4e4j - Revision history

OCA at 11:01, 1 March 2024

2024-03-01T11:01:42Z

← Older revision		Revision as of 11:01, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e4j]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Malacoplasma_penetrans_HF-2 Malacoplasma penetrans HF-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E4J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E4J FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e4j]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Malacoplasma_penetrans_HF-2 Malacoplasma penetrans HF-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E4J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E4J FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></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]] 2.3Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></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=4e4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e4j OCA], [https://pdbe.org/4e4j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e4j RCSB], [https://www.ebi.ac.uk/pdbsum/4e4j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e4j 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=4e4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e4j OCA], [https://pdbe.org/4e4j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e4j RCSB], [https://www.ebi.ac.uk/pdbsum/4e4j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e4j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/Q8EVF6_MALP2 Q8EVF6_MALP2]]		[https://www.uniprot.org/uniprot/Q8EVF6_MALP2 Q8EVF6_MALP2]
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	The metabolism of arginine towards ATP synthesis has been considered a major source of energy for microorganisms such as Mycoplasma penetrans in anaerobic conditions. Additionally, this pathway has also been implicated in pathogenic and virulence mechanism of certain microorganisms, i.e. protection from acidic stress during infection. In this work we present the crystal structures of the three enzymes composing the gene cluster of the arginine deiminase pathway from M. penetrans: arginine deiminase (ADI), ornithine carbamoyltransferase (OTC) and carbamate kinase (CK). The arginine deiminase (ADI) structure has been refined to 2.3 A resolution in its apo-form, displaying an "open" conformation of the active site of the enzyme in comparison to previous complex structures with substrate intermediates. The active site pocket of ADI is empty, with some of the catalytic and binding residues far from their active positions, suggesting major conformational changes upon substrate binding. Ornithine carbamoyltransferase (OTC) has been refined in two crystal forms at 2.5 A and 2.6 A resolution, respectively, both displaying an identical dodecameric structure with a 23-point symmetry. The dodecameric structure of OTC represents the highest level of organization in this protein family and in M.penetrans it is constituted by a novel interface between the four catalytic homotrimers. Carbamate kinase (CK) has been refined to 2.5 A resolution and its structure is characterized by the presence of two ion sulfates in the active site, one in the carbamoyl phosphate binding site and the other in the beta-phosphate ADP binding pocket of the enzyme. The CK structure also shows variations in some of the elements that regulate the catalytic activity of the enzyme. The relatively low number of metabolic pathways and the relevance in human pathogenesis of Mycoplasma penetrans places the arginine deiminase pathway enzymes as potential targets to design specific inhibitors against this human parasite.

	Structural Characterization of the Enzymes Composing the Arginine Deiminase Pathway in Mycoplasma penetrans.,Gallego P, Planell R, Benach J, Querol E, Perez-Pons JA, Reverter D PLoS One. 2012;7(10):e47886. doi: 10.1371/journal.pone.0047886. Epub 2012 Oct 17. PMID:23082227<ref>PMID:23082227</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 4e4j" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:49, 28 September 2022

2022-09-28T06:49:39Z

← Older revision		Revision as of 06:49, 28 September 2022
Line 1:		Line 1:

	==Crystal structure of arginine deiminase from Mycoplasma penetrans==		==Crystal structure of arginine deiminase from Mycoplasma penetrans==
	<StructureSection load='4e4j' size='340' side='right' caption='[[4e4j]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='4e4j' size='340' side='right'caption='[[4e4j]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e4j]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Mycpe Mycpe~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E4J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4E4J FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e4j]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Malacoplasma_penetrans_HF-2 Malacoplasma penetrans HF-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E4J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E4J FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>~~</td></tr>~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MYPE6080 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272633 MYCPE])~~</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=4e4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e4j OCA], [https://pdbe.org/4e4j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e4j RCSB], [https://www.ebi.ac.uk/pdbsum/4e4j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e4j 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=4e4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e4j OCA], [~~http~~://pdbe.org/4e4j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4e4j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4e4j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4e4j ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[[https://www.uniprot.org/uniprot/Q8EVF6_MALP2 Q8EVF6_MALP2]]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Mycpe~~]]		[[Category: Large Structures]]
	[[Category: Benach, J]]		[[Category: Malacoplasma penetrans HF-2]]
	[[Category: Gallego, P]]		[[Category: Benach J]]
	[[Category: ~~Planell, R~~]]		[[Category: Gallego P]]
	[[Category: ~~Pons, J A.Perez~~]]		[[Category: Perez Pons JA]]
	[[Category: Querol, E]]		[[Category: Planell R]]
	[[Category: Reverter, D]]		[[Category: Querol E]]
	~~[[Category: Arginine deiminase]]~~		[[Category: Reverter D]]
	~~[[Category: Hydrolase]]~~
	~~[[Category: L-arginine]]~~
	~~[[Category: L-citrulline]]~~
	~~[[Category: Nh3~~]]

