DNA Polymerases: Structural Diversity and Common Mechanisms

Abstract

Possibly the earliest enzymatic activity to appear in evolution was that of the polynucleotide polymerases, the ability to replicate the genome accurately being a prerequisite for evolution itself. Thus, one might anticipate that the mechanism by which all polymerases work would be both simple and universal. Further, these enzymatic scribes must faithfully copy the sequences of the genome into daughter nucleic acid or the information contained within would be lost; thus some mechanism of assuring fidelity is required. Finally, all classes of polynucleotide polymerases must be able to translocate along the template being copied as synthesis proceeds. The crystal structures of numerous DNA polymerases from different families suggest that they all utilize an identical two-metalioncatalyzed polymerase mechanism but differ extensively in many of their structural features. From amino acid sequence comparisons (1Delarue M. Poch O. Tordo N. Moras D. Argos P. An attempt to unify the structure of polymerases..Protein Eng. 1990; 3: 461-467Crossref PubMed Scopus (572) Google Scholar) as well as crystal structure analyses (2Joyce C.M. Steitz T.A. Function and structure relationships in DNA polymerases..Annu. Rev. Biochem. 1994; 63: 777-822Crossref PubMed Scopus (565) Google Scholar), the DNA polymerases can be divided into at least five different families, and representative crystal structures are known for enzymes in four of these families. Perhaps the best studied of these families is the DNA polymerase I (pol I) 1The abbreviations used are: pol, polymerase; RT, reverse transcriptase(s); HIV, human immunodeficiency virus. 1The abbreviations used are: pol, polymerase; RT, reverse transcriptase(s); HIV, human immunodeficiency virus. or A polymerase family, which includes the Klenow fragments of Escherichia coli and a Bacillus DNA polymerase I, Thermus aquaticusDNA polymerase, and the T7 RNA and DNA polymerases, all of whose crystal structures are known (3Ollis D.L. Brick P. Hamlin R. Xuong N.G. Steitz T.A. Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP..Nature. 1985; 313: 762-766Crossref PubMed Scopus (735) Google Scholar, 4Beese L.S. Derbyshire V. Steitz T.A. Structure of DNA polymerase I Klenow fragment bound to duplex DNA..Science. 1993; 260: 352-355Crossref PubMed Scopus (448) Google Scholar, 5Kim Y. Eom S.H. Wang J. Lee D.S. Suh S.W. Steitz T.A. Crystal structure of Thermus aquaticus DNA polymerase..Nature. 1995; 376: 612-616Crossref PubMed Scopus (328) Google Scholar, 6Eom S.H. Wang J. Steitz T.A. Structure of Taq polymerase with DNA at the polymerase active site..Nature. 1996; 382: 278-281Crossref PubMed Scopus (304) Google Scholar, 7Kiefer J.R. Mao C. Braman J.C. Beese L.S. Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal..Nature. 1998; 391: 304-307Crossref PubMed Scopus (477) Google Scholar, 8Doublié S. Tabor S. Long A.M. Richardson C.C. Ellenberger T. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. Nature. 1998; 391: 251-258Google Scholar, 9Sousa R. Chung Y.J. Rose J.P. Wang B.-C. Crystal structure of bacteriophage T7 RNA polymerase at 3.3 Å resolution..Nature. 1993; 364: 593-599Crossref PubMed Scopus (337) Google Scholar, 10Jeruzalmi D. Steitz T.A. Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme..EMBO J. 1998; 17: 4101-4113Crossref PubMed Scopus (149) Google Scholar, 11Cheetham G.M.T. Jeruzalmi D. Steitz T.A. Nature. 1999; 399: 80-83Crossref PubMed Scopus (270) Google Scholar). The second family of DNA-dependent DNA polymerases is DNA polymerase α (pol α) or B family DNA polymerase. All eukaryotic replicating DNA polymerases and the polymerases from phages T4 and RB69 belong to this family, and a crystal structure of the RB69 polymerase shows some similarities to the pol I family enzymes and numerous differences (12Wang J. Sattar A.K.M.A. Wang C.C. Karam J.D. Konigsberg W.H. Steitz T.A. Crystal structure of a pol α replication DNA polymerase from bacteriophage RB69..Cell. 1997; 89: 1087-1089Abstract Full Text Full Text PDF PubMed Scopus (421) Google Scholar). Reverse transcriptases (RT), RNA-dependent RNA polymerases, and telomerase appear to show some common structural similarities, whereas the structure of DNA polymerase β shows no structural relatedness to any of these previous families (13Sawaya M.R. Pelletier H. Kumar A. Wilson S.H. Kraut T. Crystal structure of rat DNA polymerase β: Evidence for a common polymerase mechanism..Science. 