1icj: Difference between revisions

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Revision as of 12:48, 20 March 2008

File:1icj.gif

, resolution 1.90Å

Ligands:

, and

Gene:

DEF (Escherichia coli)

Activity:

Formylmethionine deformylase, with EC number 3.5.1.31

Coordinates:

save as pdb, mmCIF, xml

PDF PROTEIN IS CRYSTALLIZED AS NI2+ CONTAINING FORM, COCRYSTALLIZED WITH INHIBITOR POLYETHYLENE GLYCOL (PEG)

OverviewOverview

Peptide deformylase is an essential metalloenzyme required for the removal of the formyl group at the N terminus of nascent polypeptide chains in eubacteria. The Escherichia coli enzyme uses Fe2+ and nearly retains its activity on substitution of the metal ion by Ni2+. We have solved the structure of the Ni2+ enzyme at 1.9-A resolution by x-ray crystallography. Each of the three monomers in the asymmetric unit contains one Ni2+ ion and, in close proximity, one molecule of polyethylene glycol. Polyethylene glycol is shown to be a competitive inhibitor with a KI value of 6 mM with respect to formylmethionine under conditions similar to those used for crystallization. We have also solved the structure of the inhibitor-free enzyme at 2.5-A resolution. The two structures are identical within the estimated errors of the models. The hydrogen bond network stabilizing the active site involves nearly all conserved amino acid residues and well defined water molecules, one of which ligates to the tetrahedrally coordinated Ni2+ ion.

About this StructureAbout this Structure

1ICJ is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.

ReferenceReference

Structure of peptide deformylase and identification of the substrate binding site., Becker A, Schlichting I, Kabsch W, Schultz S, Wagner AF, J Biol Chem. 1998 May 8;273(19):11413-6. PMID:9565550

Page seeded by OCA on Thu Mar 20 11:48:31 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1icj.gif|left|200px]]<br /><applet load="1icj" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:1icj.gif|left|200px]]
-caption="1icj, resolution 1.90&Aring;" />
-'''PDF PROTEIN IS CRYSTALLIZED AS NI2+ CONTAINING FORM, COCRYSTALLIZED WITH INHIBITOR POLYETHYLENE GLYCOL (PEG)'''<br />
+ {{Structure
+|PDB= 1icj |SIZE=350|CAPTION= <scene name='initialview01'>1icj</scene>, resolution 1.90&Aring;
+|SITE=
+|LIGAND= <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> and <scene name='pdbligand=2PE:NONAETHYLENE GLYCOL'>2PE</scene>
+|ACTIVITY= [http://en.wikipedia.org/wiki/Formylmethionine_deformylase Formylmethionine deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.31 3.5.1.31]
+|GENE= DEF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
+}}
+'''PDF PROTEIN IS CRYSTALLIZED AS NI2+ CONTAINING FORM, COCRYSTALLIZED WITH INHIBITOR POLYETHYLENE GLYCOL (PEG)'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-ICJ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=NI:'>NI</scene>, <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=2PE:'>2PE</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Formylmethionine_deformylase Formylmethionine deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.31 3.5.1.31] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ICJ OCA].
+ICJ is a [[Single protein]] structure of 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=1ICJ OCA].
 ==Reference==
-Structure of peptide deformylase and identification of the substrate binding site., Becker A, Schlichting I, Kabsch W, Schultz S, Wagner AF, J Biol Chem. 1998 May 8;273(19):11413-6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9565550 9565550]
+Structure of peptide deformylase and identification of the substrate binding site., Becker A, Schlichting I, Kabsch W, Schultz S, Wagner AF, J Biol Chem. 1998 May 8;273(19):11413-6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9565550 9565550]
 [[Category: Escherichia coli]]
 [[Category: Formylmethionine deformylase]]
@@ Line 26: / Line 35: @@
 [[Category: protein synthesis]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:10:21 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 11:48:31 2008''