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 function: nucleotide binding (GO:0000166), DNA-directed DNA polymerase activity (GO:0003887), nucleic acid binding (GO:0003676)

There are 13646 POLBc domains in 13642 proteins in SMART's nrdb database.

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

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)

% 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	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
2xhb	Crystal structure of DNA polymerase from Thermococcus gorgonarius in complex with hypoxanthine-containing DNA
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
3k57	Crystal structure of E.coli Pol II-normal DNA-dATP ternary complex
3k58	Crystal structure of E.coli Pol II-normal DNA-dTTP ternary complex
3k59	Crystal structure of E.coli Pol II-normal DNA-dCTP ternary complex
3k5l	Crystal structure of E.coli Pol II-abasic DNA-dATP Lt(0, 3) ternary complex
3k5m	Crystal structure of E.coli Pol II-abasic DNA-ddGTP Lt(-2, 2) ternary complex
3k5n	Crystal structure of E.coli Pol II-abasic DNA binary complex
3k5o	Crystal structure of E.coli Pol II
3kd1	Closed binary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP terminated primer template pair.
3kd5	Closed ternary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP terminated primer template pair and phosphonoformic acid.
3l8b	Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoin
3lds	Crystal structure of RB69 gp43 with DNA and dATP opposite 8-oxoG
3lzi	RB69 DNA Polymerase (Y567A) ternary complex with dATP Opposite 7,8-dihydro-8-oxoguanine
3lzj	RB69 DNA Polymerase (Y567A) ternary complex with dCTP Opposite 7,8-Dihydro-8-oxoguanine
3maq	Crystal structure of E.coli Pol II-normal DNA-dGTP ternary complex
3nae	RB69 DNA Polymerase (Y567A) Ternary Complex with dATP Opposite Guanidinohydantoin
3nci	RB69 DNA Polymerase Ternary Complex with dCTP Opposite dG at 1.8 angstrom resolution
3ndk	RB69 DNA Polymerase (Y567A) Ternary Complex with dCTP Opposite dG
3ne6	RB69 DNA Polymerase (S565G/Y567A) Ternary Complex with dCTP Opposite dG
3ngi	RB69 DNA Polymerase (Y567A) Ternary Complex with dTTP Opposite dG
3nhg	RB69 DNA Polymerase (S565G/Y567A) Ternary Complex with dTTP Opposite dG
3qei	RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dCTP Opposite Difluorotoluene Nucleoside
3qep	RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dTTP Opposite Difluorotoluene Nucleoside
3qer	RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dATP Opposite Difluorotoluene Nucleoside
3qes	RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dGTP Opposite Difluorotoluene Nucleoside
3qet	RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dTTP Opposite dT
3qev	RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dCTP Opposite dT
3qew	RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dDTP Opposite dT
3qex	RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dGTP Opposite dT
3qnn	RB69 DNA Polymerase (Y567A) Ternary Complex with dGT Opposite 3tCo
3qno	RB69 DNA Polymerase (Y567A) Ternary Complex with dATP Opposite 3tCo
3rma	Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol
3rmb	Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol
3rmc	Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol
3rmd	Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol
3rwu	RB69 DNA Polymerase (Y567A) Ternary Complex with dATP Opposite Difluorotoluene Nucleoside
3s9h	RB69 DNA Polymerase Triple Mutant(L561A/S565G/Y567A) ternary complex with dUpNpp and a dideoxy-terminated primer in the presence of Ca2+
