Peptide deformylase

Peptide deformylase removes the formyl group from the N terminus of nascent polypeptides as they are synthesized by the ribosome.

The function of peptide deformylase can be described by the following equation, where formyl-L-methionyl peptide and water react under the formation of formate and methionyl peptide:

:H₂O + formyl-L-methionyl peptide $\backslash rightleftharpoons$ methionyl peptide + formate

File:Peptide deformylase.svg

This reaction takes place on the surface of the ribosome, where the C-terminal alpha-helix of the peptide deformylase interacts with a grove between ribosomal proteins uL22 and bL32, and rRNA.{{cite journal | vauthors = McGrath H, Černeková M, Kolář MH | title = Binding of the peptide deformylase on the ribosome surface modulates the exit tunnel interior | journal = Biophysical Journal | volume = 121 | issue = 23 | pages = 4443–4451 | date = December 2022 | pmid = 36335428 | doi = 10.1016/j.bpj.2022.11.004 | pmc = 9748369 | bibcode = 2022BpJ...121.4443M }}

For its function this enzyme belongs to the family of hydrolases, those acting on carbon-nitrogen bonds other than peptide bonds, specifically in linear amides. The systematic name of this enzyme class is formyl-L-methionyl peptide amidohydrolase.

As of late 2007, 34 structures have been solved for this class of enzymes, with PDB accession codes {{PDB link|1IX1}}, {{PDB link|1LM4}}, {{PDB link|1LM6}}, {{PDB link|1LME}}, {{PDB link|1LQW}}, {{PDB link|1LQY}}, {{PDB link|1LRU}}, {{PDB link|1LRY}}, {{PDB link|1N5N}}, {{PDB link|1Q1Y}}, {{PDB link|1S17}}, {{PDB link|1SV2}}, {{PDB link|1SZZ}}, {{PDB link|1V3Y}}, {{PDB link|1VEV}}, {{PDB link|1VEY}}, {{PDB link|1VEZ}}, {{PDB link|1WS0}}, {{PDB link|1WS1}}, {{PDB link|1XEM}}, {{PDB link|1XEN}}, {{PDB link|1XEO}}, {{PDB link|1Y6H}}, {{PDB link|1ZXZ}}, {{PDB link|1ZY0}}, {{PDB link|1ZY1}}, {{PDB link|2AI7}}, {{PDB link|2AI8}}, {{PDB link|2AI9}}, {{PDB link|2AIA}}, {{PDB link|2AIE}}, {{PDB link|2EW5}}, {{PDB link|2EW6}}, and {{PDB link|2EW7}}.

• Actinonin

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• {{cite journal | vauthors = Adams JM | title = On the release of the formyl group from nascent protein | journal = Journal of Molecular Biology | volume = 33 | issue = 3 | pages = 571–589 | date = May 1968 | pmid = 4973445 | doi = 10.1016/0022-2836(68)90307-0 }}
• {{cite journal | vauthors = Mazel D, Pochet S, Marlière P | title = Genetic characterization of polypeptide deformylase, a distinctive enzyme of eubacterial translation | journal = The EMBO Journal | volume = 13 | issue = 4 | pages = 914–923 | date = February 1994 | pmid = 8112305 | pmc = 394892 | doi = 10.1002/j.1460-2075.1994.tb06335.x }}
• {{cite journal | vauthors = Chan MK, Gong W, Rajagopalan PT, Hao B, Tsai CM, Pei D | title = Crystal structure of the Escherichia coli peptide deformylase | journal = Biochemistry | volume = 36 | issue = 45 | pages = 13904–13909 | date = November 1997 | pmid = 9374869 | doi = 10.1021/bi9711543 }}
• {{cite journal | vauthors = Becker A, Schlichting I, Kabsch W, Schultz S, Wagner AF | title = Structure of peptide deformylase and identification of the substrate binding site | journal = The Journal of Biological Chemistry | volume = 273 | issue = 19 | pages = 11413–11416 | date = May 1998 | pmid = 9565550 | doi = 10.1074/jbc.273.19.11413 | doi-access = free }}
• {{cite journal | vauthors = Becker A, Schlichting I, Kabsch W, Groche D, Schultz S, Wagner AF | title = Iron center, substrate recognition and mechanism of peptide deformylase | journal = Nature Structural Biology | volume = 5 | issue = 12 | pages = 1053–1058 | date = December 1998 | pmid = 9846875 | doi = 10.1038/4162 | s2cid = 40528211 }}
• {{cite journal | vauthors = Rajagopalan PT, Yu XC, Pei D | year = 1997 | title = Peptide deformylase: a new type of mononuclear iron protein | journal = J. Am. Chem. Soc. | volume = 119 | pages = 12418–12419 | doi = 10.1021/ja9734096 | issue = 50 | bibcode = 1997JAChS.11912418R }}
• {{cite journal | vauthors = Groche D, Becker A, Schlichting I, Kabsch W, Schultz S, Wagner AF | title = Isolation and crystallization of functionally competent Escherichia coli peptide deformylase forms containing either iron or nickel in the active site | journal = Biochemical and Biophysical Research Communications | volume = 246 | issue = 2 | pages = 342–346 | date = May 1998 | pmid = 9610360 | doi = 10.1006/bbrc.1998.8616 | bibcode = 1998BBRC..246..342G }}
• {{cite journal | vauthors = Rajagopalan PT, Grimme S, Pei D | title = Characterization of cobalt(II)-substituted peptide deformylase: function of the metal ion and the catalytic residue Glu-133 | journal = Biochemistry | volume = 39 | issue = 4 | pages = 779–790 | date = February 2000 | pmid = 10651644 | doi = 10.1021/bi9919899 }}
• {{cite journal | vauthors = Hu YJ, Wei Y, Zhou Y, Rajagopalan PT, Pei D | title = Determination of substrate specificity for peptide deformylase through the screening of a combinatorial peptide library | journal = Biochemistry | volume = 38 | issue = 2 | pages = 643–650 | date = January 1999 | pmid = 9888804 | doi = 10.1021/bi9820412 }}
• {{cite journal | vauthors = Ragusa S, Mouchet P, Lazennec C, Dive V, Meinnel T | title = Substrate recognition and selectivity of peptide deformylase. Similarities and differences with metzincins and thermolysin | journal = Journal of Molecular Biology | volume = 289 | issue = 5 | pages = 1445–1457 | date = June 1999 | pmid = 10373378 | doi = 10.1006/jmbi.1999.2832 }}
• {{cite journal | vauthors = Giglione C, Pierre M, Meinnel T | title = Peptide deformylase as a target for new generation, broad spectrum antimicrobial agents | journal = Molecular Microbiology | volume = 36 | issue = 6 | pages = 1197–1205 | date = June 2000 | pmid = 10931273 | doi = 10.1046/j.1365-2958.2000.01908.x | s2cid = 23289620 | doi-access = free }}
• {{cite journal | vauthors = Pei D | title = Peptide deformylase: a target for novel antibiotics? | journal = Expert Opinion on Therapeutic Targets | volume = 5 | issue = 1 | pages = 23–40 | date = February 2001 | pmid = 15992166 | doi = 10.1517/14728222.5.1.23 | s2cid = 11385977 }}

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{{Carbon-nitrogen non-peptide hydrolases}}

{{Enzymes}}

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Category:EC 3.5.1

Category:Enzymes of known structure

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