SMART: POLAc domain annotation

POLAc DNA polymerase A domain

SMART accession number:	SM00482
Description:
Interpro abstract (IPR001098):	Synonym(s): DNA nucleotidyltransferase (DNA-directed) DNA-directed DNA polymerases(EC 2.7.7.7) are the key enzymes catalysing the accurate replication of DNA. They require either a small RNA molecule or a protein as a primer for the de novo synthesis of a DNA chain. A number of polymerases belong to this family [(PUBMED:2196557), (PUBMED:1870963), (PUBMED:8451181)].
GO process:	DNA replication (GO:0006260)
GO function:	DNA-directed DNA polymerase activity (GO:0003887), DNA binding (GO:0003677)
Family alignment:	View or

There are 2324 POLAc domains in 2324 proteins in SMART's nrdb database.

Click on the following links for more information.

Evolution (species in which this domain is found)
Click on to expand nodes. To display all proteins with a POLAc domain in a specific node, click on it.

This tree shows only several representative species. The complete taxonomic breakdown of all proteins with POLAc domain is also avaliable.

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Go to specific node: Anopheles gambiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Takifugu rubripes
Cellular role (predicted cellular role)
Cellular role: replication
Literature (relevant references for this domain)
Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.
- Braithwaite DK, Ito J
- Compilation, alignment, and phylogenetic relationships of DNA polymerases.
- Nucleic Acids Res. 1993; 21: 787-802
- Ollis DL, Brick P, Hamlin R, Xuong NG, Steitz TA
- Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP.
- Nature. 1985; 313: 762-6
- Display abstract
- The 3.3-A resolution crystal structure of the large proteolytic fragment of Escherichia coli DNA polymerase I complexed with deoxythymidine monophosphate consists of two domains, the smaller of which binds zinc-deoxythymidine monophosphate. The most striking feature of the larger domain is a deep crevice of the appropriate size and shape for binding double-stranded B-DNA. A flexible subdomain may allow the enzyme to surround completely the DNA substrate, thereby allowing processive nucleotide polymerization without enzyme dissociation.
Metabolism (metabolic pathways involving proteins which contain this domain)

Structure (3D structures containing this domain)

