Table 12.

Replication and Transcription Enzymes

Protein	PDB entrya, b	Reference
DNA polymerases
Pol I family (A family)
Klenow fragment from E. coli	1kln	Beese et al. (1993)
Pol α family (B family)
Bacteriophage RB69 DNA polymerase	1ih7, 1ig9	Franklin et al. (2001)
Pol β family (X family)
Polymerase β from rat	1bpd	Sawaya et al. (1994)
Lesion bypass polymerase family (Y family)
DNA polymerase IV from S. solfataricus	1jx4, 1jxl	Ling et al. (2001)
Reverse transcriptase family
HIV‐1 reverse transcriptase	2hmi	Jacobo‐Molina et al. (1993)
Small RNA polymerases
T7 polymerase family
Bacteriophage T7 polymerase	4rnp	Sousa et al. (1993)
Viral RNA‐dependent RNA polymerase family
Poliovirus 3D RNA polymerase	1rdr	Hansen et al. (1997)
dsRNA phage RNA–dependent RNA polymerase family
Bacteriophage Φ6 RNA polymerase	1hhs	Butcher et al. (2001)
Eukaryotic poly(A) RNA polymerases
Yeast poly(A) RNA polymerase	1fa0	Bard et al. (2000)
Bovine poly(A) RNA polymerase	1f5a	Martin et al. (2000)
DNA‐dependent RNA polymerases (RNAPs)
T. aquaticus core RNAP (α2ββ′ω)	1hqm, 1i6v	Zhang et al. (1999), Campbell et al. (2001)
T. aquaticus holoenzyme RNAP (α2ββ′ωσ70)	1l9u	Murakami et al. (2002a)
T. thermophilus holoenzyme RNAP (α2ββ′ωσ70)	1iw7	Vassylyev et al. (2002)
E. coli RNAP α subunit N‐terminal domain	1bdf	Zhang and Darst (1998)
E. coli RNAP α subunit C‐terminal domain	1coo	Jeon et al. (1995)
E. coli RNAP σ70 initiation factor	1sig	Malhotra et al. (1996)
T. aquaticus RNAP σA factor	1ku2, 1ku3, 1ku7	Campbell et al. (2002)
Saccharomyces cerevisiae RNAP II (10 subunits)	1en0, 1I50	Cramer et al. (2000, 2001)
DNA polymerase processivity factors
Dimeric processivity factors
E. coli β subunit of polymerase III	2pol	Kong et al. (1992)
Trimeric processivity factors
Proliferating cell nuclear antigen (PCNA)	1plq	Krishna et al. (1994)
Topoisomereases
Subtype IA
E. coli topoisomerase I 67‐kDa fragment	1ecl	Lima et al. (1994)
Subtype IB
Human topoisomerase I	1a36	Redinbo et al. (1998), Stewart et al. (1998)
Subtype IIA
Yeast topoisomerase II 92‐kDa fragment	1bgw	Berger et al. (1996)
E coli GyrB 43‐kDa fragment	1ei1	Wigley et al. (1991), Brino et al. (2000)
Subtype IIB
M. jannaschii topoisomerase VI‐A′	1d3y	Nichols et al. (1999)
RNAse H‐like polynucleotide transferases
E. coli RNase H	2m2	Katayanagi et al. (1990), Yang et al. (1990), Katayanagi et al. (1992)
HIV‐I reverse transcriptase RNase H	1hrh	Davies et al. (1991)
RuvC resolvase	1hjr	Ariyoshi et al. (1994)
HIV‐I integrase	1itg	Dyda et al. (1994)
Mu transposase	1beo	Rice and Mizuuchi (1995)
TN5 transposase	1f3i	Davies et al. (2000)
Klenow fragment 3′‐5′ exonuclease	1kln	Beese et al. (1993)

^aSee Web‐Based Structural Bioinformatics and http://www.rcsb.org/pdb.

^bDue to the large number of structures present in the PDB, only representative structures are listed in this table.

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