2def
From Proteopedia
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| - | [[Image:2def.jpg|left|200px]]< | + | [[Image:2def.jpg|left|200px]] |
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| - | '''PEPTIDE DEFORMYLASE CATALYTIC CORE (RESIDUES 1-147), NMR, 20 STRUCTURES''' | + | {{Structure |
| + | |PDB= 2def |SIZE=350|CAPTION= <scene name='initialview01'>2def</scene> | ||
| + | |SITE= <scene name='pdbsite=CAT:Catalytic+Ni+Ion'>CAT</scene> | ||
| + | |LIGAND= <scene name='pdbligand=NI:NICKEL (II) ION'>NI</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= FMS (CODONS 1-147) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | ||
| + | }} | ||
| + | |||
| + | '''PEPTIDE DEFORMYLASE CATALYTIC CORE (RESIDUES 1-147), NMR, 20 STRUCTURES''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2DEF is a [ | + | 2DEF 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=2DEF OCA]. |
==Reference== | ==Reference== | ||
| - | 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:[http:// | + | 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:[http://www.ncbi.nlm.nih.gov/pubmed/9665852 9665852] |
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Formylmethionine deformylase]] | [[Category: Formylmethionine deformylase]] | ||
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[[Category: metalloprotease]] | [[Category: metalloprotease]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:26:14 2008'' |
Revision as of 14:26, 20 March 2008
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| Sites: | |||||||
| Ligands: | |||||||
| Gene: | FMS (CODONS 1-147) (Escherichia coli) | ||||||
| Activity: | Formylmethionine deformylase, with EC number 3.5.1.31 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
PEPTIDE DEFORMYLASE CATALYTIC CORE (RESIDUES 1-147), NMR, 20 STRUCTURES
Overview
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.
About this Structure
2DEF is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
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
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