2hp0: Difference between revisions
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== | ==Crystal structure of iminodisuccinate epimerase== | ||
[[2hp0]] is a 2 chain structure with sequence from [ | <StructureSection load='2hp0' size='340' side='right'caption='[[2hp0]], [[Resolution|resolution]] 1.50Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2hp0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HP0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HP0 FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTU:(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL'>DTU</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr> | |||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ite ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=358 "Achromobacter radiobacter" (Beijerinck and van Delden 1902) Bergey et al. 1934])</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=2hp0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hp0 OCA], [https://pdbe.org/2hp0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hp0 RCSB], [https://www.ebi.ac.uk/pdbsum/2hp0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hp0 ProSAT]</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/hp/2hp0_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/main_output.php?pdb_ID=2hp0 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Iminodisuccinate (IDS) epimerase catalyzes the epimerisation of R,R-, S,S- and R,S- iminodisuccinate, one step in the biodegradation of the chelating agent iminodisuccinate by Agrobacterium tumefaciens BY6. The enzyme is a member of the MmgE/PrpD protein family, a diverse and little characterized class of proteins of prokaryotic and eukaryotic origin. IDS epimerase does not show significant overall amino acid sequence similarity to any other protein of known three-dimensional structure. The crystal structure of this novel epimerase has been determined by multi-wavelength diffraction to 1.5 A resolution using selenomethionine-substituted enzyme. In the crystal, the enzyme forms a homo-dimer, and the subunit consists of two domains. The larger domain, not consecutive in sequence and comprising residues Met1-Lys266 and Leu400-Pro446, forms a novel all alpha-helical fold with a central six-helical bundle. The second, smaller domain folds into an alpha+beta domain, related in topology to chorismate mutase by a circular permutation. IDS epimerase is thus not related in three-dimensional structure to other known epimerases. The fold of the IDS epimerase is representative for the whole MmgE/PrpD family. The putative active site is located at the interface between the two domains of the subunit, and is characterized by a positively charged surface, consistent with the binding of a highly negatively charged substrate such as iminodisuccinate. Docking experiments suggest a two-base mechanism for the epimerisation reaction. | |||
Three-dimensional structure of iminodisuccinate epimerase defines the fold of the MmgE/PrpD protein family.,Lohkamp B, Bauerle B, Rieger PG, Schneider G J Mol Biol. 2006 Sep 22;362(3):555-66. Epub 2006 Jul 29. PMID:16934291<ref>PMID:16934291</ref> | |||
<ref | |||
[[Category: | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
[[Category: Bauerle, B | </div> | ||
[[Category: Lohkamp, B | <div class="pdbe-citations 2hp0" style="background-color:#fffaf0;"></div> | ||
[[Category: Rieger, P G | == References == | ||
[[Category: Schneider, G | <references/> | ||
[[Category: | __TOC__ | ||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Bauerle, B]] | |||
[[Category: Lohkamp, B]] | |||
[[Category: Rieger, P G]] | |||
[[Category: Schneider, G]] | |||
[[Category: Helix bundle]] | |||
[[Category: Chorismate mutase like]] | [[Category: Chorismate mutase like]] | ||
[[Category: Isomerase]] | [[Category: Isomerase]] | ||
[[Category: Mmge/prpd fold]] | [[Category: Mmge/prpd fold]] | ||
Latest revision as of 10:19, 24 March 2021
Crystal structure of iminodisuccinate epimeraseCrystal structure of iminodisuccinate epimerase
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedIminodisuccinate (IDS) epimerase catalyzes the epimerisation of R,R-, S,S- and R,S- iminodisuccinate, one step in the biodegradation of the chelating agent iminodisuccinate by Agrobacterium tumefaciens BY6. The enzyme is a member of the MmgE/PrpD protein family, a diverse and little characterized class of proteins of prokaryotic and eukaryotic origin. IDS epimerase does not show significant overall amino acid sequence similarity to any other protein of known three-dimensional structure. The crystal structure of this novel epimerase has been determined by multi-wavelength diffraction to 1.5 A resolution using selenomethionine-substituted enzyme. In the crystal, the enzyme forms a homo-dimer, and the subunit consists of two domains. The larger domain, not consecutive in sequence and comprising residues Met1-Lys266 and Leu400-Pro446, forms a novel all alpha-helical fold with a central six-helical bundle. The second, smaller domain folds into an alpha+beta domain, related in topology to chorismate mutase by a circular permutation. IDS epimerase is thus not related in three-dimensional structure to other known epimerases. The fold of the IDS epimerase is representative for the whole MmgE/PrpD family. The putative active site is located at the interface between the two domains of the subunit, and is characterized by a positively charged surface, consistent with the binding of a highly negatively charged substrate such as iminodisuccinate. Docking experiments suggest a two-base mechanism for the epimerisation reaction. Three-dimensional structure of iminodisuccinate epimerase defines the fold of the MmgE/PrpD protein family.,Lohkamp B, Bauerle B, Rieger PG, Schneider G J Mol Biol. 2006 Sep 22;362(3):555-66. Epub 2006 Jul 29. PMID:16934291[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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