2ivf
From Proteopedia
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| - | == | + | |
| - | <StructureSection load='2ivf' size='340' side='right' caption='[[2ivf]], [[Resolution|resolution]] 1.88Å' scene=''> | + | ==Ethylbenzene dehydrogenase from Aromatoleum aromaticum== |
| + | <StructureSection load='2ivf' size='340' side='right'caption='[[2ivf]], [[Resolution|resolution]] 1.88Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | [[2ivf]] is a 3 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[2ivf]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Aromatoleum_aromaticum_EbN1 Aromatoleum aromaticum EbN1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IVF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IVF FirstGlance]. <br> |
| - | <b>[[Ligand|Ligands:]]</b> <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MD1:PHOSPHORIC+ACID+4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL+ESTER+GUANYLATE+ESTER'>MD1</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>MGD</scene>, <scene name='pdbligand=MO:MOLYBDENUM+ATOM'>MO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>< | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.88Å</td></tr> |
| - | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MD1:PHOSPHORIC+ACID+4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL+ESTER+GUANYLATE+ESTER'>MD1</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>MGD</scene>, <scene name='pdbligand=MO:MOLYBDENUM+ATOM'>MO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr> | |
| - | <b>Resources:</b> <span class='plainlinks'>[ | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ivf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ivf OCA], [https://pdbe.org/2ivf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ivf RCSB], [https://www.ebi.ac.uk/pdbsum/2ivf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ivf ProSAT]</span></td></tr> |
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/Q5P5I0_AROAE Q5P5I0_AROAE] | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
| - | [[Image:Consurf_key_small.gif|right]] | + | [[Image:Consurf_key_small.gif|200px|right]] |
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iv/2ivf_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iv/2ivf_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/ | + | </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=2ivf ConSurf]. |
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
Anaerobic degradation of hydrocarbons was discovered a decade ago, and ethylbenzene dehydrogenase was one of the first characterized enzymes involved. The structure of the soluble periplasmic 165 kDa enzyme was established at 1.88 A resolution. It is a heterotrimer. The alpha subunit contains the catalytic center with a molybdenum held by two molybdopterin-guanine dinucleotides, one with an open pyran ring, and an iron-sulfur cluster with a histidine ligand. During catalysis, electrons produced by substrate oxidation are transferred to a heme in the gamma subunit and then presumably to a separate cytochrome involved in nitrate respiration. The beta subunit contains four iron-sulfur clusters and is structurally related to ferredoxins. The gamma subunit is the first known protein with a methionine and a lysine as axial heme ligands. The catalytic product was modeled into the active center, showing the reaction geometry. A mechanism consistent with activity and inhibition data of ethylbenzene-related compounds is proposed. | Anaerobic degradation of hydrocarbons was discovered a decade ago, and ethylbenzene dehydrogenase was one of the first characterized enzymes involved. The structure of the soluble periplasmic 165 kDa enzyme was established at 1.88 A resolution. It is a heterotrimer. The alpha subunit contains the catalytic center with a molybdenum held by two molybdopterin-guanine dinucleotides, one with an open pyran ring, and an iron-sulfur cluster with a histidine ligand. During catalysis, electrons produced by substrate oxidation are transferred to a heme in the gamma subunit and then presumably to a separate cytochrome involved in nitrate respiration. The beta subunit contains four iron-sulfur clusters and is structurally related to ferredoxins. The gamma subunit is the first known protein with a methionine and a lysine as axial heme ligands. The catalytic product was modeled into the active center, showing the reaction geometry. A mechanism consistent with activity and inhibition data of ethylbenzene-related compounds is proposed. | ||
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Crystal structure of ethylbenzene dehydrogenase from Aromatoleum aromaticum.,Kloer DP, Hagel C, Heider J, Schulz GE Structure. 2006 Sep;14(9):1377-88. PMID:16962969<ref>PMID:16962969</ref> | Crystal structure of ethylbenzene dehydrogenase from Aromatoleum aromaticum.,Kloer DP, Hagel C, Heider J, Schulz GE Structure. 2006 Sep;14(9):1377-88. PMID:16962969<ref>PMID:16962969</ref> | ||
| - | From | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| + | </div> | ||
| + | <div class="pdbe-citations 2ivf" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: Aromatoleum aromaticum]] | + | [[Category: Aromatoleum aromaticum EbN1]] |
| - | [[Category: | + | [[Category: Large Structures]] |
| - | [[Category: Hagel | + | [[Category: Hagel C]] |
| - | [[Category: Heider | + | [[Category: Heider J]] |
| - | [[Category: Kloer | + | [[Category: Kloer DP]] |
| - | [[Category: Schulz | + | [[Category: Schulz GE]] |
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Current revision
Ethylbenzene dehydrogenase from Aromatoleum aromaticum
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