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Literature summary for 3.5.1.88 extracted from

  • Grzela, R.; Nusbaum, J.; Fieulaine, S.; Lavecchia, F.; Bienvenut, W.V.; Dian, C.; Meinnel, T.; Giglione, C.
    The C-terminal residue of phage Vp16 PDF, the smallest peptide deformylase, acts as an offset element locking the active conformation (2017), Sci. Rep., 7, 11041 .
    View publication on PubMedView publication on EuropePMC
Search for more literature for 3.5.1.88

Cloned(Commentary)

Cloned (Comment) Organism
orf60T, phylogenetic analysis Escherichia coli
orf60T, phylogenetic analysis Vibrio phage VP16T

Protein Variants

Protein Variants Comment Organism
additional information generation of several chimeric enzyme mutants PDFS with various length of their C-domain constructed from Vp16 PDF and Escherichia coli PDF, and complementation of Escherichia coli strain PAL421Tr which is deficient for enzyme PDF, substrate specificity analysis and comparison, overview Escherichia coli
additional information generation of several chimeric enzyme mutants PDFS with various length of their C-domain constructed from Vp16 PDF and Escherichia coli PDF, and complementation of Escherichia coli strain PAL421Tr which is deficient for enzyme PDF, substrate specificity analysis and comparison, overview Vibrio phage VP16T

Metals/Ions

Metals/Ions Comment Organism Structure
Zn2+ bound in the active site Escherichia coli
Zn2+ bound in the active site Vibrio phage VP16T

Organism

Organism UniProt Comment Textmining
Escherichia coli P0A6K3
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Vibrio phage VP16T Q6VT21 isolated from Vibrio parahaemolyticus strain 16
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Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
formyl-Met-Ala-Lys + H2O
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 Escherichia coli formate + Met-Ala-Lys
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 ?
formyl-Met-Ala-Lys + H2O the substrate is corresponding to the putative N-termini of viral proteins Vibrio phage VP16T formate + Met-Ala-Lys
-
 ?
formyl-Met-Ala-Ser + H2O
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 Escherichia coli formate + Met-Ala-Ser
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 ?
formyl-Met-Ala-Ser + H2O the substrate is corresponding to the putative capsid N-terminus Vibrio phage VP16T formate + Met-Ala-Ser
-
 ?
formyl-Met-Lys-Leu + H2O
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 Escherichia coli formate + Met-Lys-Leu
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 ?
formyl-Met-Lys-Leu + H2O the substrate is corresponding to the putative N-termini of viral proteins Vibrio phage VP16T formate + Met-Lys-Leu
-
 ?
formyl-Met-Ser-Asn + H2O
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 Escherichia coli formate + Met-Ser-Asn
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 ?
formyl-Met-Ser-Asn + H2O the substrate is corresponding to the putative helicase N-terminus Vibrio phage VP16T formate + Met-Ser-Asn
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 ?
formyl-Met-Thr-Thr + H2O
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 Escherichia coli formate + Met-Thr-Thr
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 ?
formyl-Met-Thr-Thr + H2O the substrate is corresponding to the putative N-termini of viral proteins Vibrio phage VP16T formate + Met-Thr-Thr
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 ?
additional information comparison of substrate specificity of the Escherichia coli PDF Vibrio phage Vp16 PDF Escherichia coli ?
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additional information Vp16 PDF shows high catalytic efficiency in vitro and with substrate specificity comparable to other PDFs, comparison to the Escherichia coli PDF Vibrio phage VP16T ?
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Subunits

Subunits Comment Organism
More the C-terminal extremity of Vp16 PDF revealed that it is tightly bound to the globular core of the protein involving (i) a hydrogen bond made between the side chains of the penultimate residue, Thr136, and that of Tyr88 located immediately after motif II (m2, composed of residues 83-87) and (ii) a salt bridge between the C-terminal carboxyl group of the last residue, Ile137, and the side chain of Lys91, with both amino acids sitting in a structured loop between strands beta4 and beta5. In addition, the side chain extremity of Lys95 is within hydrogen bonding distance of the carboxyl terminal of Ile137. The side chain of Ile137 is clamped by residues coming from beta4 and beta5 strands and their connecting loop, especially by Tyr88, Lys91, Val93 and Lys95 side chains Vibrio phage VP16T

Synonyms

Synonyms Comment Organism
PDF
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 Escherichia coli
PDF
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 Vibrio phage VP16T

General Information

General Information Comment Organism
additional information the C-terminal residue of phage Vp16 PDF, the smallest known peptide deformylase, acts as an offset element locking the active conformation. The crystal structure of Vp16 PDF reveals a classical PDF fold Vibrio phage VP16T