1994; 264: 1930-1935Crossref PubMed Scopus (396) Google Scholar, 14Steitz T.A. Smerdon S.J. Jäger J. Joyce C.M. A unified mechanism for nonhomologous DNA and RNA polymerases..Science. 1994; 266: 2022-2025Crossref PubMed Scopus (268) Google Scholar). On the basis of amino acid sequence comparisons but no crystal structures, it appears that the bacterial DNA polymerase III enzymes also form a family that is unrelated to the polymerases of known structure (1Delarue M. Poch O. Tordo N. Moras D. Argos P. An attempt to unify the structure of polymerases..Protein Eng. 1990; 3: 461-467Crossref PubMed Scopus (572) Google Scholar). Independent of their detailed domain structures, all polymerases whose structures are known presently appear to share a common overall architectural feature. They have a shape that can be compared with that of a right hand and have been described as consisting of “thumb,” “palm,” and “fingers” domains (15Kohlstaedt L.A. Wang J. Friedman J.M. Rice P.A. Steitz T.A. Crystal structure at 3.5 Å of HIV-1 reverse transcriptase complexed with an inhibitor..Science. 1992; 256: 1781-1790Crossref Scopus (1749) Google Scholar). The function of the palm domain appears to be catalysis of the phosphoryl transfer reaction whereas that of the fingers domain includes important interactions with the incoming nucleoside triphosphate as well as the template base to which it is paired. The thumb on the other hand may play a role in positioning the duplex DNA and in processivity and translocation. Although the palm domain appears to be homologous among the pol I, pol α, and RT families, the fingers and thumb domains are different in all four of these families for which structures are known to date (16Brautigam C.A. Steitz T.A. Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes..Curr. Opin. Struct. Biol. 1998; 8: 54-63Crossref PubMed Scopus (333) Google Scholar). Here the functional and structural similarities and differences among the polymerases of known structure are explored. Of particular interest are the role of editing in the fidelity of copying, the common enzymatic mechanism of polymerases, and the manners in which different domain structures function in the polymerase reaction in analogous ways. Although the palm domains of the pol I, pol α, and RT families are homologous, the fingers and thumb domains are completely different in the structures from all families (16Brautigam C.A. Steitz T.A. Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes..Curr. Opin. Struct. Biol. 1998; 8: 54-63Crossref PubMed Scopus (333) Google Scholar). In the structure of the DNA polymerase from RB69 five domains are arranged around a central hole (12Wang J. Sattar A.K.M.A. Wang C.C. Karam J.D. Konigsberg W.H. Steitz T.A. Crystal structure of a pol α replication DNA polymerase from bacteriophage RB69..Cell. 1997; 89: 1087-1089Abstract Full Text Full Text PDF PubMed Scopus (421) Google Scholar). In this enzyme the fingers domain consists largely of two very long anti-parallel coiled-coil α-helices that extend more than 20 Å out the “back.” The thumb domain is seen to be interacting directly with the exonuclease domain and providing some of the binding site for the single-stranded exonuclease substrate. After orienting the palm domains of the RB69 and Klenow fragment enzymes identically, it becomes clear that their exonuclease domains are located in completely different places relative to the polymerase active site. Although in the “standard” orientation the exonuclease domain can be described as being southeast of the polymerase active site in Klenow fragment, the corresponding domain of the RB69 polymerase is located northwest of the polymerase active site. This difference in location of the editing domain may be in part related to the fact that the RB69 enzyme, like that from T4 phage, has an exonuclease activity that is 103times larger than that of the Klenow fragment (17Huang W.H. Lehman I.R. On the direction of translation of the T4 deoxyribonucleic acid polymerase gene in vivo. J. Biol. Chem. 1972; 247: 7663-7667Google Scholar, 18Capson T.L. Peliska J.A. Kaboord B.F. Frey M.W. Lively C. Dahlberg M. Benkovic S.J. Kinetic characterization of the polymerase and exonuclease activities of the gene 43 protein of bacteriophage T4..Biochemistry. 