3D Structures of POLAc domains in PDB

PDB code	Main view	Title
1bgx		Taq polymerase in complex with tp7, an inhibitory fab
1cmw		Crystal structure of taq dna-polymerase shows a new orientation for the structure-specific nuclease domain
1d8y		Crystal structure of the complex of dna polymerase i klenow fragment with dna
1d9d		Crystall structure of the complex of dna polymerase i klenow fragment with short dna fragment carrying 2'-0- aminopropyl-rna modifications 5'-d(tcg)-ap(auc)-3'
1d9f		Crystal structure of the complex of dna polymerase i klenow fragment with dna tetramer carrying 2'-o-(3-aminopropyl)- rna modification 5'-d(tt)-ap(u)-d(t)-3'
1dpi		Structure of large fragment of escherichia coli dna polymerase i complexed with d/tmp
1jxe		Stoffel fragment of taq dna polymerase i
1kfd		Crystal structures of the klenow fragment of dna polymerase i complexed with deoxynucleoside triphosphate and pyrophosphate
1kfs		Dna polymerase i klenow fragment (e.c.2.7.7.7) mutant/dna complex
1kln		Dna polymerase i klenow fragment (e.c.2.7.7.7) mutant/dna complex
1krp		Dna polymerase i klenow fragment (e.c.2.7.7.7) mutant/dna complex
1ksp		Dna polymerase i klenow fragment (e.c.2.7.7.7) mutant/dna complex
1ktq		Dna polymerase
1l3s		Crystal structure of bacillus dna polymerase i fragment complexed to 9 base pairs of duplex dna.
1l3t		Crystal structure of bacillus dna polymerase i fragment product complex with 10 base pairs of duplex dna following addition of a single dttp residue
1l3u		Crystal structure of bacillus dna polymerase i fragment product complex with 11 base pairs of duplex dna following addition of a dttp and a datp residue.
1l3v		Crystal structure of bacillus dna polymerase i fragment product complex with 15 base pairs of duplex dna following addition of dttp, datp, dctp, and dgtp residues.
1l5u		Crystal structure of bacillus dna polymerase i fragment product complex with 12 base pairs of duplex dna following addition of a dttp, a datp, and a dctp residue.
1lv5		Crystal structure of the closed conformation of bacillus dna polymerase i fragment bound to dna and dctp
1njw		Guanine-thymine mismatch at the polymerase active site
1njx		Thymine-guanine mismatch at the polymerase active site
1njy		Thymine-thymine mismatch at the polymerase active site
1njz		Cytosine-thymine mismatch at the polymerase active site
1nk0		Adenine-guanine mismatch at the polymerase active site
1nk4		Guanine-guanine mismatch at the polymerase active site
1nk5		Adenine-adenine mismatch at the polymerase active site
1nk6		Cytosine-cytosine mismatch at the polymerase active site
1nk7		Guanine-adenine mismatch at the polymerase active site
1nk8		A bacillus dna polymerase i product complex bound to a guanine-thymine mismatch after a single round of primer extension, following incorporation of dctp.
1nk9		A bacillus dna polymerase i product complex bound to a guanine-thymine mismatch after two rounds of primer extension, following incorporation of dctp and dgtp.
1nkb		A bacillus dna polymerase i product complex bound to a guanine-thymine mismatch after three rounds of primer extension, following incorporation of dctp, dgtp, and dttp.
1nkc		A bacillus dna polymerase i product complex bound to a guanine-thymine mismatch after five rounds of primer extension, following incorporation of dctp, dgtp, dttp, and datp.
1nke		A bacillus dna polymerase i product complex bound to a cytosine-thymine mismatch after a single round of primer extension, following incorporation of dctp.
1qsl		Klenow fragment complexed with single-stranded substrate and europium (iii) ion
1qss		Ddgtp-trapped closed ternary complex of the large fragment of dna polymerase i from thermus aquaticus
1qsy		Ddatp-trapped closed ternary complex of the large fragment of dna polymerase i from thermus aquaticus
1qtm		Ddttp-trapped closed ternary complex of the large fragment of dna polymerase i from thermus aquaticus
1skr		T7 dna polymerase complexed to dna primer/template and ddatp
1sks		Binary 3' complex of t7 dna polymerase with a dna primer/template containing a cis-syn thymine dimer on the template
1skw		Binary 3' complex of t7 dna polymerase with a dna primer/template containing a disordered cis-syn thymine dimer on the template
1sl0		Ternary 3' complex of t7 dna polymerase with a dna primer/template containing a disordered cis-syn thymine dimer on the template and an incoming nucleotide
1sl1		Binary 5' complex of t7 dna polymerase with a dna primer/template containing a cis-syn thymine dimer on the template
1sl2		Ternary 5' complex of t7 dna polymerase with a dna primer/template containing a cis-syn thymine dimer on the template and an incoming nucleotide
1t7p		T7 dna polymerase complexed to dna primer/template,a nucleoside triphosphate, and its processivity factor thioredoxin
1t8e		T7 dna polymerase ternary complex with dctp at the insertion site.
1taq		Structure of taq dna polymerase
1tau		Taq polymerase (e.c.2.7.7.7)/dna/b-octylglucoside complex
1tk0		T7 dna polymerase ternary complex with 8 oxo guanosine and ddctp at the insertion site
1tk5		T7 dna polymerase binary complex with 8 oxo guanosine in the templating strand
1tk8		T7 dna polymerase ternary complex with 8 oxo guanosine and damp at the elongation site
1tkd		T7 dna polymerase ternary complex with 8 oxo guanosine and dcmp at the elongation site
1u45		8oxoguanine at the pre-insertion site of the polymerase active site
1u47		Cytosine-8-oxoguanine base pair at the polymerase active site
1u48		Extension of a cytosine-8-oxoguanine base pair
1u49		Adenine-8oxoguanine mismatch at the polymerase active site
1u4b		Extension of an adenine-8oxoguanine mismatch
1ua0		Aminofluorene dna adduct at the pre-insertion site of a dna polymerase
1ua1		Structure of aminofluorene adduct paired opposite cytosine at the polymerase active site.
1x9m		T7 dna polymerase in complex with an n-2- acetylaminofluorene-adducted dna
1x9s		T7 dna polymerase in complex with a primer/template dna containing a disordered n-2 aminofluorene on the template, crystallized with dideoxy-ctp as the incoming nucleotide.
1x9w		T7 dna polymerase in complex with a primer/template dna containing a disordered n-2 aminofluorene on the template, crystallized with dideoxy-atp as the incoming nucleotide.
1xc9		Structure of a high-fidelity polymerase bound to a benzo[a]pyrene adduct that blocks replication
1xwl		Bacillus stearothermophilus (newly identified strain as yet unnamed) dna polymerase fragment
1zyq		T7 dna polymerase in complex with 8og and incoming ddatp
2ajq		Structure of replicative dna polymerase provides insigts into the mechanisms for processivity, frameshifting and editing
2bdp		Crystal structure of bacillus dna polymerase i fragment complexed to 9 base pairs of duplex dna
2hhq		O6-methyl-guanine:t pair in the polymerase-10 basepair position
2hhs		O6-methyl:c pair in the polymerase-10 basepair position
2hht		C:o6-methyl-guanine pair in the polymerase-2 basepair position
2hhu		C:o6-methyl-guanine in the polymerase postinsertion site (- basepair position)
2hhv		T:o6-methyl-guanine in the polymerase-2 basepair position
2hhw		Ddttp:o6-methyl-guanine pair in the polymerase active site, in the closed conformation
2hhx		O6-methyl-guanine in the polymerase template preinsertion site
2hvh		Ddctp:o6meg pair in the polymerase active site (0 position)
2hvi		Ddctp:g pair in the polymerase active site (0 position)
2hw3		T:o6-methyl-guanine pair in the polymerase postinsertion site (-1 basepair position)
2kfn		Klenow fragment with bridging-sulfur substrate and manganese
2kfz		Klenow fragment with bridging-sulfur substrate and zinc only
2ktq		Open ternary complex of the large fragment of dna polymerase i from thermus aquaticus
2kzm		Klenow fragment with normal substrate and zinc and manganese
2kzz		Klenow fragment with normal substrate and zinc only
3bdp		Dna polymerase i/dna complex
3eyz		Cocrystal structure of bacillus fragment dna polymerase i with duplex dna (open form)
3ez5		Cocrystal structure of bacillus fragment dna polymerase i with duplex dna , dctp, and zinc (closed form).
3ikm		Crystal structure of human mitochondrial dna polymerase holoenzyme
3ktq		Crystal structure of an active ternary complex of the large fragment of dna polymerase i from thermus aquaticus
4bdp		Crystal structure of bacillus dna polymerase i fragment complexed to 11 base pairs of duplex dna after addition of two datp residues
4ktq		Binary complex of the large fragment of dna polymerase i from t. aquaticus bound to a primer/template dna
5ktq		Large fragment of taq dna polymerase bound to dctp

Links (links to other resources describing this domain)
PFAM DNA_pol_A
INTERPRO IPR001098
PROSITE DNA_POLYMERASE_A

PFAM	DNA_pol_A
INTERPRO	IPR001098
PROSITE	DNA_POLYMERASE_A