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Literature summary extracted from

  • Bao, X.; Pachikara, N.D.; Oey, C.B.; Balakrishnan, A.; Westblade, L.F.; Tan, M.; Chase, T.; Nickels, B.E.; Fan, H.
    Non-coding nucleotides and amino acids near the active site regulate peptide deformylase expression and inhibitor susceptibility in Chlamydia trachomatis (2011), Microbiology, 157, 2569-2581.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
3.5.1.88 expressed in Escherichia coli strain ArcticExpress Chlamydia trachomatis

Protein Variants

EC Number Protein Variants Comment Organism
3.5.1.88 F134C the mutation alters the enzyme activity (nearly 2fold higher Km and increased kcat value as compared with the wild type enzyme) and affects protein stability Chlamydia trachomatis
3.5.1.88 F134C/R137S the mutation alters the enzyme activity (nearly 10fold higher Km, increased kcat and 27% decrease in the kcat/Km value as compared with the wild type enzyme) and is 6.3fold more resistant towards inhibitor GM6001 as the wild type enzyme Chlamydia trachomatis
3.5.1.88 R137S the mutation alters the enzyme activity (nearly 2fold higher Km and increased kcat value as compared with the wild type enzyme) and affects protein stability Chlamydia trachomatis

Inhibitors

EC Number Inhibitors Comment Organism Structure
3.5.1.88 N-(R)-[2-(hydroxyaminocarbonyl)methyl]-4-methylpentanoyl-L-naphthylalanyl-L-alanine amide
-
 Chlamydia trachomatis
3.5.1.88 N-[(2R)-2-(hydroxamidocarbonylmethyl)-4-methylpentanoyl]-L-tryptophan methylamide
-
 Chlamydia trachomatis

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.5.1.88 5
-
 N-formyl-Met-Ala-Ser wild type enzyme, at pH 7.2 and 37°C Chlamydia trachomatis
3.5.1.88 9.2
-
 N-formyl-Met-Ala-Ser mutant enzyme F134C, at pH 7.2 and 37°C Chlamydia trachomatis
3.5.1.88 9.3
-
 N-formyl-Met-Ala-Ser mutant enzyme R137S, at pH 7.2 and 37°C Chlamydia trachomatis
3.5.1.88 48
-
 N-formyl-Met-Ala-Ser mutant enzyme F134C/R137S, at pH 7.2 and 37°C Chlamydia trachomatis

Organism

EC Number Organism UniProt Comment Textmining
3.5.1.88 Chlamydia trachomatis
-
-
-
3.5.1.88 Chlamydia trachomatis GR10
-
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
3.5.1.88 TALON affinity metal resin column chromatography Chlamydia trachomatis

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.5.1.88 N-formyl-Met-Ala-Ser + H2O
-
 Chlamydia trachomatis formate + Met-Ala-Ser
-
 ?
3.5.1.88 N-formyl-Met-Ala-Ser + H2O
-
 Chlamydia trachomatis GR10 formate + Met-Ala-Ser
-
 ?

Synonyms

EC Number Synonyms Comment Organism
3.5.1.88 PDF
-
 Chlamydia trachomatis

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
3.5.1.88 6.4
-
 N-formyl-Met-Ala-Ser wild type enzyme, at pH 7.2 and 37°C Chlamydia trachomatis
3.5.1.88 19.6
-
 N-formyl-Met-Ala-Ser mutant enzyme F134C, at pH 7.2 and 37°C Chlamydia trachomatis
3.5.1.88 22.1
-
 N-formyl-Met-Ala-Ser mutant enzyme R137S, at pH 7.2 and 37°C Chlamydia trachomatis
3.5.1.88 45.3
-
 N-formyl-Met-Ala-Ser mutant enzyme F134C/R137S, at pH 7.2 and 37°C Chlamydia trachomatis

Ki Value [mM]

EC Number Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
3.5.1.88 0.000148
-
 N-[(2R)-2-(hydroxamidocarbonylmethyl)-4-methylpentanoyl]-L-tryptophan methylamide mutant enzyme R137S, at pH 7.2 and 37°C Chlamydia trachomatis
3.5.1.88 0.00016
-
 N-[(2R)-2-(hydroxamidocarbonylmethyl)-4-methylpentanoyl]-L-tryptophan methylamide wild type enzyme, at pH 7.2 and 37°C Chlamydia trachomatis
3.5.1.88 0.001
-
 N-[(2R)-2-(hydroxamidocarbonylmethyl)-4-methylpentanoyl]-L-tryptophan methylamide mutant enzyme F134C/R137S, at pH 7.2 and 37°C Chlamydia trachomatis
3.5.1.88 143
-
 N-[(2R)-2-(hydroxamidocarbonylmethyl)-4-methylpentanoyl]-L-tryptophan methylamide mutant enzyme F134C, at pH 7.2 and 37°C Chlamydia trachomatis

Expression

EC Number Organism Comment Expression
3.5.1.88 Chlamydia trachomatis the GR10 mutation increases transcription from the chlamydial peptide deformylase promoter by stabilizing interactions between the C-terminal domain of the RNA polymerase alpha subunit and upstream DNA up

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
3.5.1.88 0.948
-
 N-formyl-Met-Ala-Ser mutant enzyme F134C/R137S, at pH 7.2 and 37°C Chlamydia trachomatis
3.5.1.88 1.296
-
 N-formyl-Met-Ala-Ser wild type enzyme, at pH 7.2 and 37°C Chlamydia trachomatis
3.5.1.88 2.143
-
 N-formyl-Met-Ala-Ser mutant enzyme F134C, at pH 7.2 and 37°C Chlamydia trachomatis
3.5.1.88 2.387
-
 N-formyl-Met-Ala-Ser mutant enzyme R137S, at pH 7.2 and 37°C Chlamydia trachomatis