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Literature summary for 3.5.1.88 extracted from

  • Frank, J.A.; Lorimer, D.; Youle, M.; Witte, P.; Craig, T.; Abendroth, J.; Rohwer, F.; Edwards, R.A.; Segall, A.M.; Burgin, A.B.
    Structure and function of a cyanophage-encoded peptide deformylase (2013), ISME J., 7, 1150-1160.
    View publication on PubMedView publication on EuropePMC
Search for more literature for 3.5.1.88

Cloned(Commentary)

Cloned (Comment) Organism
DNA and amino acid sequence determination and analysis, phylogenetic analysis, recombinant expression of His6-tagged enzyme in Escherichia coli strain BL21(DE3) Synechococcus phage S-SSM7
DNA and amino acid sequence determination and analysis, recombinant expression Arabidopsis thaliana

Crystallization (Commentary)

Crystallization (Comment) Organism
purified recombinant enzyme, X-ray diffraction structure determination and analysis at 1.95 A resolution Arabidopsis thaliana
purified recombinant enzyme, X-ray diffraction structure determination and analysis at 1.95 A resolution, comparison to the crystal structure of the Arabidopsis thaliana chloroplast PDF enzyme Synechococcus phage S-SSM7

Localization

Localization Comment Organism GeneOntology No. Textmining
chloroplast
-
 Arabidopsis thaliana 9507
-

Metals/Ions

Metals/Ions Comment Organism Structure
Zn2+ catalytic zinc Synechococcus phage S-SSM7

Organism

Organism UniProt Comment Textmining
Arabidopsis thaliana
-
-
-
Synechococcus phage S-SSM7 E3SLL2
-
-

Purification (Commentary)

Purification (Comment) Organism
recombinant His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity cromatography Synechococcus phage S-SSM7

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
additional information the enzyme deformylates the N-terminal tetrapeptides from D1 proteins more efficiently than those from ribosomal proteins Synechococcus phage S-SSM7 ?
-
 ?

Synonyms

Synonyms Comment Organism
PDF
-
 Arabidopsis thaliana
PDF
-
 Synechococcus phage S-SSM7

General Information

General Information Comment Organism
evolution phylogenetic analysis, the cyanophage enzyme belongs to the type 1B subclass, but lacking the C-terminal a-helix characteristic of that group. PDFs are a subclass of the metalloprotease superfamily of enzymes known as the clan MA and MB metalloproteases. Proteins from this family share a common structure containing a three-stranded beta strand facing a catalytic metal and a HEXXH motif-containing alpha helix. Activity of phage and bacterial PDFs on N-terminal tetrapeptides derived from D1 proteins and cyanobacterial ribosomal proteins, overview Synechococcus phage S-SSM7
evolution the enzyme belongs to the type 1B subclass.PDFs are a subclass of the metalloprotease superfamily of enzymes known as the clan MA and MB metalloproteases. Proteins from this family share a common structure containing a three-stranded beta strand facing a catalytic metal and a HEXXH motif-containing alpha helix Arabidopsis thaliana
physiological function synthesis of functional proteins in bacteria requires co-translational removal of the N-terminal formyl group by a peptide deformylase, enzyme PDF expression during infection might benefit phage replication Synechococcus phage S-SSM7