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| | ==PEPTIDE DEFORMYLASE CATALYTIC CORE (RESIDUES 1-147), NMR, 20 STRUCTURES== | | ==PEPTIDE DEFORMYLASE CATALYTIC CORE (RESIDUES 1-147), NMR, 20 STRUCTURES== |
| - | <StructureSection load='2def' size='340' side='right'caption='[[2def]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''> | + | <StructureSection load='2def' size='340' side='right'caption='[[2def]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2def]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DEF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DEF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2def]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DEF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DEF FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">FMS (CODONS 1-147) ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Formylmethionine_deformylase Formylmethionine deformylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.31 3.5.1.31] </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=2def FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2def OCA], [https://pdbe.org/2def PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2def RCSB], [https://www.ebi.ac.uk/pdbsum/2def PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2def 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=2def FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2def OCA], [https://pdbe.org/2def PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2def RCSB], [https://www.ebi.ac.uk/pdbsum/2def PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2def ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == 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]
| + | [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] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| - | [[Category: Formylmethionine deformylase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Dardel, F]] | + | [[Category: Dardel F]] |
| - | [[Category: Meinnel, T]] | + | [[Category: Meinnel T]] |
| - | [[Category: Hydrolase]]
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| - | [[Category: Metalloprotease]]
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| 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]
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
In the accompanying paper, we report that zinc is unlikely to be the co-factor supporting peptide deformylase activity in vivo. In contrast, nickel binding promotes full enzyme activity. The three-dimensional structure of the resulting nickel-containing peptide deformylase (catalytic domain, residues 1 to 147) was solved by NMR using a 13C-15N-doubly labelled protein sample. A set of 2261 restraints could be collected, with an average of 15.4 per amino acid. The resolution, which shows a good definition for the position of most side-chains, is greatly improved compared to that previously reported for the zinc-containing, inactive form. A comparison of the two stuctures indicates however that both share the same 3D organization. This shows that the nature of the bound metal is the primary determinant of the hydrolytic activity of this enzyme. Site-directed mutagenesis enabled us to determine the conserved residues of PDF involved in the structure of the active site. In particular, a buried arginine appears to be critical for the positioning of Cys90, one of the metal ligands. Furthermore, the 3D structure of peptide deformylase was compared to thermolysin and metzincins. Although the structural folds are very different, they all display a common structural motif involving an alpha-helix and a three-stranded beta-sheet. These conserved structural elements build a common scaffold which includes the active site, suggesting a common hydrolytic mechanism for these proteases. Finally, an invariant glycine shared by both PDF and metzincins enables us to extend the conserved motif from HEXXH to HEXXHXXG.
Solution structure of nickel-peptide deformylase.,Dardel F, Ragusa S, Lazennec C, Blanquet S, Meinnel T J Mol Biol. 1998 Jul 17;280(3):501-13. PMID:9665852[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Dardel F, Ragusa S, Lazennec C, Blanquet S, Meinnel T. Solution structure of nickel-peptide deformylase. J Mol Biol. 1998 Jul 17;280(3):501-13. PMID:9665852 doi:10.1006/jmbi.1998.1882
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