4al3: Difference between revisions

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~~[[Image:4al3.png|left|200px]]~~

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==peptide deformylase (Co-form) with mercaptoethanol==

~~The line below this paragraph~~, ~~containing~~ "~~STRUCTURE_4al3~~"~~, creates the~~ "~~Structure Box~~" ~~on the page~~.

~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~

== Structural highlights ==

~~or the SCENE parameter (which sets~~ the ~~initial scene displayed when~~ the ~~page~~ is ~~loaded),~~

<table><tr><td colspan='2'>[[4al3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AL3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4AL3 FirstGlance]. <br>

~~or leave the SCENE parameter empty~~ for the ~~default display~~.

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.98Å</td></tr>

-->

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>

~~{{STRUCTURE_4al3| PDB~~=~~4al3 | SCENE~~= }}

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4al3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4al3 OCA], [https://pdbe.org/4al3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4al3 RCSB], [https://www.ebi.ac.uk/pdbsum/4al3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4al3 ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/DEF_ECOLI DEF_ECOLI] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.[HAMAP-Rule:MF_00163]

== Publication Abstract from PubMed ==

Fluorescently labeled cobalt peptide deformylase (Co-PDF) can be efficiently used as a fluorescence-resonance-energy-transfer-based sensing device for hydrogen sulfide (H(2)S). The proof of concept of our sensor system is substantiated by spectroscopic, structural, and theoretical results. Monohydrogen sulfide coordination to Co-PDF and Ni-PDF was verified by X-ray crystallography. Density functional theory calculations were performed to gain insight into the characteristics of the coordination adduct between H(2)S and the cobalt cofactor in Co-PDF.

~~===peptide deformylase~~ (Co-~~form) with mercaptoethanol===~~

A FRET Enzyme-Based Probe for Monitoring Hydrogen Sulfide.,Strianese M, Palm GJ, Milione S, Kuhl O, Hinrichs W, Pellecchia C Inorg Chem. 2012 Nov 5;51(21):11220-2. doi: 10.1021/ic301363d. Epub 2012 Oct 16. PMID:23072298<ref>PMID:23072298</ref>

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

~~==About this Structure==~~

</div>

~~[[4al3]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca~~-~~bin~~/~~ocashort?id~~=~~4AL3 OCA].~~

~~[[Category: Escherichia coli]]~~

== References ==

[[Category: ~~Peptide deformylase~~]]

[[Category: Hinrichs, W.]]

__TOC__

[[Category: Palm~~, G J.]]~~

</StructureSection>

~~[[Category: Hydrolase]]~~

[[Category: Large Structures]]

~~[[Category: Oxidation-reduction~~]]

[[Category: Hinrichs W]]

[[Category: Palm GJ]]

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@@ Line 1: / Line 1: @@
-[[Image:4al3.png|left|200px]]
-<!--
+==peptide deformylase (Co-form) with mercaptoethanol==
-The line below this paragraph, containing "STRUCTURE_4al3", creates the "Structure Box" on the page.
+<StructureSection load='4al3' size='340' side='right'caption='[[4al3]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[4al3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AL3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4AL3 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.98&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
-{{STRUCTURE_4al3|  PDB=4al3  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4al3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4al3 OCA], [https://pdbe.org/4al3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4al3 RCSB], [https://www.ebi.ac.uk/pdbsum/4al3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4al3 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DEF_ECOLI DEF_ECOLI] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.[HAMAP-Rule:MF_00163]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Fluorescently labeled cobalt peptide deformylase (Co-PDF) can be efficiently used as a fluorescence-resonance-energy-transfer-based sensing device for hydrogen sulfide (H(2)S). The proof of concept of our sensor system is substantiated by spectroscopic, structural, and theoretical results. Monohydrogen sulfide coordination to Co-PDF and Ni-PDF was verified by X-ray crystallography. Density functional theory calculations were performed to gain insight into the characteristics of the coordination adduct between H(2)S and the cobalt cofactor in Co-PDF.
-===peptide deformylase (Co-form) with mercaptoethanol===
+A FRET Enzyme-Based Probe for Monitoring Hydrogen Sulfide.,Strianese M, Palm GJ, Milione S, Kuhl O, Hinrichs W, Pellecchia C Inorg Chem. 2012 Nov 5;51(21):11220-2. doi: 10.1021/ic301363d. Epub 2012 Oct 16. PMID:23072298<ref>PMID:23072298</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-==About this Structure==
+</div>
-[[4al3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AL3 OCA].
+<div class="pdbe-citations 4al3" style="background-color:#fffaf0;"></div>
-[[Category: Escherichia coli]]
+== References ==
-[[Category: Peptide deformylase]]
+<references/>
-[[Category: Hinrichs, W.]]
+__TOC__
-[[Category: Palm, G J.]]
+</StructureSection>
-[[Category: Hydrolase]]
+[[Category: Large Structures]]
-[[Category: Oxidation-reduction]]
+[[Category: Hinrichs W]]
+[[Category: Palm GJ]]