1XEN
High Resolution Crystal Structure of Escherichia coli Iron- Peptide Deformylase Bound To Formate
Summary for 1XEN
| Entry DOI | 10.2210/pdb1xen/pdb |
| Related | 1BSK 1DFF |
| Descriptor | Peptide deformylase, FE (III) ION, FORMIC ACID, ... (4 entities in total) |
| Functional Keywords | iron deformylase, formate, hydrolase |
| Biological source | Escherichia coli |
| Total number of polymer chains | 1 |
| Total formula weight | 19558.24 |
| Authors | Jain, R.,Hao, B.,Liu, R.-P.,Chan, M.K. (deposition date: 2004-09-10, release date: 2005-03-29, Last modification date: 2024-02-14) |
| Primary citation | Jain, R.,Hao, B.,Liu, R.-P.,Chan, M.K. Structures of E. coli peptide deformylase bound to formate: insight into the preference for Fe2+ over Zn2+ as the active site metal J.Am.Chem.Soc., 127:4558-4559, 2005 Cited by PubMed Abstract: E. coli peptide deformylase (PDF) catalyzes the deformylation of nascent polypeptides generated during protein synthesis. While PDF was originally thought to be a zinc enzyme, subsequent studies revealed that the active site metal is iron. In an attempt to understand this unusual metal preference, high-resolution structures of Fe-, Co-, and Zn-PDF were determined in complex with its deformylation product, formate. In all three structures, the formate ion binds the metal and forms hydrogen-bonding interactions with the backbone nitrogen of Leu91, the amide side chain of Gln50, and the carboxylate side chain of Glu133. One key difference, however, is how the formate binds the metal. In Fe-PDF and Co-PDF, formate binds in a bidentate fashion, while in Zn-PDF, it binds in a monodentate fashion. Importantly, these structural results provide the first clues into the origins of PDF's metal-dependent activity differences. On the basis of these structures, we propose that the basis for the higher activity of Fe-PDF stems from the better ability of iron to bind and activate the tetrahedral transition state required for cleavage of the N-terminal formyl group. PubMed: 15796505DOI: 10.1021/ja0503074 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.85 Å) |
Structure validation
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