This study was done to investigate the DNA binding ability of a diagnostic biomarker, 45-kDa calcium oxalate monohydrate (COM) binding protein, isolated from human kidney and its effect on transcription. The 45-kDa COM binding protein was isolated and purified from human kidney. The subcellular localization of the protein and the amino acid composition of the protein were analyzed. Oxalate-binding activity in the presence or absence of DNA was determined. The possibility of forming DNA-protein adducts was checked by diethylaminoethyl (DEAE)-Sephadex column chromatography. The effect of the protein on in vitro transcription was also studied. The isolated 45-kDa protein was found to be basic in nature and its AACompIdent analysis showed it to be related to known transcription factors. The protein was found to be present in kidney cytosol and nucleus. The decreased oxalate binding activity in the presence of the DNA, and the shift in the DEAE-Sephadex elution profile established the DNA-binding ability of the protein. The in vitro transcription assay demonstrated the repression effect of the protein on gene expression during hyperoxaluria. Transcriptional repression by the 45-kDa COM binding protein in an in vitro transcription assay system was reduced in the presence of oxalate. Hence, altered expression of certain genes involved in the prognosis of urolithiasis might be mediated by this 45-kDa protein.