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A pectin lyase gene pnlzj5b from Aspergillus niger ZJ5 was identified and overexpressed successfully in Pichia pastoris. Recombinant PNLZJ5B exhibited high activity towards citrus pectin (150 U ml−1). Through further codon optimization, the expression efficiency of PNLZJ5B in P. pastoris increased to 3·5‐fold (532/150 U ml−1). PNLZJ5B was purified by ultrafiltration, anion exchange and gel chromatography...