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Literature summary for 1.5.1.B8 extracted from

  • McFarlane, J.S.; Davis, C.L.; Lamb, A.L.
    Staphylopine, pseudopaline, and yersinopine dehydrogenases A structural and kinetic analysis of a new functional class of opine dehydrogenase (2018), J. Biol. Chem., 293, 8009-8019 .
    View publication on PubMedView publication on EuropePMC
Search for more literature for 1.5.1.B8

Crystallization (Commentary)

Crystallization (Comment) Organism
purified recombinant, wild-type or selenomethionine-labeled YpODH in apoform or complexed with NADP+, X-ray diffraction structure determination and analysis, single wavelength anomalous dispersion, at 2.15-2.85 A resolution, molecular replacement and modelling Yersinia pestis

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
 additional information steady-state kinetic analysis, overview Yersinia pestis
0.073
-
 pyruvate recombinant enzyme, with NADPH and L-histidine nicotianamine, pH 8.0, 22°C Yersinia pestis
1.9
-
 oxaloacetate recombinant enzyme, with NADPH and L-histidine nicotianamine, pH 8.0, 22°C Yersinia pestis
1.9
-
 glyoxylate recombinant enzyme, with NADPH and L-histidine nicotianamine, pH 8.0, 22°C Yersinia pestis

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
(2S)-2-amino-4-([(1S)-1-carboxy-2-(1H-imidazol-4-yl)ethyl]amino)butanoate + pyruvate + NADPH + H+ Yersinia pestis
-
 yersinopine + NADP+ + H2O
-
 ?

Organism

Organism UniProt Comment Textmining
Yersinia pestis Q8CKU7
-
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
(2S)-2-amino-4-([(1S)-1-carboxy-2-(1H-imidazol-4-yl)ethyl]amino)butanoate + glyoxylate + NADPH + H+
-
 Yersinia pestis ? + NADP+ + H2O
-
 ?
(2S)-2-amino-4-([(1S)-1-carboxy-2-(1H-imidazol-4-yl)ethyl]amino)butanoate + oxaloacetate + NADPH + H+
-
 Yersinia pestis ? + NADP+ + H2O
-
 ?
(2S)-2-amino-4-([(1S)-1-carboxy-2-(1H-imidazol-4-yl)ethyl]amino)butanoate + pyruvate + NADH + H+
-
 Yersinia pestis yersinopine + NAD+ + H2O
-
 ?
(2S)-2-amino-4-([(1S)-1-carboxy-2-(1H-imidazol-4-yl)ethyl]amino)butanoate + pyruvate + NADPH + H+
-
 Yersinia pestis yersinopine + NADP+ + H2O
-
 ?
additional information L-histidine nicotianamine is preferred over D-histidine nicotianamine, no activity with D-histidine nicotianamine Yersinia pestis ?
-
-

Subunits

Subunits Comment Organism
dimer YpODH is composed of three domains. NADPH binds along a canonical GXGXXA loop within the N-terminal NAD(P)H-binding domain. This domain forms one half of the active site. The other half, and the proposed location for substrate binding, is formed by the catalytic domain. These domains are separated by a central cleft. Embedded within the catalytic domain is a third domain that forms a dimerization interface. The NAD(P)H-binding domain has a Rossmann-like fold. This domain contains twelve beta-strands, five alpha-helices, and one 310 helix. Helix G acts as a linker connecting the NAD(P)H-binding domain with the C-terminal, predominantly alpha-helical, domains, structure overview Yersinia pestis

Synonyms

Synonyms Comment Organism
ODH
-
 Yersinia pestis
opine dehydrogenase
-
 Yersinia pestis
YpODH
-
 Yersinia pestis

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
22
-
 assay at Yersinia pestis

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.013
-
 NADH recombinant enzyme, with pyruvate and L-histidine nicotianamine, pH 8.0, 22°C Yersinia pestis
0.22
-
 glyoxylate recombinant enzyme, with NADPH and L-histidine nicotianamine, pH 8.0, 22°C Yersinia pestis
0.29
-
 oxaloacetate recombinant enzyme, with NADPH and L-histidine nicotianamine, pH 8.0, 22°C Yersinia pestis
0.3
-
 pyruvate recombinant enzyme, with NADPH and L-histidine nicotianamine, pH 8.0, 22°C Yersinia pestis
0.38
-
 NADPH recombinant enzyme, with pyruvate and L-histidine nicotianamine, pH 8.0, 22°C Yersinia pestis

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
8
-
 assay at Yersinia pestis

Cofactor

Cofactor Comment Organism Structure
additional information YpODH shows little turnover with NADH and a 26fold lower kcat compared to NADPH Yersinia pestis
NADP+ binding structure, overview Yersinia pestis
NADPH
-
 Yersinia pestis

General Information

General Information Comment Organism
metabolism opine dehydrogenases (ODHs) from the bacterial pathogens, e.g. Staphylococcus aureus, Pseudomonas aeruginosa, and Yersinia pestis, perform the final enzymatic step in the biosynthesis of the class of opine metallophores, which includes staphylopine, pseudopaline, and yersinopine, respectively. Comparison of structure-function relationships, overview Yersinia pestis
additional information structure-function analysis, stereochemic reaction, overview. Active site structure involving Asp153 and substrate binding analysis. The histidine is positioned to act as a general acid/general base deprotonating the nucleophile and then donating the proton back to the 2-carbon hydroxyl leading to water release and Schiff base formation. HisNA is oriented with the imidazole moiety deep in the active site to confer stereoselectivity. This places the primary amine of the amino butyrate proximal to the plane between the hydride and His242, positioning the substrate for nucleophilic attack. The nicotinamide ring hydride is 8.5 A distant from the histidine proton, too far for catalysis, further supporting the necessity of domain closure Yersinia pestis
physiological function opine dehydrogenases (ODHs) from the bacterial pathogens, e.g. Staphylococcus aureus, Pseudomonas aeruginosa, and Yersinia pestis, perform the final enzymatic step in the biosynthesis of the class of opine metallophores, which includes staphylopine, pseudopaline, and yersinopine, respectively. Important role for this pathway in metal acquisition and virulence Yersinia pestis

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
0.12
-
 glyoxylate recombinant enzyme, with NADPH and L-histidine nicotianamine, pH 8.0, 22°C Yersinia pestis
0.15
-
 oxaloacetate recombinant enzyme, with NADPH and L-histidine nicotianamine, pH 8.0, 22°C Yersinia pestis
4.11
-
 pyruvate recombinant enzyme, with NADPH and L-histidine nicotianamine, pH 8.0, 22°C Yersinia pestis