1992; 31: 10984-10994Crossref PubMed Scopus (225) Google Scholar). A detailed comparison of the structures from four polymerase families (Fig. 1) shows that the fingers and thumbs are different in all four families for which structures are known (12Wang J. Sattar A.K.M.A. Wang C.C. Karam J.D. Konigsberg W.H. Steitz T.A. Crystal structure of a pol α replication DNA polymerase from bacteriophage RB69..Cell. 1997; 89: 1087-1089Abstract Full Text Full Text PDF PubMed Scopus (421) Google Scholar, 16Brautigam C.A. Steitz T.A. Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes..Curr. Opin. Struct. Biol. 1998; 8: 54-63Crossref PubMed Scopus (333) Google Scholar). (To make a suitable comparison between structural elements having similar functions, the names of the pol β thumb and fingers domains have been switched from the Pelletier et al. image (19Pelletier H. Sawaya M.R. Kumar A. Wilson S.H. Kraut J. Structure of ternary complexes of rat DNA polymerase β, a DNA template-primer, and ddCTP..Science. 1994; 264: 1981Crossref Scopus (754) Google Scholar).) Although the structures of the thumb domains are not homologous, they do exhibit analogous features that consist of largely parallel or anti-parallel α-helices and in each case at least one α-helix seems to be making important interactions across the minor groove of the primer-template product. In the case of the pol I family, loops at the top of the thumb also make important and conserved interactions with the DNA backbone (6Eom S.H. Wang J. Steitz T.A. Structure of Taq polymerase with DNA at the polymerase active site..Nature. 1996; 382: 278-281Crossref PubMed Scopus (304) Google Scholar, 8Doublié S. Tabor S. Long A.M. Richardson C.C. Ellenberger T. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. Nature. 1998; 391: 251-258Google Scholar). Although the fingers domains of all four families are also not homologous, there are some striking structural analogies among the families as with the thumbs. In three of the four DNA polymerase families with known structures, the pol I, pol α, and pol β families, an α-helix in the fingers domain is positioned at the blunt end of the primer-template; it contains side chains that are conserved within the families (the B motif) and provides important orienting interactions with the incoming deoxynucleoside triphosphate. In the case of the reverse transcriptase family, however, it appears that some of these functions have been taken over by an anti-parallel β-ribbon, which lies in a similar position, as seen in a recent ternary complex with the primer-template and deoxynucleoside triphosphate (27Huang H. Chopra R. Verdine G.L. Harrison S.C. Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: Implications for drug resistance..Science. 1998; 282: 1669-1675Crossref PubMed Scopus (1346) Google Scholar). The perhaps surprising diversity of polymerase structures found in these families leads one to wonder why the structures of DNA polymerases turn out to be so diverse when the structures of most metabolic enzymes, such as glyceraldehyde-3-phosphate dehydrogenase, are almost identical from microbe to man. One possibility is that the RT, pol I, and pol β families are later evolutionary additions to all cellular replicating polymerases, which could turn out to be divergently related to the pol α family polymerases; however, sequence comparisons do not presently show such a relationship between the eukaryotic pol α and the prokaryotic pol III DNA polymerases. An alternative speculation might imagine that a ribozyme DNA polymerase originating in the “RNA world” may have persisted beyond the divergence of eukaryotes and prokaryotes and was replaced domain by domain differently. The greatest insights into the mechanisms by which polymerases achieve faithful copying of the template come from structural and biochemical studies of the pol I family of polymerases (2Joyce C.M. Steitz T.A. Function and structure relationships in DNA polymerases..Annu. Rev. Biochem. 