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| | ==E.coli deformylase with Co(II) and hydrosulfide== | | ==E.coli deformylase with Co(II) and hydrosulfide== |
| - | <StructureSection load='4az4' size='340' side='right' caption='[[4az4]], [[Resolution|resolution]] 1.80Å' scene=''> | + | <StructureSection load='4az4' size='340' side='right'caption='[[4az4]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4az4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecobd Ecobd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AZ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4AZ4 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4az4]] 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=4AZ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4AZ4 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </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=4az4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4az4 OCA], [https://pdbe.org/4az4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4az4 RCSB], [https://www.ebi.ac.uk/pdbsum/4az4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4az4 ProSAT]</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=4az4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4az4 OCA], [http://pdbe.org/4az4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4az4 RCSB], [http://www.ebi.ac.uk/pdbsum/4az4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4az4 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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] | + | [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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ecobd]] | + | [[Category: Large Structures]] |
| - | [[Category: Peptide deformylase]]
| + | [[Category: Hinrichs W]] |
| - | [[Category: Hinrichs, W]] | + | [[Category: Palm GJ]] |
| - | [[Category: Palm, G J]] | + | |
| - | [[Category: Cobalt]]
| + | |
| - | [[Category: Hydrogen sulfide sensor]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Strianese M, Palm GJ, Milione S, Kuhl O, Hinrichs W, Pellecchia C. A FRET Enzyme-Based Probe for Monitoring Hydrogen Sulfide. Inorg Chem. 2012 Nov 5;51(21):11220-2. doi: 10.1021/ic301363d. Epub 2012 Oct 16. PMID:23072298 doi:http://dx.doi.org/10.1021/ic301363d
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