4d9n - Revision history

OCA at 13:42, 8 November 2023

OCA — Wed, 08 Nov 2023 13:42:37 GMT

←Older revision		Revision as of 13:42, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4d9n]] is a 2 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=4D9N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D9N FirstGlance]. <br>		<table><tr><td colspan='2'>[[4d9n]] is a 2 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=4D9N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D9N FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DSN:D-SERINE'>DSN</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.5Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DSN:D-SERINE'>DSN</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</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=4d9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d9n OCA], [https://pdbe.org/4d9n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d9n RCSB], [https://www.ebi.ac.uk/pdbsum/4d9n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d9n 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=4d9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d9n OCA], [https://pdbe.org/4d9n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d9n RCSB], [https://www.ebi.ac.uk/pdbsum/4d9n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d9n ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DPAL_ECOLI DPAL_ECOLI]] Catalyzes the alpha,beta-elimination reaction of both L- and D-alpha,beta-diaminopropionate (DAP) to form pyruvate and ammonia. In vitro the D-isomer of serine is degraded to pyruvate, though very poorly; other amino acids (L-serine, D- and L-threonine, D- and L-beta-Cl-alanine) are not substrates. In vivo allows poor growth on L-DAP or a DL-DAP mixture but not on D-DAP alone, this may be due to a poor promoter. DL-DAP is toxic in the absence of this enzyme, it may inhibit enzymes involved in the synthesis of pyruvate and aspartate, as well as amino acids derived from them.<ref>PMID:12596860</ref> <ref>PMID:12821154</ref> <ref>PMID:22904288</ref> <ref>PMID:22505717</ref>	+	[https://www.uniprot.org/uniprot/DPAL_ECOLI DPAL_ECOLI] Catalyzes the alpha,beta-elimination reaction of both L- and D-alpha,beta-diaminopropionate (DAP) to form pyruvate and ammonia. In vitro the D-isomer of serine is degraded to pyruvate, though very poorly; other amino acids (L-serine, D- and L-threonine, D- and L-beta-Cl-alanine) are not substrates. In vivo allows poor growth on L-DAP or a DL-DAP mixture but not on D-DAP alone, this may be due to a poor promoter. DL-DAP is toxic in the absence of this enzyme, it may inhibit enzymes involved in the synthesis of pyruvate and aspartate, as well as amino acids derived from them.<ref>PMID:12596860</ref> <ref>PMID:12821154</ref> <ref>PMID:22904288</ref> <ref>PMID:22505717</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 08:07, 21 September 2022