3scx	RB69 DNA Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Complex with dUpNpp and a Deoxy-terminated Primer in the Presence of Ca2+
3si6	RB69 DNA Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with dUpNpp and a Deoxy-terminated Primer in the presence of Mg2+
3sjj	RB69 DNA Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with dUpNpp and a Deoxy-terminated Primer in the presence of Mn2+
3snn	RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dCTP Opposite dG in the presence of Mg2+
3spy	RB69 DNA Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with dUpCpp Opposite dA
3spz	DNA Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with dUpCpp Opposite dA (Ca2+)
3sq0	DNA Polymerase(L561A/S565G/Y567A) Ternary Complex with dUpNpp Opposite dA (Mn2+)
3sq1	RB69 DNA Polymerase Ternary Complex with dUpCpp Opposite dA
3sq2	RB69 DNA Polymerase Ternary Complex with dTTP Opposite 2AP (AT rich sequence)
3sq4	RB69 DNA Polymerase Ternary Complex with dTTP Opposite 2AP (GC rich sequence)
3sun	RB69 DNA Polymerase (Y567A) Ternary Complex with dTTP Opposite 2AP (AT rich sequence)
3suo	RB69 DNA Polymerase (Y567A) Ternary Complex with dTTP Opposite 2AP (GC rich sequence)
3sup	RB69 DNA Polymerase (Y567A) Ternary Complex with dCTP Opposite 2AP (GC rich sequence)
3suq	RB69 DNA Polymerase (Y567A) Ternary Complex with dCTP Opposite 2AP (AT rich sequence)
3tab	5-hydroxycytosine paired with dGMP in RB69 gp43
3tae	5-hydroxycytosine paired with dAMP in RB69 gp43
3taf	5-fluorocytosine paired with ddGMP in RB69 gp43
3tag	5-fluorocytosine paired with dAMP in RB69 gp43
3uiq	RB69 DNA Polymerase Ternary Complex containing dUpNpp
4ahc	Crystal Structure of an Evolved Replicating DNA Polymerase
4ail	Crystal Structure of an Evolved Replicating DNA Polymerase
4b08	Yeast DNA polymerase alpha, Selenomethionine protein
4dtj	RB69 DNA Polymerase Ternary Complex with dTTP Opposite an Abasic Site and ddT/dA as the Penultimate Base-pair
4dtm	RB69 DNA Polymerase Ternary Complex with dCTP Opposite an Abasic Site and ddG/dC as the Penultimate Base-pair
4dtn	RB69 DNA Polymerase Ternary Complex with dATP Opposite an Abasic Site and ddA/dT as the Penultimate Base-pair
4dto	RB69 DNA Polymerase Ternary Complex with dCTP Opposite an Abasic Site and ddA/dT as the Penultimate Base-pair
4dtp	RB69 DNA Polymerase Ternary Complex with dGTP Opposite an Abasic Site and ddA/dT as the Penultimate Base-pair
4dtr	RB69 DNA Polymerase Ternary Complex with dATP Opposite an Abasic Site and ddC/dG as the Penultimate Base-pair
4dts	RB69 DNA Polymerase Ternary Complex with dCTP Opposite an Abasic Site and ddC/dG as the Penultimate Base-pair
4dtu	RB69 DNA Polymerase Ternary Complex with dGTP Opposite an Abasic Site and ddC/dG as the Penultimate Base-pair
4dtx	RB69 DNA Polymerase Ternary Complex with dTTP Opposite an Abasic Site and ddC/dG as the Penultimate Base-pair
4du1	RB69 DNA Polymerase Ternary Complex with dATP Opposite dT
4du3	RB69 DNA Polymerase Ternary Complex with dDTP Opposite dT with 3-Deaza-adenine at the N-1 Position of Template Strand
4du4	RB69 DNA Polymerase Ternary Complex with dATP Opposite dT with 3-Deaza-adenine at the N-3 Position of Primer Strand
4e3s	RB69 DNA Polymerase Ternary Complex with dQTP Opposite dT
4fj5	RB69 DNA polymerase ternary complex with dATP/dT
4fj7	RB69 DNA polymerase ternary complex with dGTP/dT
4fj8	RB69 DNA polymerase ternary complex with dCTP/dT
4fj9	RB69 DNA polymerase ternary complex with dTTP/dT
4fjg	RB69 DNA polymerase ternary complex with dATP/dC
4fjh	RB69 DNA polymerase ternary complex with dGTP/dC
4fji	RB69 DNA polymerase ternary complex with dcTP/dC
4fjj	RB69 DNA polymerase ternary complex with dTTP/dC
