Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95, 5857-5864
Letunic et al. (2012) Nucleic Acids Res , doi:10.1093/nar/gkr931

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POLBc DNA polymerase type-B family

SMART accession number:	SM00486
Description:	DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Interpro abstract (IPR006172):	DNA is the biological information that instructs cells how to exist in an ordered fashion: accurate replication is thus one of the most important events in the life cycle of a cell. This function is performed by DNA- directed DNA-polymerases (EC 2.7.7.7) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family polymerases. The most conserved region (I) includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known. However, it has been suggested [(PUBMED:2461550)] that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain [(PUBMED:8679562)], a DNA binding domain, and binding domains for both dNTP's and pyrophosphate [(PUBMED:9757117)].
GO process:	nucleobase-containing compound metabolic process (GO:0006139)
GO function:	DNA-directed DNA polymerase activity (GO:0003887), nucleotide binding (GO:0000166), nucleic acid binding (GO:0003676)
Family alignment:	View or CHROMA formatCLUSTALW formatMSF formatFASTA formatPIR format

There are 1709 POLBc domains in 1709 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 POLBc domain in a specific node, click on it.

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

  Useful shortcuts: Expand all nodes or Collapse tree
  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.

  • Wang J, Yu P, Lin TC, Konigsberg WH, Steitz TA
  • Crystal structures of an NH2-terminal fragment of T4 DNA polymerase and its complexes with single-stranded DNA and with divalent metal ions.
  • Biochemistry. 1996; 35: 8110-9
  • Display abstract

  • We report the crystal structure of an NH2-terminal 388-residue fragment of T4 DNA polymerase (protein N388) refined at 2.2 A resolution. This fragment contains both the 3'-5' exonuclease active site and part of the autologous mRNA binding site (J. D. Karam, personal communication). The structure of a complex between the apoprotein N388 and a substrate, p(dT)3, has been refined at 2.5 A resolution to a crystallographic R-factor of 18.7%. Two divalent metal ion cofactors, Zn(II) and Mn(II), have been located in crystals of protein N388 which had been soaked in solutions containing Zn(II), Mn(II), or both. The structure of the 3'-5' exonuclease domain of protein N388 closely resembles the corresponding region in the Klenow fragment despite minimal sequence identity. The side chains of four carboxylate residues that serve as ligands for the two metal ions required for catalysis are located in geometrically equivalent positions in both proteins with a rms deviation of 0.87 A. There are two main differences between the 3'-5' exonuclease active site regions of the two proteins: (I) the OH of Tyr-497 in the Klenow fragment interacts with the scissile phosphate in the active site whereas the OH of the equivalent tyrosine (Tyr-320) in protein N388 points away from the active center; (II) different residues form of the binding pocket for the 3'-terminal bases of the substrate. In the protein N388 complex the 3'-terminal base of p(dT)3 is rotated approximately 60 degrees relative to the position that the corresponding base occupies in the p(dT)3 complex with the Klenow fragment. Finally, a separate domain (residues 1-96) of protein N388 may be involved in mRNA binding that results in translational regulation of T4 DNA polymerase (Pavlov & Karam, 1994).

• Metabolism (metabolic pathways involving proteins which contain this domain)

• Click the image to view the interactive version of the map in iPath

  % proteins involved KEGG pathway ID Description 43.07 map03030 DNA replication 28.47 map00240 Pyrimidine metabolism 28.47 map00230 Purine metabolism This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with POLBc domain which could be assigned to a KEGG orthologous group, and not all proteins containing POLBc domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

• Structure (3D structures containing this domain)