OCA — Wed, 21 Sep 2022 08:07:53 GMT

←Older revision		Revision as of 08:07, 21 September 2022
Line 3:		Line 3:
	<StructureSection load='4d9n' size='340' side='right'caption='[[4d9n]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='4d9n' size='340' side='right'caption='[[4d9n]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4d9n]] is a 2 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=4D9N OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4D9N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4d9n]] is a 2 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=4D9N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D9N FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DSN:D-SERINE'>DSN</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DSN:D-SERINE'>DSN</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</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=4d9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d9n OCA], [https://pdbe.org/4d9n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d9n RCSB], [https://www.ebi.ac.uk/pdbsum/4d9n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d9n ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d9g\|4d9g]], [[4d9i\|4d9i]], [[4d9k\|4d9k]], [[4d9m\|4d9m]]</td></tr>~~	+
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2871, JW2839, ygeX ([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/Diaminopropionate_ammonia-lyase Diaminopropionate ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.15 4.3.1.15] </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=4d9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d9n OCA], [~~http~~://pdbe.org/4d9n PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4d9n RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4d9n PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4d9n ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DPAL_ECOLI DPAL_ECOLI]] Catalyzes the alpha,beta-elimination reaction of both L- and D-alpha,beta-diaminopropionate (DAP) to form pyruvate and ammonia. In vitro the D-isomer of serine is degraded to pyruvate, though very poorly; other amino acids (L-serine, D- and L-threonine, D- and L-beta-Cl-alanine) are not substrates. In vivo allows poor growth on L-DAP or a DL-DAP mixture but not on D-DAP alone, this may be due to a poor promoter. DL-DAP is toxic in the absence of this enzyme, it may inhibit enzymes involved in the synthesis of pyruvate and aspartate, as well as amino acids derived from them.<ref>PMID:12596860</ref> <ref>PMID:12821154</ref> <ref>PMID:22904288</ref> <ref>PMID:22505717</ref>	+	[[https://www.uniprot.org/uniprot/DPAL_ECOLI DPAL_ECOLI]] Catalyzes the alpha,beta-elimination reaction of both L- and D-alpha,beta-diaminopropionate (DAP) to form pyruvate and ammonia. In vitro the D-isomer of serine is degraded to pyruvate, though very poorly; other amino acids (L-serine, D- and L-threonine, D- and L-beta-Cl-alanine) are not substrates. In vivo allows poor growth on L-DAP or a DL-DAP mixture but not on D-DAP alone, this may be due to a poor promoter. DL-DAP is toxic in the absence of this enzyme, it may inhibit enzymes involved in the synthesis of pyruvate and aspartate, as well as amino acids derived from them.<ref>PMID:12596860</ref> <ref>PMID:12821154</ref> <ref>PMID:22904288</ref> <ref>PMID:22505717</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Diaminopropionate ammonia~~-~~lyase]]~~	+	[[Category: Escherichia coli K-12]]
-	~~[[Category: Ecoli~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bharath~~, S R~~]]	+	[[Category: Bharath SR]]
-	[[Category: Bisht, S]]	+	[[Category: Bisht S]]
-	[[Category: Murthy~~, M R.N~~]]	+	[[Category: Murthy MRN]]
-	[[Category: Rajaram, V]]	+	[[Category: Rajaram V]]
-	~~[[Category: Fold type ii plp-dependent enzyme]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Tryptophan synthase beta subunit-like plp-dependent enzymes superfamily~~]]	+

OCA at 08:15, 27 March 2019

OCA — Wed, 27 Mar 2019 08:15:31 GMT

←Older revision		Revision as of 08:15, 27 March 2019
Line 1:		Line 1:

	==Crystal structure of Diaminopropionate ammonia lyase from Escherichia coli in complex with D-serine==		==Crystal structure of Diaminopropionate ammonia lyase from Escherichia coli in complex with D-serine==
-	<StructureSection load='4d9n' size='340' side='right' caption='[[4d9n]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='4d9n' size='340' side='right'caption='[[4d9n]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4d9n]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D9N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D9N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4d9n]] is a 2 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=4D9N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D9N FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DSN:D-SERINE'>DSN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DSN:D-SERINE'>DSN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d9g\|4d9g]], [[4d9i\|4d9i]], [[4d9k\|4d9k]], [[4d9m\|4d9m]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d9g\|4d9g]], [[4d9i\|4d9i]], [[4d9k\|4d9k]], [[4d9m\|4d9m]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2871, JW2839, ygeX ([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/Diaminopropionate_ammonia-lyase Diaminopropionate ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.15 4.3.1.15] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopropionate_ammonia-lyase Diaminopropionate ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.15 4.3.1.15] </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=4d9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d9n OCA], [http://pdbe.org/4d9n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d9n RCSB], [http://www.ebi.ac.uk/pdbsum/4d9n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4d9n ProSAT]</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=4d9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d9n OCA], [http://pdbe.org/4d9n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d9n RCSB], [http://www.ebi.ac.uk/pdbsum/4d9n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4d9n ProSAT]</span></td></tr>
Line 26:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Diaminopropionate ammonia-lyase]]		[[Category: Diaminopropionate ammonia-lyase]]
		+	[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Bharath, S R]]		[[Category: Bharath, S R]]
	[[Category: Bisht, S]]		[[Category: Bisht, S]]

