3emr

From Proteopedia

(Difference between revisions)

Revision as of 09:10, 23 February 2022

Crystal Structure Analysis of the ectoine hydroxylase ECTD from Salibacillus salexigens

Structural highlights

3emr is a 1 chain structure with sequence from Atcc 700290. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
NonStd Res:
Gene:	ectD (ATCC 700290)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[ECTD_VIRSA] Involved in the biosynthesis of ectoine ((S)-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid) which is a highly soluble organic osmolyte, called compatible solute, use to avoid excessive water efflux, plasmolysis, molecular crowding of the cytoplasm, and cessation of growth in high salinity environments. Catalyzes the 2-oxoglutarate-dependent selective hydroxylation of L-ectoine to yield (4S,5S)-5-hydroxyectoine.^[1]

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 PubMed

As a response to high osmolality, many microorganisms synthesize various types of compatible solutes. These organic osmolytes aid in offsetting the detrimental effects of low water activity on cell physiology. One of these compatible solutes is ectoine. A sub-group of the ectoine producer's enzymatically convert this tetrahydropyrimidine into a hydroxylated derivative, 5-hydroxyectoine. This compound also functions as an effective osmostress protectant and compatible solute but it possesses properties that differ in several aspects from those of ectoine. The enzyme responsible for ectoine hydroxylation (EctD) is a member of the non-heme iron(II)-containing and 2-oxoglutarate-dependent dioxygenases (EC 1.14.11). These enzymes couple the decarboxylation of 2-oxoglutarate with the formation of a high-energy ferryl-oxo intermediate to catalyze the oxidation of the bound organic substrate. We report here the crystal structure of the ectoine hydroxylase EctD from the moderate halophile Virgibacillus salexigens in complex with Fe(3+) at a resolution of 1.85 A. Like other non-heme iron(II) and 2-oxoglutarate dependent dioxygenases, the core of the EctD structure consists of a double-stranded beta-helix forming the main portion of the active-site of the enzyme. The positioning of the iron ligand in the active-site of EctD is mediated by an evolutionarily conserved 2-His-1-carboxylate iron-binding motif. The side chains of the three residues forming this iron-binding site protrude into a deep cavity in the EctD structure that also harbours the 2-oxoglutarate co-substrate-binding site. Database searches revealed a widespread occurrence of EctD-type proteins in members of the Bacteria but only in a single representative of the Archaea, the marine crenarchaeon Nitrosopumilus maritimus. The EctD crystal structure reported here can serve as a template to guide further biochemical and structural studies of this biotechnologically interesting enzyme family.

Synthesis of 5-hydroxyectoine from ectoine: crystal structure of the non-heme iron(II) and 2-oxoglutarate-dependent dioxygenase EctD.,Reuter K, Pittelkow M, Bursy J, Heine A, Craan T, Bremer E PLoS One. 2010 May 14;5(5):e10647. PMID:20498719^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Bursy J, Pierik AJ, Pica N, Bremer E. Osmotically induced synthesis of the compatible solute hydroxyectoine is mediated by an evolutionarily conserved ectoine hydroxylase. J Biol Chem. 2007 Oct 26;282(43):31147-55. Epub 2007 Jul 18. PMID:17636255 doi:http://dx.doi.org/10.1074/jbc.M704023200
↑ Reuter K, Pittelkow M, Bursy J, Heine A, Craan T, Bremer E. Synthesis of 5-hydroxyectoine from ectoine: crystal structure of the non-heme iron(II) and 2-oxoglutarate-dependent dioxygenase EctD. PLoS One. 2010 May 14;5(5):e10647. PMID:20498719 doi:10.1371/journal.pone.0010647

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3emr"

@@ Line 1: / Line 1: @@
 ==Crystal Structure Analysis of the ectoine hydroxylase ECTD from Salibacillus salexigens==
-<StructureSection load='3emr' size='340' side='right' caption='[[3emr]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+<StructureSection load='3emr' size='340' side='right'caption='[[3emr]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3emr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_700290 Atcc 700290]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EMR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EMR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3emr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_700290 Atcc 700290]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EMR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EMR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ectD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=61016 ATCC 700290])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ectD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=61016 ATCC 700290])</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=3emr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3emr OCA], [http://pdbe.org/3emr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3emr RCSB], [http://www.ebi.ac.uk/pdbsum/3emr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3emr 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=3emr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3emr OCA], [https://pdbe.org/3emr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3emr RCSB], [https://www.ebi.ac.uk/pdbsum/3emr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3emr ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ECTD_VIRSA ECTD_VIRSA]] Involved in the biosynthesis of ectoine ((S)-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid) which is a highly soluble organic osmolyte, called compatible solute, use to avoid excessive water efflux, plasmolysis, molecular crowding of the cytoplasm, and cessation of growth in high salinity environments. Catalyzes the 2-oxoglutarate-dependent selective hydroxylation of L-ectoine to yield (4S,5S)-5-hydroxyectoine.<ref>PMID:17636255</ref>
+[[https://www.uniprot.org/uniprot/ECTD_VIRSA ECTD_VIRSA]] Involved in the biosynthesis of ectoine ((S)-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid) which is a highly soluble organic osmolyte, called compatible solute, use to avoid excessive water efflux, plasmolysis, molecular crowding of the cytoplasm, and cessation of growth in high salinity environments. Catalyzes the 2-oxoglutarate-dependent selective hydroxylation of L-ectoine to yield (4S,5S)-5-hydroxyectoine.<ref>PMID:17636255</ref>
 == 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/em/3emr_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/em/3emr_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 30: / Line 30: @@
 </div>
 <div class="pdbe-citations 3emr" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Hydroxylases 3D structures|Hydroxylases 3D structures]]
 == References ==
 <references/>
@@ Line 35: / Line 38: @@
 </StructureSection>
 [[Category: Atcc 700290]]
+[[Category: Large Structures]]
 [[Category: Heine, A]]
 [[Category: Reuter, K]]
 [[Category: Double stranded beta helix]]
 [[Category: Oxidoreductase]]

3emr

From Proteopedia

Revision as of 09:10, 23 February 2022

Crystal Structure Analysis of the ectoine hydroxylase ECTD from Salibacillus salexigens

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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