2dkh - Revision history

OCA at 13:47, 13 March 2024

2024-03-13T13:47:40Z

← Older revision		Revision as of 13:47, 13 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dkh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Comamonas_testosteroni Comamonas testosteroni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DKH FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dkh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Comamonas_testosteroni Comamonas testosteroni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DKH FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=3HB:3~~-~~HYDROXYBENZOIC+ACID'>3HB</scene>~~, ~~<scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.8Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[2dki\|2dki]]~~</~~div~~><~~/td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3HB:3-HYDROXYBENZOIC+ACID'>3HB</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/3-hydroxybenzoate_4-monooxygenase 3-hydroxybenzoate 4-monooxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.23 1.14.13.23]~~ </~~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=2dkh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkh OCA], [https://pdbe.org/2dkh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dkh RCSB], [https://www.ebi.ac.uk/pdbsum/2dkh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dkh 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=2dkh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkh OCA], [https://pdbe.org/2dkh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dkh RCSB], [https://www.ebi.ac.uk/pdbsum/2dkh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dkh ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/MOBA_COMTE MOBA_COMTE]] Converts 3-hydroxybenzoate (m-hydroxybenzoate), and to a lesser extent p-hydroxybenzoate, to 3,4-dihydroxybenzoate (protocatechuate). Also acts on a number of analogs of 3-hydroxybenzoate substituted in the 2, 4, 5 and 6 positions.<ref>PMID:18417078</ref>		[https://www.uniprot.org/uniprot/MOBA_COMTE MOBA_COMTE] Converts 3-hydroxybenzoate (m-hydroxybenzoate), and to a lesser extent p-hydroxybenzoate, to 3,4-dihydroxybenzoate (protocatechuate). Also acts on a number of analogs of 3-hydroxybenzoate substituted in the 2, 4, 5 and 6 positions.<ref>PMID:18417078</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=2dkh 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=2dkh ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	The 3-hydroxybenzoate hydroxylase (MHBH) from Comamonas testosteroni KH122-3s is a single-component flavoprotein monooxygenase, a member of the glutathione reductase (GR) family. It catalyzes the conversion of 3-hydroxybenzoate to 3,4-dihydroxybenzoate with concomitant requirements for equimolar amounts of NADPH and molecular oxygen. The production of dihydroxy-benzenoid derivative by hydroxylation is the first step in the aerobic degradation of various phenolic compounds in soil microorganisms. To establish the structural basis for substrate recognition, the crystal structure of MHBH in complex with its substrate was determined at 1.8 A resolution. The enzyme is shown to form a physiologically active homodimer with crystallographic 2-fold symmetry, in which each subunit consists of the first two domains comprising an active site and the C-terminal domain involved in oligomerization. The protein fold of the catalytic domains and the active-site architecture, including the FAD and substrate-binding sites, are similar to those of 4-hydroxybenzoate hydroxylase (PHBH) and phenol hydroxylase (PHHY), which are members of the GR family, providing evidence that the flavoprotein aromatic hydroxylases share similar catalytic actions for hydroxylation of the respective substrates. Structural comparison of MHBH with the homologous enzymes suggested that a large tunnel connecting the substrate-binding pocket to the protein surface serves for substrate transport in this enzyme. The internal space of the large tunnel is distinctly divided into hydrophilic and hydrophobic regions. The characteristically stratified environment in the tunnel interior and the size of the entrance would allow the enzyme to select its substrate by amphiphilic nature and molecular size. In addition, the structure of the Xe-derivative at 2.5 A resolution led to the identification of a putative oxygen-binding site adjacent to the substrate-binding pocket. The hydrophobic nature of the xenon-binding site extends to the solvent through the tunnel, suggesting that the tunnel could be involved in oxygen transport.

	Crystal structure of 3-hydroxybenzoate hydroxylase from Comamonas testosteroni has a large tunnel for substrate and oxygen access to the active site.,Hiromoto T, Fujiwara S, Hosokawa K, Yamaguchi H J Mol Biol. 2006 Dec 15;364(5):878-96. Epub 2006 Sep 16. PMID:17045293<ref>PMID:17045293</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2dkh" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: 3-hydroxybenzoate 4-monooxygenase]]~~
	[[Category: Comamonas testosteroni]]		[[Category: Comamonas testosteroni]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Fujiwara, S]]		[[Category: Fujiwara S]]
	[[Category: Hiromoto, T]]		[[Category: Hiromoto T]]
	[[Category: Hosokawa, K]]		[[Category: Hosokawa K]]
	[[Category: Yamaguchi, H]]		[[Category: Yamaguchi H]]
	~~[[Category: 3-hydroxybenzoate hydroxylase]]~~
	~~[[Category: Flavoprotein]]~~
	~~[[Category: Monooxygenase]]~~
	~~[[Category: Oxidoreductase]]~~
	~~[[Category: Substrate complex~~]]