OCA at 06:15, 10 May 2017

OCA — Wed, 10 May 2017 06:15:51 GMT

←Older revision		Revision as of 06:15, 10 May 2017
Line 3:		Line 3:
	<StructureSection load='4d9n' size='340' side='right' caption='[[4d9n]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='4d9n' size='340' side='right' caption='[[4d9n]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4d9n]] is a 2 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=4D9N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D9N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4d9n]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D9N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D9N FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DSN:D-SERINE'>DSN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DSN:D-SERINE'>DSN</scene></td></tr>
-	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~IT1~~:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>~~IT1~~</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d9g\|4d9g]], [[4d9i\|4d9i]], [[4d9k\|4d9k]], [[4d9m\|4d9m]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d9g\|4d9g]], [[4d9i\|4d9i]], [[4d9k\|4d9k]], [[4d9m\|4d9m]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2871, JW2839, ygeX ([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/Diaminopropionate_ammonia-lyase Diaminopropionate ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.15 4.3.1.15] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopropionate_ammonia-lyase Diaminopropionate ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.15 4.3.1.15] </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=4d9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d9n OCA], [http://pdbe.org/4d9n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d9n RCSB], [http://www.ebi.ac.uk/pdbsum/4d9n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4d9n ProSAT]</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=4d9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d9n OCA], [http://pdbe.org/4d9n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d9n RCSB], [http://www.ebi.ac.uk/pdbsum/4d9n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4d9n ProSAT]</span></td></tr>
Line 27:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Diaminopropionate ammonia-lyase]]		[[Category: Diaminopropionate ammonia-lyase]]
-	[[Category: Ecoli]]
	[[Category: Bharath, S R]]		[[Category: Bharath, S R]]
	[[Category: Bisht, S]]		[[Category: Bisht, S]]

OCA at 15:22, 5 August 2016

OCA — Fri, 05 Aug 2016 15:22:58 GMT

←Older revision		Revision as of 15:22, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Diaminopropionate ammonia lyase from Escherichia coli in complex with D-serine==		==Crystal structure of Diaminopropionate ammonia lyase from Escherichia coli in complex with D-serine==
	<StructureSection load='4d9n' size='340' side='right' caption='[[4d9n]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='4d9n' size='340' side='right' caption='[[4d9n]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4d9n]] is a 2 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=4D9N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D9N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4d9n]] is a 2 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=4D9N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D9N FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DSN:D-SERINE'>DSN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DSN:D-SERINE'>DSN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=IT1:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>IT1</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=IT1:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>IT1</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d9g\|4d9g]], [[4d9i\|4d9i]], [[4d9k\|4d9k]], [[4d9m\|4d9m]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d9g\|4d9g]], [[4d9i\|4d9i]], [[4d9k\|4d9k]], [[4d9m\|4d9m]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2871, JW2839, ygeX ([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">b2871, JW2839, ygeX ([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/Diaminopropionate_ammonia-lyase Diaminopropionate ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.15 4.3.1.15] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopropionate_ammonia-lyase Diaminopropionate ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.15 4.3.1.15] </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=4d9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d9n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4d9n RCSB], [http://www.ebi.ac.uk/pdbsum/4d9n 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=4d9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d9n OCA], [http://pdbe.org/4d9n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d9n RCSB], [http://www.ebi.ac.uk/pdbsum/4d9n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4d9n ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 21:
	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 4d9n" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Diaminopropionate ammonia-lyase]]		[[Category: Diaminopropionate ammonia-lyase]]
-	[[Category: ~~Escherichia coli~~]]	+	[[Category: Ecoli]]
	[[Category: Bharath, S R]]		[[Category: Bharath, S R]]
	[[Category: Bisht, S]]		[[Category: Bisht, S]]

