|
|
| (2 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | + | |
| | ==Crystal structure of Arabidopsis thaliana peptide deformylase 1B (AtPDF1B) in complex with inhibitor 6b== | | ==Crystal structure of Arabidopsis thaliana peptide deformylase 1B (AtPDF1B) in complex with inhibitor 6b== |
| - | <StructureSection load='3o3j' size='340' side='right' caption='[[3o3j]], [[Resolution|resolution]] 3.00Å' scene=''> | + | <StructureSection load='3o3j' size='340' side='right'caption='[[3o3j]], [[Resolution|resolution]] 3.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3o3j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O3J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3O3J FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3o3j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O3J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O3J FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BB4:2-(5-BROMO-1H-INDOL-3-YL)-N-HYDROXYACETAMIDE'>BB4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3m6o|3m6o]], [[3m6p|3m6p]], [[3m6q|3m6q]], [[3m6r|3m6r]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BB4:2-(5-BROMO-1H-INDOL-3-YL)-N-HYDROXYACETAMIDE'>BB4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">def ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])</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=3o3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o3j OCA], [https://pdbe.org/3o3j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o3j RCSB], [https://www.ebi.ac.uk/pdbsum/3o3j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o3j 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>
| + | |
| - | <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=3o3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o3j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3o3j RCSB], [http://www.ebi.ac.uk/pdbsum/3o3j PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DEF1B_ARATH DEF1B_ARATH]] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Has a preferred substrate specificity towards the photosystem II (PS II) D1 polypeptide.<ref>PMID:11060042</ref> | + | [https://www.uniprot.org/uniprot/DEF1B_ARATH DEF1B_ARATH] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Has a preferred substrate specificity towards the photosystem II (PS II) D1 polypeptide.<ref>PMID:11060042</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 19: |
Line 18: |
| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 3o3j" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| Line 24: |
Line 24: |
| | </StructureSection> | | </StructureSection> |
| | [[Category: Arabidopsis thaliana]] | | [[Category: Arabidopsis thaliana]] |
| - | [[Category: Peptide deformylase]] | + | [[Category: Large Structures]] |
| - | [[Category: Fieulaine, S]] | + | [[Category: Fieulaine S]] |
| - | [[Category: Giglione, C]] | + | [[Category: Giglione C]] |
| - | [[Category: Meinnel, T]] | + | [[Category: Meinnel T]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Hydrolase-hydrolase inhibitor complex]]
| + | |
| - | [[Category: Induced-fit]]
| + | |
| - | [[Category: N-terminal excision pathway]]
| + | |
| - | [[Category: Nme]]
| + | |
| - | [[Category: Pdf]]
| + | |
| Structural highlights
Function
DEF1B_ARATH Removes the formyl group from the N-terminal Met of newly synthesized proteins. Has a preferred substrate specificity towards the photosystem II (PS II) D1 polypeptide.[1]
Publication Abstract from PubMed
For several decades, molecular recognition has been considered one of the most fundamental processes in biochemistry. For enzymes, substrate binding is often coupled to conformational changes that alter the local environment of the active site to align the reactive groups for efficient catalysis and to reach the transition state. Adaptive substrate recognition is a well-known concept; however, it has been poorly characterized at a structural level because of its dynamic nature. Here, we provide a detailed mechanism for an induced-fit process at atomic resolution. We take advantage of a slow, tight binding inhibitor-enzyme system, actinonin-peptide deformylase. Crystal structures of the initial open state and final closed state were solved, as well as those of several intermediate mimics captured during the process. Ligand-induced reshaping of a hydrophobic pocket drives closure of the active site, which is finally "zipped up" by additional binding interactions. Together with biochemical analyses, these data allow a coherent reconstruction of the sequence of events leading from the encounter complex to the key-lock binding state of the enzyme. A "movie" that reconstructs this entire process can be further extrapolated to catalysis.
Trapping conformational States along ligand-binding dynamics of Peptide deformylase: the impact of induced fit on enzyme catalysis.,Fieulaine S, Boularot A, Artaud I, Desmadril M, Dardel F, Meinnel T, Giglione C PLoS Biol. 2011 May;9(5):e1001066. Epub 2011 May 24. PMID:21629676[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Giglione C, Serero A, Pierre M, Boisson B, Meinnel T. Identification of eukaryotic peptide deformylases reveals universality of N-terminal protein processing mechanisms. EMBO J. 2000 Nov 1;19(21):5916-29. PMID:11060042 doi:10.1093/emboj/19.21.5916
- ↑ Fieulaine S, Boularot A, Artaud I, Desmadril M, Dardel F, Meinnel T, Giglione C. Trapping conformational States along ligand-binding dynamics of Peptide deformylase: the impact of induced fit on enzyme catalysis. PLoS Biol. 2011 May;9(5):e1001066. Epub 2011 May 24. PMID:21629676 doi:10.1371/journal.pbio.1001066
|