OCA at 10:32, 8 December 2021

2021-12-08T10:32:24Z

← Older revision		Revision as of 10:32, 8 December 2021
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	<StructureSection load='2dkh' size='340' side='right'caption='[[2dkh]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2dkh' size='340' side='right'caption='[[2dkh]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dkh]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Comamonas_testosteroni Comamonas testosteroni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DKH FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dkh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Comamonas_testosteroni Comamonas testosteroni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DKH FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3HB:3-HYDROXYBENZOIC+ACID'>3HB</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3HB:3-HYDROXYBENZOIC+ACID'>3HB</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dki\|2dki]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2dki\|2dki]]</div></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/3-hydroxybenzoate_4-monooxygenase 3-hydroxybenzoate 4-monooxygenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.23 1.14.13.23] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/3-hydroxybenzoate_4-monooxygenase 3-hydroxybenzoate 4-monooxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.23 1.14.13.23] </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=2dkh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkh OCA], [~~http~~://pdbe.org/2dkh PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2dkh RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2dkh PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2dkh 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=2dkh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkh OCA], [https://pdbe.org/2dkh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dkh RCSB], [https://www.ebi.ac.uk/pdbsum/2dkh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dkh ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/MOBA_COMTE MOBA_COMTE]] Converts 3-hydroxybenzoate (m-hydroxybenzoate), and to a lesser extent p-hydroxybenzoate, to 3,4-dihydroxybenzoate (protocatechuate). Also acts on a number of analogs of 3-hydroxybenzoate substituted in the 2, 4, 5 and 6 positions.<ref>PMID:18417078</ref>		[[https://www.uniprot.org/uniprot/MOBA_COMTE MOBA_COMTE]] Converts 3-hydroxybenzoate (m-hydroxybenzoate), and to a lesser extent p-hydroxybenzoate, to 3,4-dihydroxybenzoate (protocatechuate). Also acts on a number of analogs of 3-hydroxybenzoate substituted in the 2, 4, 5 and 6 positions.<ref>PMID:18417078</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:48, 4 March 2020

2020-03-04T07:48:34Z

← Older revision		Revision as of 07:48, 4 March 2020
Line 1:		Line 1:

	==Crystal structure of 3-hydroxybenzoate hydroxylase from Comamonas testosteroni, in complex with the substrate==		==Crystal structure of 3-hydroxybenzoate hydroxylase from Comamonas testosteroni, in complex with the substrate==
	<StructureSection load='2dkh' size='340' side='right' caption='[[2dkh]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2dkh' size='340' side='right'caption='[[2dkh]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dkh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Comamonas_testosteroni Comamonas testosteroni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DKH FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dkh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Comamonas_testosteroni Comamonas testosteroni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DKH FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 2dkh" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2dkh" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Hydroxylases 3D structures\|Hydroxylases 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: 3-hydroxybenzoate 4-monooxygenase]]		[[Category: 3-hydroxybenzoate 4-monooxygenase]]
	[[Category: Comamonas testosteroni]]		[[Category: Comamonas testosteroni]]
			[[Category: Large Structures]]
	[[Category: Fujiwara, S]]		[[Category: Fujiwara, S]]
	[[Category: Hiromoto, T]]		[[Category: Hiromoto, T]]

OCA at 06:36, 30 May 2018

2018-05-30T06:36:20Z

← Older revision		Revision as of 06:36, 30 May 2018
Line 1:		Line 1:

	==Crystal structure of 3-hydroxybenzoate hydroxylase from Comamonas testosteroni, in complex with the substrate==		==Crystal structure of 3-hydroxybenzoate hydroxylase from Comamonas testosteroni, in complex with the substrate==
	<StructureSection load='2dkh' size='340' side='right' caption='[[2dkh]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2dkh' size='340' side='right' caption='[[2dkh]], [[Resolution\|resolution]] 1.80Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dki\|2dki]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dki\|2dki]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxybenzoate_4-monooxygenase 3-hydroxybenzoate 4-monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.23 1.14.13.23] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxybenzoate_4-monooxygenase 3-hydroxybenzoate 4-monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.23 1.14.13.23] </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=2dkh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkh OCA], [http://pdbe.org/2dkh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dkh RCSB], [http://www.ebi.ac.uk/pdbsum/2dkh 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=2dkh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkh OCA], [http://pdbe.org/2dkh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dkh RCSB], [http://www.ebi.ac.uk/pdbsum/2dkh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dkh ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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/dk/2dkh_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dk/2dkh_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>
	</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=2dkh ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:20, 11 September 2015

