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| | ==Crystal Structure of Peptide Deformylase from Streptococcus pneumoniae== | | ==Crystal Structure of Peptide Deformylase from Streptococcus pneumoniae== |
| - | <StructureSection load='1lm6' size='340' side='right' caption='[[1lm6]], [[Resolution|resolution]] 1.75Å' scene=''> | + | <StructureSection load='1lm6' size='340' side='right'caption='[[1lm6]], [[Resolution|resolution]] 1.75Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1lm6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"diplococcus_pneumoniae"_(klein_1884)_weichselbaum_1886 "diplococcus pneumoniae" (klein 1884) weichselbaum 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LM6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LM6 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1lm6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LM6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LM6 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></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]] 1.75Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></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=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1lm4|1lm4]], [[1lme|1lme]]</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=1lm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lm6 OCA], [https://pdbe.org/1lm6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lm6 RCSB], [https://www.ebi.ac.uk/pdbsum/1lm6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lm6 ProSAT]</span></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>
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| - | <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=1lm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lm6 OCA], [http://pdbe.org/1lm6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lm6 RCSB], [http://www.ebi.ac.uk/pdbsum/1lm6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lm6 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DEF_STRPN DEF_STRPN]] 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 (By similarity). | + | [https://www.uniprot.org/uniprot/DEF_STRPN DEF_STRPN] 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 (By similarity). |
| | == 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: Peptide deformylase]] | + | [[Category: Large Structures]] |
| - | [[Category: Ericson, C]] | + | [[Category: Streptococcus pneumoniae]] |
| - | [[Category: Klock, H]] | + | [[Category: Ericson C]] |
| - | [[Category: Kreusch, A]] | + | [[Category: Klock H]] |
| - | [[Category: Lee, C C]] | + | [[Category: Kreusch A]] |
| - | [[Category: Lesley, S A]] | + | [[Category: Lee CC]] |
| - | [[Category: McMullan, D]] | + | [[Category: Lesley SA]] |
| - | [[Category: Ng, K]] | + | [[Category: McMullan D]] |
| - | [[Category: Shin, T]] | + | [[Category: Ng K]] |
| - | [[Category: Spraggon, G]] | + | [[Category: Shin T]] |
| - | [[Category: Vincent, J]] | + | [[Category: Spraggon G]] |
| - | [[Category: Warner, I]] | + | [[Category: Vincent J]] |
| - | [[Category: Hydrolase]]
| + | [[Category: Warner I]] |
| - | [[Category: Metalloenzyme]]
| + | |
| - | [[Category: Pdf]]
| + | |
| Structural highlights
Function
DEF_STRPN 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 (By similarity).
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
Peptide deformylase (PDF) has received considerable attention during the last few years as a potential target for a new type of antibiotics. It is an essential enzyme in eubacteria for the removal of the formyl group from the N terminus of the nascent polypeptide chain. We have solved the X-ray structures of four members of this enzyme family, two from the Gram-positive pathogens Streptococcus pneumoniae and Staphylococcus aureus, and two from the Gram-negative bacteria Thermotoga maritima and Pseudomonas aeruginosa. Combined with the known structures from the Escherichia coli enzyme and the recently solved structure of the eukaryotic deformylase from Plasmodium falciparum, a complete picture of the peptide deformylase structure and function relationship is emerging. This understanding could help guide a more rational design of inhibitors. A structure-based comparison between PDFs reveals some conserved differences between type I and type II enzymes. Moreover, our structures provide insights into the known instability of PDF caused by oxidation of the metal-ligating cysteine residue.
Structure analysis of peptide deformylases from Streptococcus pneumoniae, Staphylococcus aureus, Thermotoga maritima and Pseudomonas aeruginosa: snapshots of the oxygen sensitivity of peptide deformylase.,Kreusch A, Spraggon G, Lee CC, Klock H, McMullan D, Ng K, Shin T, Vincent J, Warner I, Ericson C, Lesley SA J Mol Biol. 2003 Jul 4;330(2):309-21. PMID:12823970[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kreusch A, Spraggon G, Lee CC, Klock H, McMullan D, Ng K, Shin T, Vincent J, Warner I, Ericson C, Lesley SA. Structure analysis of peptide deformylases from Streptococcus pneumoniae, Staphylococcus aureus, Thermotoga maritima and Pseudomonas aeruginosa: snapshots of the oxygen sensitivity of peptide deformylase. J Mol Biol. 2003 Jul 4;330(2):309-21. PMID:12823970
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