OCA at 02:38, 11 December 2016

2016-12-11T02:38:32Z

← Older revision		Revision as of 02:38, 11 December 2016
Line 1:		Line 1:

	==Crystal structure of arginine deiminase from Mycoplasma penetrans==		==Crystal structure of arginine deiminase from Mycoplasma penetrans==
	<StructureSection load='4e4j' size='340' side='right' caption='[[4e4j]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='4e4j' size='340' side='right' caption='[[4e4j]], [[Resolution\|resolution]] 2.30Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MYPE6080 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272633 MYCPE])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MYPE6080 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272633 MYCPE])</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=4e4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e4j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e4j RCSB], [http://www.ebi.ac.uk/pdbsum/4e4j 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=4e4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e4j OCA], [http://pdbe.org/4e4j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4e4j RCSB], [http://www.ebi.ac.uk/pdbsum/4e4j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4e4j ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 4e4j" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:23, 9 December 2014

2014-12-09T14:23:25Z

← Older revision		Revision as of 14:23, 9 December 2014
Line 1:		Line 1:
	[[~~Image~~:~~4e4j~~.~~jpg~~\|~~left~~\|~~200px~~]]		==Crystal structure of arginine deiminase from Mycoplasma penetrans==
			<StructureSection load='4e4j' size='340' side='right' caption='[[4e4j]], [[Resolution\|resolution]] 2.30Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[4e4j]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycpe Mycpe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E4J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E4J FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MYPE6080 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272633 MYCPE])</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=4e4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e4j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e4j RCSB], [http://www.ebi.ac.uk/pdbsum/4e4j PDBsum]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The metabolism of arginine towards ATP synthesis has been considered a major source of energy for microorganisms such as Mycoplasma penetrans in anaerobic conditions. Additionally, this pathway has also been implicated in pathogenic and virulence mechanism of certain microorganisms, i.e. protection from acidic stress during infection. In this work we present the crystal structures of the three enzymes composing the gene cluster of the arginine deiminase pathway from M. penetrans: arginine deiminase (ADI), ornithine carbamoyltransferase (OTC) and carbamate kinase (CK). The arginine deiminase (ADI) structure has been refined to 2.3 A resolution in its apo-form, displaying an "open" conformation of the active site of the enzyme in comparison to previous complex structures with substrate intermediates. The active site pocket of ADI is empty, with some of the catalytic and binding residues far from their active positions, suggesting major conformational changes upon substrate binding. Ornithine carbamoyltransferase (OTC) has been refined in two crystal forms at 2.5 A and 2.6 A resolution, respectively, both displaying an identical dodecameric structure with a 23-point symmetry. The dodecameric structure of OTC represents the highest level of organization in this protein family and in M.penetrans it is constituted by a novel interface between the four catalytic homotrimers. Carbamate kinase (CK) has been refined to 2.5 A resolution and its structure is characterized by the presence of two ion sulfates in the active site, one in the carbamoyl phosphate binding site and the other in the beta-phosphate ADP binding pocket of the enzyme. The CK structure also shows variations in some of the elements that regulate the catalytic activity of the enzyme. The relatively low number of metabolic pathways and the relevance in human pathogenesis of Mycoplasma penetrans places the arginine deiminase pathway enzymes as potential targets to design specific inhibitors against this human parasite.