2015-09-11T09:20:36Z

← Older revision		Revision as of 09:20, 11 September 2015
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dki\|2dki]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dki\|2dki]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxybenzoate_4-monooxygenase 3-hydroxybenzoate 4-monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.23 1.14.13.23] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxybenzoate_4-monooxygenase 3-hydroxybenzoate 4-monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.23 1.14.13.23] </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=2dkh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dkh RCSB], [http://www.ebi.ac.uk/pdbsum/2dkh 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=2dkh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkh OCA], [http://pdbe.org/2dkh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dkh RCSB], [http://www.ebi.ac.uk/pdbsum/2dkh PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/MOBA_COMTE MOBA_COMTE]] Converts 3-hydroxybenzoate (m-hydroxybenzoate), and to a lesser extent p-hydroxybenzoate, to 3,4-dihydroxybenzoate (protocatechuate). Also acts on a number of analogs of 3-hydroxybenzoate substituted in the 2, 4, 5 and 6 positions.<ref>PMID:18417078</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	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 2dkh" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:47, 15 January 2015

2015-01-15T16:47:32Z

← Older revision		Revision as of 16:47, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dkh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Comamonas_testosteroni Comamonas testosteroni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DKH FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dkh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Comamonas_testosteroni Comamonas testosteroni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DKH FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3HB:3-HYDROXYBENZOIC+ACID'>3HB</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3HB:3-HYDROXYBENZOIC+ACID'>3HB</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dki\|2dki]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dki\|2dki]]</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxybenzoate_4-monooxygenase 3-hydroxybenzoate 4-monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.23 1.14.13.23] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxybenzoate_4-monooxygenase 3-hydroxybenzoate 4-monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.23 1.14.13.23] </span></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=2dkh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dkh RCSB], [http://www.ebi.ac.uk/pdbsum/2dkh 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=2dkh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dkh RCSB], [http://www.ebi.ac.uk/pdbsum/2dkh 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 32:		Line 32:
	[[Category: 3-hydroxybenzoate 4-monooxygenase]]		[[Category: 3-hydroxybenzoate 4-monooxygenase]]
	[[Category: Comamonas testosteroni]]		[[Category: Comamonas testosteroni]]
	[[Category: Fujiwara, S.]]		[[Category: Fujiwara, S]]
	[[Category: Hiromoto, T.]]		[[Category: Hiromoto, T]]
	[[Category: Hosokawa, K.]]		[[Category: Hosokawa, K]]
	[[Category: Yamaguchi, H.]]		[[Category: Yamaguchi, H]]
	[[Category: 3-hydroxybenzoate hydroxylase]]		[[Category: 3-hydroxybenzoate hydroxylase]]
	[[Category: Flavoprotein]]		[[Category: Flavoprotein]]

OCA at 01:58, 30 September 2014

2014-09-30T01:58:31Z

← Older revision		Revision as of 01:58, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2dkh~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure of 3-hydroxybenzoate hydroxylase from Comamonas testosteroni, in complex with the substrate==
			<StructureSection load='2dkh' size='340' side='right' caption='[[2dkh]], [[Resolution\|resolution]] 1.80Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2dkh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Comamonas_testosteroni Comamonas testosteroni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DKH FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3HB:3-HYDROXYBENZOIC+ACID'>3HB</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dki\|2dki]]</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxybenzoate_4-monooxygenase 3-hydroxybenzoate 4-monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.23 1.14.13.23] </span></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=2dkh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dkh RCSB], [http://www.ebi.ac.uk/pdbsum/2dkh 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/dk/2dkh_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 ==
			The 3-hydroxybenzoate hydroxylase (MHBH) from Comamonas testosteroni KH122-3s is a single-component flavoprotein monooxygenase, a member of the glutathione reductase (GR) family. It catalyzes the conversion of 3-hydroxybenzoate to 3,4-dihydroxybenzoate with concomitant requirements for equimolar amounts of NADPH and molecular oxygen. The production of dihydroxy-benzenoid derivative by hydroxylation is the first step in the aerobic degradation of various phenolic compounds in soil microorganisms. To establish the structural basis for substrate recognition, the crystal structure of MHBH in complex with its substrate was determined at 1.8 A resolution. The enzyme is shown to form a physiologically active homodimer with crystallographic 2-fold symmetry, in which each subunit consists of the first two domains comprising an active site and the C-terminal domain involved in oligomerization. The protein fold of the catalytic domains and the active-site architecture, including the FAD and substrate-binding sites, are similar to those of 4-hydroxybenzoate hydroxylase (PHBH) and phenol hydroxylase (PHHY), which are members of the GR family, providing evidence that the flavoprotein aromatic hydroxylases share similar catalytic actions for hydroxylation of the respective substrates. Structural comparison of MHBH with the homologous enzymes suggested that a large tunnel connecting the substrate-binding pocket to the protein surface serves for substrate transport in this enzyme. The internal space of the large tunnel is distinctly divided into hydrophilic and hydrophobic regions. The characteristically stratified environment in the tunnel interior and the size of the entrance would allow the enzyme to select its substrate by amphiphilic nature and molecular size. In addition, the structure of the Xe-derivative at 2.5 A resolution led to the identification of a putative oxygen-binding site adjacent to the substrate-binding pocket. The hydrophobic nature of the xenon-binding site extends to the solvent through the tunnel, suggesting that the tunnel could be involved in oxygen transport.