4fjk	RB69 DNA polymerase ternary complex with dATP/dA
4fjl	RB69 DNA polymerase ternary complex with dGTP/dA
4fjm	RB69 DNA polymerase ternary complex with dCTP/dA
4fjn	RB69 DNA polymerase ternary complex with dTTP/dA
4fjx	RB69 DNA polymerase ternary complex with dATP/dG
4fk0	RB69 DNA polymerase ternary complex with dCTP/dG
4fk2	RB69 DNA polymerase ternary complex with dTTP/dG
4fk4	RB69 DNA polymerase ternary complex with dGTP/dG
4flt	Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode
4flu	Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode
4flv	Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode
4flw	Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode
4flx	Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode
4fly	Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode
4flz	Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode
4fm0	Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode
4fm1	Pyrococcus abyssi B family DNA polymerase bound to a dsDNA, in edition mode
4fm2	Pyrococcus abyssi B family DNA polymerase (triple mutant) bound to a dsDNA, in edition mode
4fvm	Crystal structure of yeast DNA polymerase alpha
4fxd	Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA
4fyd	Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA and dGTP
4i9l	Crystal structure of the D714A mutant of RB69 DNA polymerase
4i9q	Crystal structure of the ternary complex of the D714A mutant of RB69 DNA polymerase
4j2a	RB69 DNA Polymerase L415A Ternary Complex
4j2b	RB69 DNA Polymerase L415G Ternary Complex
4j2d	RB69 DNA Polymerase L415K Ternary Complex
4j2e	RB69 DNA Polymerase L415M Ternary Complex
4k8x	Binary complex of 9N DNA polymerase in the replicative state
4k8z	KOD Polymerase in binary complex with dsDNA
4khn	Crystal structure of the ternary complex of the D714A mutant of RB69 DNA polymerase
4khq	Ternary complex of RB69 mutant L415F wit DUMPNPP
4khs	Ternary complex of RB69 mutant L415F with a ribonucleotide at 0 position
4khu	Ternary complex of rb69 mutant L415F with a ribonucleotide at -1 position
4khw	Ternary complex of RB69 mutant L415F with ribonucleotide at -2 position
4khy	Ternary complex of rb69 mutant L415F with ribonucleotide at -3 position
4ki4	Ternary complex of rb69 mutant L415F with ribonucleotides at 0 and -1 position
4ki6	Ternary complex of rb69 mutant l415f with ribonucleotides at -1 and -2 position
4m3r	RB69 DNA polymerase ternary complex with dT/dG at position n-1 of primer/template duplex
4m3t	RB69 DNA polymerase ternary complex with dT/dG at position n-2 of primer/template duplex
4m3u	RB69 DNA polymerase ternary complex with dT/dG at position n-3 of primer/template duplex
4m3w	RB69 DNA polymerase ternary complex with dT/dG at position n-4 of primer/template duplex
4m3x	RB69 DNA polymerase ternary complex with dT/dG at position n-5 of primer/template duplex
4m3y	RB69 DNA polymerase ternary complex with dG/dT at position n-1 of primer/template duplex
4m3z	RB69 DNA polymerase ternary complex with dG/dT at position n-2 of primer/tempLate duplex
4m41	RB69 DNA polymerase ternary complex with dG/dT at position n-3 of primer/tempLate duplex
4m42	RB69 DNA polymerase ternary complex with dG/dT at position n-4 of primer/tempLate duplex
4m45	RB69 DNA polymerase ternary complex with dG/dT at position n-5 of primer/template duplex
4m8o	TERNARY COMPLEX OF DNA POLYMERASE EPSILON WITH AN INCOMING dATP
4ptf	Ternary crystal structure of yeast DNA polymerase epsilon with template G
4q5v	4Q5V
4qcl	4QCL
5exr	5EXR
5iud	5IUD

Links (links to other resources describing this domain)

• PROSITE: DNA_POLYMERASE_B
• INTERPRO: IPR006172
• PFAM: DNA_pol_B