Structural analysis of N-acetylglucosamine-6-phosphate deacetylase apoenzyme from Escherichia coli. 2006

Frederico M Ferreira, and Guillermo Mendoza-Hernandez, and Maria Castañeda-Bueno, and Ricardo Aparicio, and Hannes Fischer, and Mario L Calcagno, and Glaucius Oliva
Instituto de Física de São Carlos, Universidade de São Paulo, C.P. 369, 13560-970 São Carlos, SP, Brazil.

We report the crystal structure of the apoenzyme of N-acetylglucosamine-6-phosphate (GlcNAc6P) deacetylase from Escherichia coli (EcNAGPase) and the spectrometric evidence of the presence of Zn2+ in the native protein. The GlcNAc6P deacetylase is an enzyme of the amino sugar catabolic pathway that catalyzes the conversion of the GlcNAc6P into glucosamine 6-phosphate (GlcN6P). The crystal structure was phased by the single isomorphous replacement with anomalous scattering (SIRAS) method using low-resolution (2.9 A) iodine anomalous scattering and it was refined against a native dataset up to 2.0 A resolution. The structure is similar to two other NAGPases whose structures are known from Thermotoga maritima (TmNAGPase) and Bacillus subtilis (BsNAGPase); however, it shows a phosphate ion bound at the metal-binding site. Compared to these previous structures, the apoenzyme shows extensive conformational changes in two loops adjacent to the active site. The E. coli enzyme is a tetramer and its dimer-dimer interface was analyzed. The tetrameric structure was confirmed in solution by small-angle X-ray scattering data. Although no metal ions were detected in the present structure, experiments of photon-induced X-ray emission (PIXE) spectra and of inductively coupled plasma emission spectroscopy (ICP-AES) with enzyme that was neither exposed to chelating agents nor metal ions during purification, revealed the presence of 1.4 atoms of Zn per polypeptide chain. Enzyme inactivation by metal-sequestering agents and subsequent reactivation by the addition of several divalent cations, demonstrate the role of metal ions in EcNAGPase structure and catalysis.

UI MeSH Term Description Entries
D008667 Metalloproteins Proteins that have one or more tightly bound metal ions forming part of their structure. (Dorland, 28th ed) Metalloprotein
D008958 Models, Molecular Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures. Molecular Models,Model, Molecular,Molecular Model
D008969 Molecular Sequence Data Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. Sequence Data, Molecular,Molecular Sequencing Data,Data, Molecular Sequence,Data, Molecular Sequencing,Sequencing Data, Molecular
D004926 Escherichia coli A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc. Alkalescens-Dispar Group,Bacillus coli,Bacterium coli,Bacterium coli commune,Diffusely Adherent Escherichia coli,E coli,EAggEC,Enteroaggregative Escherichia coli,Enterococcus coli,Diffusely Adherent E. coli,Enteroaggregative E. coli,Enteroinvasive E. coli,Enteroinvasive Escherichia coli
D000581 Amidohydrolases Any member of the class of enzymes that catalyze the cleavage of amide bonds and result in the addition of water to the resulting molecules. Amidases,Amidohydrolase
D000595 Amino Acid Sequence The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION. Protein Structure, Primary,Amino Acid Sequences,Sequence, Amino Acid,Sequences, Amino Acid,Primary Protein Structure,Primary Protein Structures,Protein Structures, Primary,Structure, Primary Protein,Structures, Primary Protein
D001412 Bacillus subtilis A species of gram-positive bacteria that is a common soil and water saprophyte. Natto Bacteria,Bacillus subtilis (natto),Bacillus subtilis subsp. natto,Bacillus subtilis var. natto
D001665 Binding Sites The parts of a macromolecule that directly participate in its specific combination with another molecule. Combining Site,Binding Site,Combining Sites,Site, Binding,Site, Combining,Sites, Binding,Sites, Combining
D015032 Zinc A metallic element of atomic number 30 and atomic weight 65.38. It is a necessary trace element in the diet, forming an essential part of many enzymes, and playing an important role in protein synthesis and in cell division. Zinc deficiency is associated with ANEMIA, short stature, HYPOGONADISM, impaired WOUND HEALING, and geophagia. It is known by the symbol Zn.
D016415 Sequence Alignment The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms. Sequence Homology Determination,Determination, Sequence Homology,Alignment, Sequence,Alignments, Sequence,Determinations, Sequence Homology,Sequence Alignments,Sequence Homology Determinations

Related Publications

Frederico M Ferreira, and Guillermo Mendoza-Hernandez, and Maria Castañeda-Bueno, and Ricardo Aparicio, and Hannes Fischer, and Mario L Calcagno, and Glaucius Oliva
January 1975, Methods in enzymology,
Frederico M Ferreira, and Guillermo Mendoza-Hernandez, and Maria Castañeda-Bueno, and Ricardo Aparicio, and Hannes Fischer, and Mario L Calcagno, and Glaucius Oliva
October 1967, The Biochemical journal,
Frederico M Ferreira, and Guillermo Mendoza-Hernandez, and Maria Castañeda-Bueno, and Ricardo Aparicio, and Hannes Fischer, and Mario L Calcagno, and Glaucius Oliva
April 1997, Archives of biochemistry and biophysics,
Frederico M Ferreira, and Guillermo Mendoza-Hernandez, and Maria Castañeda-Bueno, and Ricardo Aparicio, and Hannes Fischer, and Mario L Calcagno, and Glaucius Oliva
August 2020, Proteins,
Frederico M Ferreira, and Guillermo Mendoza-Hernandez, and Maria Castañeda-Bueno, and Ricardo Aparicio, and Hannes Fischer, and Mario L Calcagno, and Glaucius Oliva
August 1982, Indian journal of biochemistry & biophysics,
Frederico M Ferreira, and Guillermo Mendoza-Hernandez, and Maria Castañeda-Bueno, and Ricardo Aparicio, and Hannes Fischer, and Mario L Calcagno, and Glaucius Oliva
January 1999, Journal of bioscience and bioengineering,
Frederico M Ferreira, and Guillermo Mendoza-Hernandez, and Maria Castañeda-Bueno, and Ricardo Aparicio, and Hannes Fischer, and Mario L Calcagno, and Glaucius Oliva
October 1987, Analytical biochemistry,
Frederico M Ferreira, and Guillermo Mendoza-Hernandez, and Maria Castañeda-Bueno, and Ricardo Aparicio, and Hannes Fischer, and Mario L Calcagno, and Glaucius Oliva
August 1996, Bioscience, biotechnology, and biochemistry,
Frederico M Ferreira, and Guillermo Mendoza-Hernandez, and Maria Castañeda-Bueno, and Ricardo Aparicio, and Hannes Fischer, and Mario L Calcagno, and Glaucius Oliva
December 1996, British journal of haematology,
Frederico M Ferreira, and Guillermo Mendoza-Hernandez, and Maria Castañeda-Bueno, and Ricardo Aparicio, and Hannes Fischer, and Mario L Calcagno, and Glaucius Oliva
June 2018, The Journal of biological chemistry,
Copied contents to your clipboard!