	~~{{STRUCTURE_4e4j\| PDB=4e4j \| SCENE= }}~~		Structural Characterization of the Enzymes Composing the Arginine Deiminase Pathway in Mycoplasma penetrans.,Gallego P, Planell R, Benach J, Querol E, Perez-Pons JA, Reverter D PLoS One. 2012;7(10):e47886. doi: 10.1371/journal.pone.0047886. Epub 2012 Oct 17. PMID:23082227<ref>PMID:23082227</ref>

	~~===Crystal structure~~ of ~~arginine deiminase from Mycoplasma penetrans===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_23082227}}~~		== References ==
			<references/>
	==~~About this Structure~~==		__TOC__
	~~[[4e4j]] is a 12 chain structure with sequence from [http:~~//~~en.wikipedia.org/wiki/Mycoplasma_penetrans_hf-2 Mycoplasma penetrans hf-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E4J OCA].~~		</StructureSection>
	[[Category: ~~Mycoplasma penetrans hf-2~~]]		[[Category: Mycpe]]
	[[Category: Benach, J.]]		[[Category: Benach, J]]
	[[Category: Gallego, P.]]		[[Category: Gallego, P]]
	[[Category: Planell, R.]]		[[Category: Planell, R]]
	[[Category: Pons, J A.Perez.]]		[[Category: Pons, J A.Perez]]
	[[Category: Querol, E.]]		[[Category: Querol, E]]
	[[Category: Reverter, D.]]		[[Category: Reverter, D]]
	[[Category: Arginine deiminase]]		[[Category: Arginine deiminase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 09:00, 31 October 2012

2012-10-31T09:00:20Z

← Older revision		Revision as of 09:00, 31 October 2012
Line 1:		Line 1:
	~~'''Unreleased structure'''~~		[[Image:4e4j.jpg\|left\|200px]]

	~~The entry~~ 4e4j ~~is ON HOLD~~ ~~until Paper Publication~~		{{STRUCTURE_4e4j\| PDB=4e4j \| SCENE= }}

	~~Authors: Benach, J., Gallego, P., Planell, R., Querol, E., Perez Pons, J.A., Reverter, D.~~		===Crystal structure of arginine deiminase from Mycoplasma penetrans===

	~~Description~~: ~~Crystal structure of arginine deiminase~~ from Mycoplasma penetrans		{{ABSTRACT_PUBMED_23082227}}

			==About this Structure==
			[[4e4j]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycoplasma_penetrans_hf-2 Mycoplasma penetrans hf-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E4J OCA].
			[[Category: Mycoplasma penetrans hf-2]]
			[[Category: Benach, J.]]
			[[Category: Gallego, P.]]
			[[Category: Planell, R.]]
			[[Category: Pons, J A.Perez.]]
			[[Category: Querol, E.]]
			[[Category: Reverter, D.]]
			[[Category: Arginine deiminase]]
			[[Category: Hydrolase]]
			[[Category: L-arginine]]
			[[Category: L-citrulline]]
			[[Category: Nh3]]

OCA at 07:14, 6 June 2012

2012-06-06T07:14:43Z

← Older revision		Revision as of 07:14, 6 June 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 4e4j is ON HOLD		The entry 4e4j is ON HOLD until Paper Publication

	Authors: Benach, J., Gallego, P., Planell, R., Querol, E., Perez Pons, J.A., Reverter, D.		Authors: Benach, J., Gallego, P., Planell, R., Querol, E., Perez Pons, J.A., Reverter, D.

	Description: Crystal structure of arginine deiminase from Mycoplasma penetrans		Description: Crystal structure of arginine deiminase from Mycoplasma penetrans

OCA: Protected "4e4j" [edit=sysop:move=sysop]

2012-03-21T07:16:56Z

Protected "4e4j" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:16, 21 March 2012
(No difference)

OCA: New page: '''Unreleased structure''' The entry 4e4j is ON HOLD Authors: Benach, J., Gallego, P., Planell, R., Querol, E., Perez Pons, J.A., Reverter, D. Description: Crystal structure of arginin...

2012-03-21T07:16:55Z

New page: '''Unreleased structure''' The entry 4e4j is ON HOLD Authors: Benach, J., Gallego, P., Planell, R., Querol, E., Perez Pons, J.A., Reverter, D. Description: Crystal structure of arginin...

New page

'''Unreleased structure'''

The entry 4e4j is ON HOLD

Authors: Benach, J., Gallego, P., Planell, R., Querol, E., Perez Pons, J.A., Reverter, D.

Description: Crystal structure of arginine deiminase from Mycoplasma penetrans