OCA at 03:34, 25 December 2014

OCA — Thu, 25 Dec 2014 03:34:55 GMT

←Older revision		Revision as of 03:34, 25 December 2014
Line 1:		Line 1:
-	[[~~Image:~~4d9n.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of Diaminopropionate ammonia lyase from Escherichia coli in complex with D-serine==
		+	<StructureSection load='4d9n' size='340' side='right' caption='[[4d9n]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4d9n]] is a 2 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=4D9N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D9N FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DSN:D-SERINE'>DSN</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=IT1:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>IT1</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d9g\|4d9g]], [[4d9i\|4d9i]], [[4d9k\|4d9k]], [[4d9m\|4d9m]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b2871, JW2839, ygeX ([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/Diaminopropionate_ammonia-lyase Diaminopropionate ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.15 4.3.1.15] </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=4d9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d9n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4d9n RCSB], [http://www.ebi.ac.uk/pdbsum/4d9n PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPAL_ECOLI DPAL_ECOLI]] Catalyzes the alpha,beta-elimination reaction of both L- and D-alpha,beta-diaminopropionate (DAP) to form pyruvate and ammonia. In vitro the D-isomer of serine is degraded to pyruvate, though very poorly; other amino acids (L-serine, D- and L-threonine, D- and L-beta-Cl-alanine) are not substrates. In vivo allows poor growth on L-DAP or a DL-DAP mixture but not on D-DAP alone, this may be due to a poor promoter. DL-DAP is toxic in the absence of this enzyme, it may inhibit enzymes involved in the synthesis of pyruvate and aspartate, as well as amino acids derived from them.<ref>PMID:12596860</ref> <ref>PMID:12821154</ref> <ref>PMID:22904288</ref> <ref>PMID:22505717</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pyridoxal 5'-phosphate (PLP)-dependent enzymes utilize the unique chemistry of a pyridine ring to carry out diverse reactions involving amino acids. Diaminopropionate (DAP) ammonia-lyase (DAPAL) is a prokaryotic PLP-dependent enzyme that catalyzes the degradation of d- and l-forms of DAP to pyruvate and ammonia. Here, we report the first crystal structure of DAPAL from Escherichia coli (EcDAPAL) in tetragonal and monoclinic forms at 2.0 and 2.2 A resolutions, respectively. Structures of EcDAPAL soaked with substrates were also determined. EcDAPAL has a typical fold type II PLP-dependent enzyme topology consisting of a large and a small domain with the active site at the interface of the two domains. The enzyme is a homodimer with a unique biological interface not observed earlier. Structure of the enzyme in the tetragonal form had PLP bound at the active site, whereas the monoclinic structure was in the apo-form. Analysis of the apo and holo structures revealed that the region around the active site undergoes transition from a disordered to ordered state and assumes a conformation suitable for catalysis only upon PLP binding. A novel disulfide was found to occur near a channel that is likely to regulate entry of ligands to the active site. EcDAPAL soaked with dl-DAP revealed density at the active site appropriate for the reaction intermediate aminoacrylate, which is consistent with the observation that EcDAPAL has low activity under crystallization conditions. Based on the analysis of the structure and results of site-directed mutagenesis, a two-base mechanism of catalysis involving Asp(120) and Lys(77) is suggested.

-	~~{{STRUCTURE_4d9n\| PDB=4d9n \| SCENE= }}~~	+	Crystal Structure of Escherichia coli Diaminopropionate Ammonia-lyase Reveals Mechanism of Enzyme Activation and Catalysis.,Bisht S, Rajaram V, Bharath SR, Kalyani JN, Khan F, Rao AN, Savithri HS, Murthy MR J Biol Chem. 2012 Jun 8;287(24):20369-81. Epub 2012 Apr 13. PMID:22505717<ref>PMID:22505717</ref>

-	~~===Crystal structure~~ of ~~Diaminopropionate ammonia lyase from Escherichia coli in complex with D-serine===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_22505717}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[4d9n]] is a 2 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=4D9N OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022505717<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Diaminopropionate ammonia-lyase]]		[[Category: Diaminopropionate ammonia-lyase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Bharath, S R.]]	+	[[Category: Bharath, S R]]
-	[[Category: Bisht, S.]]	+	[[Category: Bisht, S]]
-	[[Category: Murthy, M R.N.]]	+	[[Category: Murthy, M R.N]]
-	[[Category: Rajaram, V.]]	+	[[Category: Rajaram, V]]
	[[Category: Fold type ii plp-dependent enzyme]]		[[Category: Fold type ii plp-dependent enzyme]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Tryptophan synthase beta subunit-like plp-dependent enzymes superfamily]]		[[Category: Tryptophan synthase beta subunit-like plp-dependent enzymes superfamily]]

