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Literature summary extracted from

  • Huang, N.; Sorci, L.; Zhang, X.; Brautigam, C.A.; Li, X.; Raffaelli, N.; Magni, G.; Grishin, N.V.; Osterman, A.L.; Zhang, H.
    Bifunctional NMN adenylyltransferase/ADP-ribose pyrophosphatase: structure and function in bacterial NAD metabolism (2008), Structure, 16, 196-209.
    View publication on PubMedView publication on EuropePMC

Application

EC Number Application Comment Organism
2.7.7.1 drug development development of NMNATase inhibitors as potential therapeutics against tularemia Francisella tularensis

Cloned(Commentary)

EC Number Cloned (Comment) Organism
3.6.1.13 expression of GST-tagged nezyme in Escherichia coli Francisella tularensis
3.6.1.13 expression of the His-tagged enzyme in Escherichia coli strain Bl21 Synechocystis sp.

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
2.7.7.1 the enzyme is complexed with the co-purified NAD and pyrophosphate in the NadM-domain active site, and with ADPR substrate in the Nudix-domain, X-ray diffraction structure determination and analysis at 2.6 A resolution Synechocystis sp.
2.7.7.1 X-ray diffraction structure determination and analysis at 2.3 A resolution, molecular replacement method, co-crystallization of ftNadM-Nudix complexed with the product AMP and Mn2+ ions in the Nudix active site Francisella tularensis
3.6.1.13 purified recombinant enzyme in complex with the product AMP and Mn2+ ions in its Nudix active site, sitting drop vapor diffusion method, 20°C, 0.001 ml of 15 mg/ml protein solution is mixed with an equal volume of reservoir solution containing 0.1 M Tris, pH 7.5, 200 mM MgCl2, and 19% PEG 3350, with or without 30 mM AMP, equilibration against the reservoir, X-ray diffraction structure determination and analysis at 2.3 A resolution, molecular replacement method Francisella tularensis
3.6.1.13 purified recombinant His-tagged enzyme in complex with co-purified NAD and diphosphate complexed in the NadM-domain active site, and with ADPR substrate complexed in the Nudix-domain, hanging drop vapor diffusion method, 0.0015 ml of 15 mg/ml protein solution is mixed with an equal volume of reservoir solution containing 100 mM Tris, pH 7.5, and 1.5 M Li2SO4, 20°C, 3 days to 2 weeks, X-ray diffraction structure determination and analysis at 2.6 A resolution, selenomethionyl MAD phasing method Synechocystis sp.

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
2.7.7.1 additional information
-
 additional information steady state kinetics Francisella tularensis
2.7.7.1 additional information
-
 additional information steady state kinetics Synechocystis sp.
2.7.7.1 0.041
-
 ADP-ribose pH 8.2, 37°C Francisella tularensis

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
2.7.7.1 Mg2+ presence of a metal ion cluster in the active site of the enzyme's Nudix domain, structure analysis and determination of the metal ion positions Francisella tularensis
2.7.7.1 Mn2+ presence of a metal ion cluster in the active site of the enzyme's Nudix domain, structure analysis and determination of the metal ion positions Francisella tularensis
3.6.1.13 Mg2+
-
 Francisella tularensis
3.6.1.13 Mg2+
-
 Synechocystis sp.

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.7.7.1 ATP + NMN Synechocystis sp. the enzyme from Synechocystis sp. is primarily involved in NAD savage/recycling pathways diphosphate + NAD+
-
 ?
2.7.7.1 ATP + NMN Francisella tularensis the enzyme likely plays a central role in the pathway of NAD de novo synthesis in Francisella tularensis diphosphate + NAD+
-
 ?
3.6.1.13 ADP-ribose + H2O Francisella tularensis
-
 AMP + D-ribose 5-phosphate
-
 ?
3.6.1.13 ADP-ribose + H2O Synechocystis sp.
-
 AMP + D-ribose 5-phosphate
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.7.7.1 Francisella tularensis Q5NHR1
-
-
2.7.7.1 Synechocystis sp. Q55928
-
-
3.6.1.13 Francisella tularensis Q5NHR1
-
-
3.6.1.13 Synechocystis sp. Q55928
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
3.6.1.13 recombinant GST-tagged enzyme from Escherichia coli by glutathione affinity chromatography, the tag is cleaved off by TEV protease, and the detagged protein is further purified by anion exchange chromatography Francisella tularensis
3.6.1.13 recombinant His-tagged enzyme from Escherichia coli strain Bl21 by nickel affinity and anion exchange chromatography, and gel filtration Synechocystis sp.

