Structural and nucleotide-binding properties of YajQ and YnaF, two Escherichia coli proteins of unknown function.
Structural genomics is a new approach in functional assignment of proteins identified via whole-genome sequencing programs. Its rationale is that nonhomologous proteins performing similar or related biological functions might have similar tertiary structure. We used dye pseudoaffinity chromatography, two-dimensional gel electrophoresis, and mass spectrometry to identify two novel Escherichia coli nucleotide-binding proteins, YnaF and YajQ. YnaF exhibited significant sequence identity with MJ0577, an ATP-binding protein from a hyperthermophile (Methanococcus jannaschii), and with UspA, a protein from Haemophilus influenzae that belongs to the Universal Stress Protein family. YnaF conserves the ATP-binding site and the dimeric structure observed in the crystal of MJ0577. The protein YajQ, present in many bacterial genomes, is missing in eukaryotes. In the absence of significant similarities of YajQ to any solved structure, we determined its structural and ligand-binding properties by NMR and isothermal titration calorimetry. We demonstrate that YajQ is composed of two domains, each centered on a beta-sheet, that are connected by two helical segments. NMR studies, corroborated with local sequence conservation among YajQ homologs in various bacteria, indicate that one of the beta-sheets is mostly involved in biological activity.
Saveanu
Cosmin
C
Laboratoire de Chimie Structurale des Macromolécules, (CNRS URA 2185) Institut Pasteur, 75724 Paris Cédex 15, France.
Miron
Simona
S
Borza
Tudor
T
Craescu
Constantin T
CT
Labesse
Gilles
G
Gagyi
Cristina
C
Popescu
Aurel
A
Schaeffer
Francis
F
Namane
Abdelkader
A
Laurent-Winter
Christine
C
Bârzu
Octavian
O
Gilles
Anne-Marie
AM
D000255:Adenosine Triphosphate / Q000378:metabolism; D000595:Amino Acid Sequence; D002151:Calorimetry; D002942:Circular Dichroism; D019281:Dimerization; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D019906:Nuclear Magnetic Resonance, Biomolecular; D009711:Nucleotides / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D020543:Proteome; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment
D029968:Escherichia coli Proteins; D008024:Ligands; D009711:Nucleotides; D020543:Proteome; D016601:RNA-Binding Proteins; D011994:Recombinant Proteins; C473713:YajQ protein, E coli; C473716:YnaF protein, E coli; D000255:Adenosine Triphosphate