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Literature summary for 4.1.1.23 extracted from

  • Iiams, V.; Desai, B.J.; Fedorov, A.A.; Fedorov, E.V.; Almo, S.C.; Gerlt, J.A.
    Mechanism of the orotidine 5-monophosphate decarboxylase-catalyzed reaction: importance of residues in the orotate binding site (2011), Biochemistry, 50, 8497-8507.
    View publication on PubMedView publication on EuropePMC
Search for more literature for 4.1.1.23

Crystallization (Commentary)

Crystallization (Comment) Organism
crystal structures of hydrophobic pocket mutants I96S, I96T, L123N, L123S, V155D, and V155S in the presence of 1-(5'-phospho-beta-D-ribofuranosyl)barbituric acid or azaUMP. The interactions of the transition state/vinyl carbanion intermediate with the active site are preserved in each mutant Methanobacterium thermoautotrophicus

Protein Variants

Protein Variants Comment Organism
D70N 0.002% of wild-type activity Methanobacterium thermoautotrophicus
D70N/I96S complete loss of activity Methanobacterium thermoautotrophicus
D70N/L123S complete loss of activity Methanobacterium thermoautotrophicus
D70N/V155S complete loss of activity Methanobacterium thermoautotrophicus
I96S 0.5% of wild-type activity Methanobacterium thermoautotrophicus
I96T 15% of wild-type activity Methanobacterium thermoautotrophicus
L123N 10% of wild-type activity Methanobacterium thermoautotrophicus
L123S 8% of wild-type activity Methanobacterium thermoautotrophicus
additional information substitutions of hydrophobic residues in a pocket proximal to the carboxylate group of the substrate, i.e. Ile 96, Leu 123, and Val 155 with neutral hydrophilic residues decrease the value of kcat by as much as 400fold but have minimal effect on the value of kex for exchange of H6 of the 5-fluoro-UMP product analog with solvent deuterium Methanobacterium thermoautotrophicus
V155D less than 0.001% of wild-type activity Methanobacterium thermoautotrophicus
V155S 1% of wild-type activity Methanobacterium thermoautotrophicus

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.001
-
 orotidine 5'-phosphate mutant I96S, pH 7.1, 25°C Methanobacterium thermoautotrophicus
0.0016
-
 orotidine 5'-phosphate wild-type, pH 7.1, 25°C Methanobacterium thermoautotrophicus
0.0023
-
 orotidine 5'-phosphate mutant I96T, pH 7.1, 25°C Methanobacterium thermoautotrophicus
0.003
-
 orotidine 5'-phosphate mutant L123S, pH 7.1, 25°C Methanobacterium thermoautotrophicus
0.0035
-
 orotidine 5'-phosphate mutant L123N, pH 7.1, 25°C Methanobacterium thermoautotrophicus
0.0046
-
 orotidine 5'-phosphate mutant V155D, pH 7.1, 25°C Methanobacterium thermoautotrophicus
0.0047
-
 orotidine 5'-phosphate mutant V155S, pH 7.1, 25°C Methanobacterium thermoautotrophicus
0.006
-
 orotidine 5'-phosphate mutant D70N, pH 7.1, 25°C Methanobacterium thermoautotrophicus

Organism

Organism UniProt Comment Textmining
Methanobacterium thermoautotrophicus O26232
-
-
Methanobacterium thermoautotrophicus DSM 1053 O26232
-
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
Orotidine 5'-phosphate
-
 Methanobacterium thermoautotrophicus UMP + CO2
-
 ?
Orotidine 5'-phosphate
-
 Methanobacterium thermoautotrophicus DSM 1053 UMP + CO2
-
 ?

Synonyms

Synonyms Comment Organism
OMPDC
-
 Methanobacterium thermoautotrophicus

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.0005
-
 orotidine 5'-phosphate mutant V155D, pH 7.1, 25°C Methanobacterium thermoautotrophicus
0.01 1 orotidine 5'-phosphate mutant I96S, pH 7.1, 25°C Methanobacterium thermoautotrophicus
0.01 1 orotidine 5'-phosphate mutant V155S, pH 7.1, 25°C Methanobacterium thermoautotrophicus
0.024
-
 orotidine 5'-phosphate mutant D70N, pH 7.1, 25°C Methanobacterium thermoautotrophicus
0.36
-
 orotidine 5'-phosphate mutant L123S, pH 7.1, 25°C Methanobacterium thermoautotrophicus
0.64
-
 orotidine 5'-phosphate mutant L123N, pH 7.1, 25°C Methanobacterium thermoautotrophicus
0.69
-
 orotidine 5'-phosphate mutant I96T, pH 7.1, 25°C Methanobacterium thermoautotrophicus
4
-
 orotidine 5'-phosphate wild-type, pH 7.1, 25°C Methanobacterium thermoautotrophicus

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
0.46
-
 orotidine 5'-phosphate mutant V155D, pH 7.1, 25°C Methanobacterium thermoautotrophicus
4
-
 orotidine 5'-phosphate mutant D70N, pH 7.1, 25°C Methanobacterium thermoautotrophicus
10
-
 orotidine 5'-phosphate mutant I96S, pH 7.1, 25°C Methanobacterium thermoautotrophicus
22
-
 orotidine 5'-phosphate mutant V155S, pH 7.1, 25°C Methanobacterium thermoautotrophicus
120
-
 orotidine 5'-phosphate mutant L123S, pH 7.1, 25°C Methanobacterium thermoautotrophicus
190
-
 orotidine 5'-phosphate mutant L123N, pH 7.1, 25°C Methanobacterium thermoautotrophicus
300
-
 orotidine 5'-phosphate mutant I96T, pH 7.1, 25°C Methanobacterium thermoautotrophicus
2000
-
 orotidine 5'-phosphate wild-type, pH 7.1, 25°C Methanobacterium thermoautotrophicus