Reaction

EC Number Reaction Comment Organism Reaction ID
2.7.7.1 ATP + nicotinamide ribonucleotide = diphosphate + NAD+ catalytic mechanism, overview Francisella tularensis
a
2.7.7.1 ATP + nicotinamide ribonucleotide = diphosphate + NAD+ catalytic mechanism, overview Synechocystis sp.
a
3.6.1.13 ADP-D-ribose + H2O = AMP + D-ribose 5-phosphate substrate binding mode in the active site of the ADPRase domain and catalytic mechanism Francisella tularensis
a
3.6.1.13 ADP-D-ribose + H2O = AMP + D-ribose 5-phosphate substrate binding mode in the active site of the ADPRase domain and catalytic mechanism Synechocystis sp.
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.7.7.1 ATP + NMN the enzyme from Synechocystis sp. is primarily involved in NAD savage/recycling pathways Synechocystis sp. diphosphate + NAD+
-
 ?
2.7.7.1 ATP + NMN the enzyme likely plays a central role in the pathway of NAD de novo synthesis in Francisella tularensis Francisella tularensis diphosphate + NAD+
-
 ?
2.7.7.1 ATP + NMN the enzyme is a bifunctional NMN adenylyltransferase/ADP-ribose pyrophosphatase, structural aspects of the catalytic mechanism, overview Francisella tularensis diphosphate + NAD+
-
 ?
2.7.7.1 ATP + NMN the enzyme is a bifunctional NMN adenylyltransferase/ADP-ribose pyrophosphatase, structural aspects of the catalytic mechanism, overview Synechocystis sp. diphosphate + NAD+
-
 ?
3.6.1.13 ADP-ribose + H2O
-
 Francisella tularensis AMP + D-ribose 5-phosphate
-
 ?
3.6.1.13 ADP-ribose + H2O
-
 Synechocystis sp. AMP + D-ribose 5-phosphate
-
 ?
3.6.1.13 ADP-ribose + H2O substrate binding structure, overview Francisella tularensis AMP + D-ribose 5-phosphate
-
 ?
3.6.1.13 ADP-ribose + H2O substrate binding structure, overview Synechocystis sp. AMP + D-ribose 5-phosphate
-
 ?
3.6.1.13 additional information the enzyme is a bifunctional NMN adenylyltransferase/ADP-ribose diphosphatase, NMN specificity of the enzyme, overview Francisella tularensis ?
-
 ?
3.6.1.13 additional information the enzyme is a bifunctional NMN adenylyltransferase/ADP-ribose diphosphatase, NMN specificity of the enzyme, overview Synechocystis sp. ?
-
 ?

Subunits

EC Number Subunits Comment Organism
2.7.7.1 hexamer syNadM-Nudix forms hexamer in both crystal and solution with two types of dimer interfaces, the dimer interface is formed primarily through ADPRase domain of each monomer, overview Synechocystis sp.
2.7.7.1 More bacterial NadM-Nudix is a bifunctional enzyme containing a nicotinamide mononucleotide adenylyltransferase and an ADP-ribose diphosphatase domain, structures of the N-terminal NadM domain and ADPR domain, overview Francisella tularensis
2.7.7.1 More bacterial NadM-Nudix is a bifunctional enzyme containing a nicotinamide mononucleotide adenylyltransferase and an ADP-ribose diphosphatase domain, structures of the N-terminal NadM domain and ADPR domain, overview Synechocystis sp.
3.6.1.13 More ADPRase Nudix domain of NadM-Nudix and bacterial monofunctional ADPRase are connected by a long alpha helix with ADPRase active site facing away from the NMNATase domain, while the NMNATase active site opens partially toward the ADPRase domain, structure of the ADPRase domain, overview Francisella tularensis
3.6.1.13 More ADPRase Nudix domain of NadM-Nudix and bacterial monofunctional ADPRase are connected by a long alpha helix with ADPRase active site facing away from the NMNATase domain, while the NMNATase active site opens partially toward the ADPRase domain, structure of the ADPRase domain, overview Synechocystis sp.

Synonyms

EC Number Synonyms Comment Organism
2.7.7.1 More the enzyme belongs to the (H/T)IGH motif containing nucleotidyltransferase superfamily, NadM family, bacterial NadM-Nudix subfamily Francisella tularensis
2.7.7.1 More the enzyme belongs to the (H/T)IGH motif containing nucleotidyltransferase superfamily, NadM family, bacterial NadM-Nudix subfamily Synechocystis sp.
2.7.7.1 NadM-Nudix
-
 Francisella tularensis
2.7.7.1 NadM-Nudix
-
 Synechocystis sp.
2.7.7.1 NMN adenylyltransferase/ADP-ribose pyrophosphatase
-
 Francisella tularensis
2.7.7.1 NMN adenylyltransferase/ADP-ribose pyrophosphatase
-
 Synechocystis sp.
2.7.7.1 NMNATase
-
 Francisella tularensis
2.7.7.1 NMNATase
-
 Synechocystis sp.
3.6.1.13 NadM-Nudix
-
 Francisella tularensis
3.6.1.13 NadM-Nudix
-
 Synechocystis sp.
3.6.1.13 NMN adenylyltransferase/ADP-ribose pyrophosphatase
-
 Francisella tularensis
3.6.1.13 NMN adenylyltransferase/ADP-ribose pyrophosphatase
-
 Synechocystis sp.

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
3.6.1.13 37
-
 assay at Francisella tularensis
3.6.1.13 37
-
 assay at Synechocystis sp.

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
2.7.7.1 3.6
-
 ADP-ribose pH 8.2, 37°C Francisella tularensis

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
3.6.1.13 8.2
-
 assay at Francisella tularensis
3.6.1.13 8.2
-
 assay at Synechocystis sp.