Transcription factor IIH (TFIIH) is a multisubunit complex required for transcription and for DNA nucleotide excision repair. TFIIH possesses three enzymatic activities: (i) an ATP-dependent DNA helicase, (ii) a DNAdependent ATPase, and (iii) a kinase with specificity for the carboxyl-terminal domain of RNA polymerase II. The kinase activity was recently identified as the cdk (cyclin-dependent kinase) activating kinase, CAK, composed of cdk7, cyclin H, and MAT-1. Here we report the isolation and characterization of three distinct CAK-containing complexes from HeLa nuclear extracts: CAK, a novel CAK-ERCC2 complex, and TFIIH. CAK-ERCC2 can efficiently associate with core-TFIIH to reconstitute holo-TFIIH transcription activity. We present evidence proposing a critical role for ERCC2 in mediating the association of CAK with core TFIIH subunits.RNA polymerase II (RNAPII) requires six auxiliary factors, called the general transcription factors (GTFs), to accurately initiate transcription from promoters of protein coding genes (1). These transcription factors (TF) include TFIID, TFIIA, TFIIB, TFIIF, TFIIE, and TFIIH. Through a combination of specific protein-DNA and protein-protein interactions, RNA-PII is escorted to the promoter by the GTFs to form a transcription competent complex (2). Interestingly, the largest subunit of RNAPII contains an unusual carboxyl-terminal domain (CTD) consisting of 52 tandemly repeated copies of the heptapeptide YSPTSPS. This domain is essential for viability and is not present in any other RNAP (3,4). The CTD further distinguishes itself by the extensive phosphorylations on serine, threonine, and tyrosine residues. The presence of both hypo-and hyperphosphorylated forms of RNAPII in vivo (3) has been correlated with a function for this domain in transcription. The unphosphorylated form has been shown to form transcription preinitiation complexes, whereas the hyperphosphorylated form is present in actively elongating RNAPII complexes (5, 6). These observations suggested that transition from initiation to elongation by RNAPII is accompanied by phosphorylation of the CTD.Studies from a number of groups showed that the CTD is phosphorylated by TFIIH (for review, see ref. 7). TFIIH is a multisubunit complex consisting of approximately nine polypeptides ranging in size from 32 to 89 kDa. TFIIH also exhibits ATP-dependent helicase and DNA-dependent ATPase activities (7). Analysis of the TFIIH polypeptides revealed that many of them are proteins known to participate in DNA nucleotide excision repair (7). This intriguing connection between transcription and nucleotide excision repair proteins was extended by the demonstration that the TFIIH complex functions as an essential nucleotide excision repair factor, as well as a GTF (7,8).Recently, the CTD kinase component of TFIIH was identified as the cell cycle regulatory cdk (cyclin-dependent kinase)-activating kinase (CAK), composed of the catalytic subunit cdk7 and its regulatory subunit cyclin H (9-12). Studies in different species reveal...