• 3D Structures of POLBc domains in PDB

  PDB code	Main view	Title
  1clq		Crystal structure of a replication fork dna polymerase editing complex at 2.7 a resolution
  1d5a		Crystal structure of an archaebacterial dna polymerase d.tok. deposition of second native structure at 2.4 angstrom
  1ig9		Structure of the replicating complex of a pol alpha family dna polymerase
  1ih7		High-resolution structure of apo rb69 dna polymerase
  1noy		Dna polymerase (e.c.2.7.7.7)/dna complex
  1noz		T4 dna polymerase fragment (residues 1-388) at 110k
  1q8i		Crystal structure of escherichia coli dna polymerase ii
  1q9x		Crystal structure of enterobacteria phage rb69 gp43 dna polymerase complexed with tetrahydrofuran containing dna
  1q9y		Crystal structure of enterobacteria phage rb69 gp43 dna polymerase complexed with 8-oxoguanosine containing dna
  1qht		Dna polymerase from thermococcus sp. 9on-7 archaeon
  1qqc		Crystal structure of an archaebacterial dna polymerase d.tok
  1s5j		Insight in dna replication: the crystal structure of dna polymerase b1 from the archaeon sulfolobus solfataricus
  1tgo		Thermostable b type dna polymerase from thermococcus gorgonarius
  1waf		Dna polymerase from bacteriophage rb69
  1waj		Dna polymerase from bacteriophage rb69
  1wn7		Crystal structure of archaeal family b dna polymerase mutant
  1wns		Crystal structure of family b dna polymerase from hyperthermophilic archaeon pyrococcus kodakaraensis kod1
  1xhx		Phi29 dna polymerase, orthorhombic crystal form
  1xhz		Phi29 dna polymerase, orthorhombic crystal form, ssdna complex
  1xi1		Phi29 dna polymerase ssdna complex, monoclinic crystal form
  2atq		Rb69 single-stranded dna binding protein-dna polymerase fusion
  2dtu		Crystal structure of the beta hairpin loop deletion variant of rb69 gp43 in complex with dna containing an abasic site analog
  2dy4		Crystal structure of rb69 gp43 in complex with dna containing thymine glycol
  2ex3		Bacteriophage phi29 dna polymerase bound to terminal protein
  2gv9		Crystal structure of the herpes simplex virus type 1 dna polymerase
  2jgu		Crystal structure of dna-directed dna polymerase
  2oyq		Crystal structure of rb69 gp43 in complex with dna with 5- nimp opposite an abasic site analog
  2ozm		Crystal structure of rb69 gp43 in complex with dna with 5- nitp opposite an abasic site analog
  2ozs		Crystal structure of rb69 gp43 in complex with dna with datp opposite dtmp
  2p5g		Crystal structure of rb69 gp43 in complex with dna with damp opposite an abasic site analog in a 21mer template
  2p5o		Crystal structure of rb69 gp43 in complex with dna containing an abasic site analog
  2py5		Phi29 dna polymerase complexed with single-stranded dna
  2pyj		Phi29 dna polymerase complexed with primer-template dna and incoming nucleotide substrates (ternary complex)
  2pyl		Phi29 dna polymerase complexed with primer-template dna and incoming nucleotide substrates (ternary complex)
  2pzs		Phi29 dna polymerase complexed with primer-template dna (post-translocation binary complex)
  2vwj		Uracil recognition in archaeal dna polymerases captured by x-ray crystallography.
  2vwk		Uracil recognition in archaeal dna polymerases captured by x-ray crystallography. v93q polymerase variant
  3a2f		Crystal structure of pyrococcus furiosus dna polymerase/pcna monomer mutant complex
  3cfo		Triple mutant apo structure
  3cfp		Structure of the replicating complex of a pol alpha family dna polymerase, ternary complex 1
  3cfr		Structure of the replicating complex of a pol alpha family dna polymerase, ternary complex 2
  3cq8		Ternary complex of the l415f mutant rb69 exo(-)polymerase
  3iay		Ternary complex of dna polymerase delta

• Links (links to other resources describing this domain)

• PFAM	DNA_pol_B
  INTERPRO	IPR006172
  PROSITE	DNA_POLYMERASE_B

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