehydrogenases from functioning as alpha-hydroxy acid dehydrogenases.

-	~~==About this Structure==~~	+	Rhodococcus L-phenylalanine dehydrogenase: kinetics, mechanism, and structural basis for catalytic specificity.,Brunhuber NM, Thoden JB, Blanchard JS, Vanhooke JL Biochemistry. 2000 Aug 8;39(31):9174-87. PMID:10924111<ref>PMID:10924111</ref>
-	~~[[1c1d]] is a 2 chain structure with sequence from [http~~:~~//en~~.~~wikipedia~~.~~org/wiki/Rhodococcus_sp. Rhodococcus sp.]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1C1D OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:010924111</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Rhodococcus sp.]]		[[Category: Rhodococcus sp.]]
	[[Category: Thoden, J B.]]		[[Category: Thoden, J B.]]

OCA at 08:35, 30 October 2013

OCA — Wed, 30 Oct 2013 08:35:23 GMT

←Older revision		Revision as of 08:35, 30 October 2013
Line 1:		Line 1:
-	[[Image:1c1d.png\|left\|200px]]
-
	{{STRUCTURE_1c1d\| PDB=1c1d \| SCENE= }}		{{STRUCTURE_1c1d\| PDB=1c1d \| SCENE= }}
-
	===L-PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NADH AND L-PHENYLALANINE===		===L-PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NADH AND L-PHENYLALANINE===
-
	{{ABSTRACT_PUBMED_10924111}}		{{ABSTRACT_PUBMED_10924111}}

Line 11:		Line 7:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:010924111</ref><references group="xtra"/>	+	<ref group="xtra">PMID:010924111</ref><references group="xtra"/><references/>
	[[Category: Rhodococcus sp.]]		[[Category: Rhodococcus sp.]]
	[[Category: Thoden, J B.]]		[[Category: Thoden, J B.]]

OCA: Protected "1c1d" [edit=sysop:move=sysop]

OCA — Sun, 21 Oct 2012 20:48:03 GMT

Protected "1c1d" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:48, 21 October 2012