1994; 63: 777-822Crossref PubMed Scopus (565) Google Scholar, 20Brautigam C.A. Steitz T.A. Structural principles for the inhibition of the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates..J. Mol. Biol. 1998; 277: 363-377Crossref PubMed Scopus (160) Google Scholar). Fidelity arises both from constraints imposed on base pairing at the polymerase active site as well as the editing of base at a active site. The crystal structure of the Klenow fragment of DNA polymerase I that this enzyme is divided into two one of which the polymerase reaction and the second of which has an active site more than Å from the polymerase active site and the reaction (3Ollis D.L. Brick P. Hamlin R. Xuong N.G. Steitz T.A. Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP..Nature. 1985; 313: 762-766Crossref PubMed Scopus (735) Google Scholar). The structure of Klenow fragment with duplex DNA a shows that the single-stranded end into the exonuclease active site L.S. Derbyshire V. Steitz T.A. Structure of DNA polymerase I Klenow fragment bound to duplex DNA..Science. 1993; 260: 352-355Crossref PubMed Scopus (448) Google Scholar). and biochemical studies of single-stranded bound to the exonuclease active site to the of a mechanism of phosphoryl transfer C.A. Steitz T.A. Structural principles for the inhibition of the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates..J. Mol. Biol. 1998; 277: 363-377Crossref PubMed Scopus (160) Google Scholar, Friedman J.M. Beese L.S. M.R. Steitz T.A. structure of an editing complex of Klenow fragment with S. A. PubMed Scopus Google Scholar, V. Joyce C.M. The 3′-5′ exonuclease of DNA polymerase I of Escherichia of each amino acid at the active site to the J. PubMed Scopus Google Scholar). duplex DNA is bound to the aquaticus DNA polymerase, which not a exonuclease active the end of the is found to in the polymerase active site to conserved known to be important for the polymerase reaction (6Eom S.H. Wang J. Steitz T.A. Structure of Taq polymerase with DNA at the polymerase active site..Nature. 1996; 382: 278-281Crossref PubMed Scopus (304) Google Scholar). in the ternary complex between T7 DNA polymerase, primer-template and the end is in the polymerase active site. Although the duplex of lies in the to the thumb the primer-template is bound to the enzyme in polymerase or in exonuclease the are located in active that are by more than The mechanism the exonuclease domain editing function is (Fig. to a between these two active for the end of the and a of the between (2Joyce C.M. Steitz T.A. Function and structure relationships in DNA polymerases..Annu. Rev. Biochem. 1994; 63: 777-822Crossref PubMed Scopus (565) Google Scholar, 4Beese L.S. Derbyshire V. Steitz T.A. Structure of DNA polymerase I Klenow fragment bound to duplex DNA..Science. 1993; 260: 352-355Crossref PubMed Scopus (448) Google Scholar, Friedman J.M. Beese L.S. M.R. Steitz T.A. structure of an editing complex of Klenow fragment with S. A. PubMed Scopus Google Scholar). The active site single-stranded DNA whereas the polymerase active site duplex DNA with the of to for duplex DNA T.L. Peliska J.A. Kaboord B.F. Frey M.W. Lively C. Dahlberg M. Benkovic S.J. Kinetic characterization of the polymerase and exonuclease activities of the gene 43 protein of bacteriophage T4..Biochemistry. 1992; 31: 10984-10994Crossref PubMed Scopus (225) Google Scholar). base the duplex DNA and the binding of the single-stranded DNA to the exonuclease active site. is of base of of the of the which the is to be this of the reaction to the of by the exonuclease The role that the polymerase domain in fidelity is Structural studies as well as sequence comparisons among polymerases suggest the that the phosphoryl transfer reaction of all polymerases is by a mechanism (Fig. L.S. Steitz T.A. Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase a two J. PubMed Scopus Google Scholar, T.A. and RNA-dependent DNA Opin. Struct. Biol. 1993; 3: Scopus Google Scholar) by to the well studied mechanism in the reaction C.A. Steitz T.A. Structural principles for the inhibition of the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates..J. Mol. Biol. 1998; 277: 363-377Crossref PubMed Scopus (160) Google Scholar, Friedman J.M. Beese L.S. M.R. Steitz T.A. structure of an editing complex of Klenow fragment with S. A. PubMed Scopus Google Scholar, L.S. Steitz T.A. Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase a two J. PubMed Scopus Google Scholar, V. Joyce C.M. The 3′-5′ exonuclease of DNA polymerase I of Escherichia of each amino acid at the active site to the J. PubMed Scopus Google Scholar). The of a polymerase complex with both primer-template DNA and bound to the polymerase active site that directly the structural basis of a mechanism was a complex with rat pol β (19Pelletier H. Sawaya M.R. Kumar A. Wilson S.H. Kraut J. Structure of ternary complexes of rat DNA polymerase β, a DNA template-primer, and ddCTP..Science. 1994; 264: 1981Crossref Scopus (754) Google Scholar). are bound by three contained in a domain that is not homologous to other polymerases T.A. Smerdon S.J. Jäger J. Joyce C.M. A unified mechanism for nonhomologous DNA and RNA polymerases..Science. 1994; 266: 2022-2025Crossref PubMed Scopus (268) Google Scholar). A structure of human pol β complexed with a DNA substrate and shows of the of two interacting with the three M.R. R. Wilson S.H. Kraut J. Pelletier H. Crystal structures of human DNA polymerase β complexed with and Evidence for an 1997; PubMed Scopus Google Scholar). In the homologous domains of the pol I and RT families these are to to the enzyme two completely conserved but in the primer-template complex with the S. Tabor S. Long A.M. Richardson C.C. Ellenberger T. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. Nature. 1998; 391: 251-258Google Scholar). are by Å in the ternary complex of T7 DNA polymerase complexed with primer-template DNA and S. Tabor S. Long A.M. Richardson C.C. Ellenberger T. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. Nature. 1998; 391: 251-258Google Scholar). A with the of the and is T.A. and RNA-dependent DNA Opin. Struct. Biol. 1993; 3: Scopus Google Scholar) to the of the on the of the incoming A and B are also to both the structure and of the that the of this Finally, B to and is to the of the and similar mechanisms of phosphoryl transfer are used by many enzymes T.A. Steitz J.A. A mechanism for catalytic S. A. 1993; PubMed Scopus Google Scholar). Although amino acid sequence comparisons that there three conserved in the active of all classes of polymerases, comparison of the crystal structures of Klenow fragment, HIV-1 RT, RB69 pol α polymerase, and the T7 RNA polymerase (12Wang J. Sattar A.K.M.A. Wang C.C. Karam J.D. Konigsberg W.H. Steitz T.A. Crystal structure of a pol α replication DNA polymerase from bacteriophage RB69..Cell. 1997; 89: 1087-1089Abstract Full Text Full Text PDF PubMed Scopus (421) Google Scholar) shows that two acid are conserved among these four the crystal structure of T7 DNA polymerase complexed with a primer-template and a deoxynucleoside triphosphate S. Tabor S. Long A.M. Richardson C.C. Ellenberger T. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. Nature. 1998; 391: 251-258Google Scholar) shows that the two are bound by one acid from conserved sequence A and one from conserved sequence and of Klenow Further, comparison of the pol α and pol I structures shows that previous sequence of the which positioned the of a sequence on the of a sequence (1Delarue M. Poch O. Tordo N. Moras D. Argos P. An attempt to unify the structure of polymerases..Protein Eng. 1990; 3: 461-467Crossref PubMed Scopus (572) Google Scholar), to be so the second of the pol α family sequence on the of the RT family sequence or the pol I family sequence (1Delarue M. Poch O. Tordo N. Moras D. Argos P. An attempt to unify the structure of polymerases..Protein Eng. 1990; 3: 461-467Crossref PubMed Scopus (572) Google Scholar). In of the fingers domains of the pol β, RT, pol I, and pol α DNA polymerases all having different evolutionary they share some similar functional features. The binding of to the pol β, RT, and T7 DNA polymerases complexed with primer-template DNA in a of the fingers domain when compared with the corresponding polymerase complexes with DNA or S. Tabor S. Long A.M. Richardson C.C. Ellenberger T. