4dcx: Difference between revisions
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[[ | ==X-ray structure of NikA in complex with Fe(1R,2R)-N,N'-Bis(2-pyridylmethyl)-N,N'-dicarboxymethyl-1,2-cyclohexanediamine== | ||
<StructureSection load='4dcx' size='340' side='right' caption='[[4dcx]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4dcx]] is a 2 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=4DCX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DCX FirstGlance]. <br> | |||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=L2D:{2,2-[(1R,2R)-CYCLOHEXANE-1,2-DIYLBIS{[(PYRIDIN-2-YL-KAPPAN)METHYL]IMINO-KAPPAN}]DIACETATO-KAPPAO(2-)}IRON'>L2D</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br> | |||
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1zlq|1zlq]], [[4dcy|4dcy]]</td></tr> | |||
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b3476, JW3441, nikA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr> | |||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4dcx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dcx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dcx RCSB], [http://www.ebi.ac.uk/pdbsum/4dcx PDBsum]</span></td></tr> | |||
<table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Understanding the interaction of a protein with a relevant ligand is crucial for the design of an artificial metalloenzyme. Our own interest is focused on the synthesis of artificial monooxygenases. In an initial effort, we have used the periplasmic nickel-binding protein NikA from Escherichia coli and iron complexes in which N(2)Py(2) ligands (where Py is pyridine) have been varied in terms of charge, aromaticity, and size. Six "NikA/iron complex" hybrids have been characterized by X-ray crystallography, and their interactions and solution properties have been studied. The hybrids are stable as indicated by their K (d) values, which are all in the micromolar range. The X-ray structures show that the ligands interact with NikA through salt bridges with arginine residues and pi-stacking with a tryptophan residue. We have further characterized these interactions using quantum mechanical calculations and determined that weak CH/pi hydrogen bonds finely modulate the stability differences between hybrids. We emphasize the important role of the tryptophan residues. Thus, our study aims at the complete characterization of the factors that condition the interaction of an artificial ligand and a protein and their implications for catalysis. Besides its potential usefulness in the synthesis of artificial monooxygenases, our approach should be generally applicable in the field of artificial metalloenzymes. | |||
The structure of the periplasmic nickel-binding protein NikA provides insights for artificial metalloenzyme design.,Cherrier MV, Girgenti E, Amara P, Iannello M, Marchi-Delapierre C, Fontecilla-Camps JC, Menage S, Cavazza C J Biol Inorg Chem. 2012 Apr 21. PMID:22526565<ref>PMID:22526565</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
< | |||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Amara, P.]] | [[Category: Amara, P.]] | ||
Revision as of 10:43, 5 June 2014
X-ray structure of NikA in complex with Fe(1R,2R)-N,N'-Bis(2-pyridylmethyl)-N,N'-dicarboxymethyl-1,2-cyclohexanediamineX-ray structure of NikA in complex with Fe(1R,2R)-N,N'-Bis(2-pyridylmethyl)-N,N'-dicarboxymethyl-1,2-cyclohexanediamine
Structural highlights
Publication Abstract from PubMedUnderstanding the interaction of a protein with a relevant ligand is crucial for the design of an artificial metalloenzyme. Our own interest is focused on the synthesis of artificial monooxygenases. In an initial effort, we have used the periplasmic nickel-binding protein NikA from Escherichia coli and iron complexes in which N(2)Py(2) ligands (where Py is pyridine) have been varied in terms of charge, aromaticity, and size. Six "NikA/iron complex" hybrids have been characterized by X-ray crystallography, and their interactions and solution properties have been studied. The hybrids are stable as indicated by their K (d) values, which are all in the micromolar range. The X-ray structures show that the ligands interact with NikA through salt bridges with arginine residues and pi-stacking with a tryptophan residue. We have further characterized these interactions using quantum mechanical calculations and determined that weak CH/pi hydrogen bonds finely modulate the stability differences between hybrids. We emphasize the important role of the tryptophan residues. Thus, our study aims at the complete characterization of the factors that condition the interaction of an artificial ligand and a protein and their implications for catalysis. Besides its potential usefulness in the synthesis of artificial monooxygenases, our approach should be generally applicable in the field of artificial metalloenzymes. The structure of the periplasmic nickel-binding protein NikA provides insights for artificial metalloenzyme design.,Cherrier MV, Girgenti E, Amara P, Iannello M, Marchi-Delapierre C, Fontecilla-Camps JC, Menage S, Cavazza C J Biol Inorg Chem. 2012 Apr 21. PMID:22526565[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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