OCA at 07:28, 11 July 2012

OCA — Wed, 11 Jul 2012 07:28:11 GMT

←Older revision		Revision as of 07:28, 11 July 2012
Line 1:		Line 1:
-	[[Image:4d9n.~~jpg~~\|left\|200px]]	+	[[Image:4d9n.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_4d9n", 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_4d9n\| PDB=4d9n \| SCENE= }}		{{STRUCTURE_4d9n\| PDB=4d9n \| SCENE= }}

	===Crystal structure of Diaminopropionate ammonia lyase from Escherichia coli in complex with D-serine===		===Crystal structure of Diaminopropionate ammonia lyase from Escherichia coli in complex with D-serine===

		+	{{ABSTRACT_PUBMED_22505717}}

	==About this Structure==		==About this Structure==
	[[4d9n]] is a 2 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=4D9N OCA].		[[4d9n]] is a 2 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=4D9N OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022505717</ref><references group="xtra"/>
	[[Category: Diaminopropionate ammonia-lyase]]		[[Category: Diaminopropionate ammonia-lyase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

OCA at 09:26, 25 April 2012

OCA — Wed, 25 Apr 2012 09:26:16 GMT

←Older revision		Revision as of 09:26, 25 April 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4d9n.jpg\|left\|200px]]

-	The ~~entry 4d9n~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_4d9n", 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_4d9n\| PDB=4d9n \| SCENE= }}

-	~~Authors: Bisht, S., Rajaram, V., Bharath, S.R., Murthy, M.R.N.~~	+	===Crystal structure of Diaminopropionate ammonia lyase from Escherichia coli in complex with D-serine===

-	~~Description: Crystal~~ structure of Diaminopropionate ammonia lyase ~~from~~ Escherichia coli ~~in complex with D~~-~~serine~~	+
		+	==About this Structure==
		+	[[4d9n]] is a 2 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=4D9N OCA].
		+	[[Category: Diaminopropionate ammonia-lyase]]
		+	[[Category: Escherichia coli]]
		+	[[Category: Bharath, S R.]]
		+	[[Category: Bisht, S.]]
		+	[[Category: Murthy, M R.N.]]
		+	[[Category: Rajaram, V.]]
		+	[[Category: Fold type ii plp-dependent enzyme]]
		+	[[Category: Lyase]]
		+	[[Category: Tryptophan synthase beta subunit-like plp-dependent enzymes superfamily]]

OCA at 06:09, 8 February 2012

OCA — Wed, 08 Feb 2012 06:09:38 GMT

←Older revision		Revision as of 06:09, 8 February 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4d9n is ON HOLD	+	The entry 4d9n is ON HOLD until Paper Publication

	Authors: Bisht, S., Rajaram, V., Bharath, S.R., Murthy, M.R.N.		Authors: Bisht, S., Rajaram, V., Bharath, S.R., Murthy, M.R.N.

	Description: Crystal structure of Diaminopropionate ammonia lyase from Escherichia coli in complex with D-serine		Description: Crystal structure of Diaminopropionate ammonia lyase from Escherichia coli in complex with D-serine

OCA at 06:58, 1 February 2012

OCA — Wed, 01 Feb 2012 06:58:54 GMT

←Older revision		Revision as of 06:58, 1 February 2012
Line 3:		Line 3:
	The entry 4d9n is ON HOLD		The entry 4d9n is ON HOLD

-	Authors: Bisht, S., V, ~~Rajaram~~, S.R~~, Bharath~~, Murthy, M.R.N.	+	Authors: Bisht, S., Rajaram, V., Bharath, S.R., Murthy, M.R.N.

	Description: Crystal structure of Diaminopropionate ammonia lyase from Escherichia coli in complex with D-serine		Description: Crystal structure of Diaminopropionate ammonia lyase from Escherichia coli in complex with D-serine