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. Nature. 1998; 391: 251-258Google H. Sawaya M.R. Kumar A. Wilson S.H. Kraut J. Structure of ternary complexes of rat DNA polymerase β, a DNA template-primer, and ddCTP..Science. 1994; 264: 1981Crossref Scopus (754) Google Scholar, H. Chopra R. Verdine G.L. Harrison S.C. Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: Implications for drug resistance..Science. 1998; 282: 1669-1675Crossref PubMed Scopus (1346) Google Scholar). The orientation of the in the complex from orientation in the ternary in the of the is a ternary complex in which the fingers and the incoming a base with the In ternary complexes in which the fingers do not the as in the All of the structures S. Tabor S. Long A.M. Richardson C.C. Ellenberger T. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. Nature. 1998; 391: 251-258Google Scholar, H. Sawaya M.R. Kumar A. Wilson S.H. Kraut J. Structure of ternary complexes of rat DNA polymerase β, a DNA template-primer, and ddCTP..Science. 1994; 264: 1981Crossref Scopus (754) Google Scholar, M.R. R. Wilson S.H. Kraut J. Pelletier H. Crystal structures of human DNA polymerase β complexed with and Evidence for an 1997; PubMed Scopus Google Scholar, H. Chopra R. Verdine G.L. Harrison S.C. Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: Implications for drug resistance..Science. 1998; 282: 1669-1675Crossref PubMed Scopus (1346) Google Scholar) are with the that to a primer-template complex with the polymerase in a but a binding is template Benkovic S.J. in the DNA polymerase I reaction PubMed Scopus (149) Google Scholar). The has been that with the base pairing between template and the fingers for catalysis M.R. R. Wilson S.H. Kraut J. Pelletier H. Crystal structures of human DNA polymerase β complexed with and Evidence for an 1997; PubMed Scopus Google Scholar). fidelity for of the at the is by this catalytically which the of a base the four known fingers domains similar to the incoming for the functional in HIV-1 RT and in T7 DNA pol with a of the in a that would the of the analogous from the fingers domains with the of From the and studies of polynucleotide polymerases there are that can be this of all polynucleotide polymerases may the mechanism to the polymerase phosphoryl transfer T.A. and RNA-dependent DNA Opin. Struct. Biol. 1993; 3: Scopus Google Scholar). is perhaps of interest to that such a which the of two positioned could be used by an enzyme of RNA and thus could function in an all RNA the fidelity of DNA synthesis from a of interactions at the polymerase active site S. Tabor S. Long A.M. Richardson C.C. Ellenberger T. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. Nature. 1998; 391: 251-258Google Scholar, H. Sawaya M.R. Kumar A. Wilson S.H. Kraut J. Structure of ternary complexes of rat DNA polymerase β, a DNA template-primer, and ddCTP..Science. 1994; 264: 1981Crossref Scopus (754) Google Scholar, M.R. R. Wilson S.H. Kraut J. Pelletier H. Crystal structures of human DNA polymerase β complexed with and Evidence for an 1997; PubMed Scopus Google Scholar) and editing at the active site L.S. Derbyshire V. Steitz T.A. Structure of DNA polymerase I Klenow fragment bound to duplex DNA..Science. 1993; 260: 352-355Crossref PubMed Scopus (448) Google Scholar, 6Eom S.H. Wang J. Steitz T.A. Structure of Taq polymerase with DNA at the polymerase active site..Nature. 1996; 382: 278-281Crossref PubMed Scopus (304) Google Scholar, Friedman J.M. Beese L.S. M.R. Steitz T.A. structure of an editing complex of Klenow fragment with S. A. PubMed Scopus Google Scholar). duplex and binding to the exonuclease active site. the catalytically important palm domains are seen to be homologous in the pol I, RT, and pol α families, the pol β family palm domain is unrelated T.A. Smerdon S.J. Jäger J. Joyce C.M. A unified mechanism for nonhomologous DNA and RNA polymerases..Science. 1994; 266: 2022-2025Crossref PubMed Scopus (268) Google the catalytic domains from the DNA polymerase III and the RNA polymerase families are to be different as from amino acid sequence the thumb and domains are different in all of the polymerase families for which representative crystal structures are positioned structures function in similar ways.