	~~{{STRUCTURE_2dkh\| PDB=2dkh \| SCENE= }}~~		Crystal structure of 3-hydroxybenzoate hydroxylase from Comamonas testosteroni has a large tunnel for substrate and oxygen access to the active site.,Hiromoto T, Fujiwara S, Hosokawa K, Yamaguchi H J Mol Biol. 2006 Dec 15;364(5):878-96. Epub 2006 Sep 16. PMID:17045293<ref>PMID:17045293</ref>

	~~===Crystal structure~~ of ~~3-hydroxybenzoate hydroxylase from Comamonas testosteroni, in complex with~~ the ~~substrate===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_17045293}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2dkh]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Comamonas_testosteroni Comamonas testosteroni]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2DKH OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:017045293<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: 3-hydroxybenzoate 4-monooxygenase]]		[[Category: 3-hydroxybenzoate 4-monooxygenase]]
	[[Category: Comamonas testosteroni]]		[[Category: Comamonas testosteroni]]

OCA: Protected "2dkh" [edit=sysop:move=sysop]

2013-01-06T11:12:05Z

Protected "2dkh" [edit=sysop:move=sysop]

← Older revision	Revision as of 11:12, 6 January 2013
(No difference)

OCA at 11:12, 6 January 2013

2013-01-06T11:12:01Z

← Older revision		Revision as of 11:12, 6 January 2013
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	~~{{Seed}}~~
	[[Image:2dkh.png\|left\|200px]]		[[Image:2dkh.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2dkh", 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_2dkh\| PDB=2dkh \| SCENE= }}		{{STRUCTURE_2dkh\| PDB=2dkh \| SCENE= }}

	===Crystal structure of 3-hydroxybenzoate hydroxylase from Comamonas testosteroni, in complex with the substrate===		===Crystal structure of 3-hydroxybenzoate hydroxylase from Comamonas testosteroni, in complex with the substrate===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_17045293}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 17045293 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_17045293}}		{{ABSTRACT_PUBMED_17045293}}

	==About this Structure==		==About this Structure==
	~~2DKH~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Comamonas_testosteroni Comamonas testosteroni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKH OCA].		[[2dkh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Comamonas_testosteroni Comamonas testosteroni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKH OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~17045293~~</ref><references group="xtra"/>		<ref group="xtra">PMID:017045293</ref><references group="xtra"/>
	[[Category: 3-hydroxybenzoate 4-monooxygenase]]		[[Category: 3-hydroxybenzoate 4-monooxygenase]]
	[[Category: Comamonas testosteroni]]		[[Category: Comamonas testosteroni]]
Line 35:		Line 23:
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Substrate complex]]		[[Category: Substrate complex]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:39:00 2009''~~

OCA at 16:39, 17 February 2009

2009-02-17T16:39:01Z

← Older revision		Revision as of 16:39, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	2DKH is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Comamonas_testosteroni Comamonas testosteroni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKH OCA].		2DKH is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Comamonas_testosteroni Comamonas testosteroni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKH OCA].

	==Reference==		==Reference==
	Crystal structure of 3-hydroxybenzoate hydroxylase from Comamonas testosteroni has a large tunnel for substrate and oxygen access to the active site., Hiromoto T, Fujiwara S, Hosokawa K, Yamaguchi H, J Mol Biol. 2006 Dec 15;364(5):878-96. Epub 2006 Sep 16. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17045293 17045293]~~		<ref group="xtra">PMID:17045293</ref><references group="xtra"/>
	[[Category: 3-hydroxybenzoate 4-monooxygenase]]		[[Category: 3-hydroxybenzoate 4-monooxygenase]]
	[[Category: Comamonas testosteroni]]		[[Category: Comamonas testosteroni]]
	~~[[Category: Single protein]]~~
	[[Category: Fujiwara, S.]]		[[Category: Fujiwara, S.]]
	[[Category: Hiromoto, T.]]		[[Category: Hiromoto, T.]]
Line 37:		Line 36:
	[[Category: Substrate complex]]		[[Category: Substrate complex]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 02~~:39:~~21 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:39:00 2009''