DNA polymerase

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{{STRUCTURE_1taq| PDB=1taq | SIZE=350| SCENE=DNA_polymerase/Cv/1 |right|CAPTION=DNA polymerase complex with octylglucoside [[1taq]] }}
{{STRUCTURE_1taq| PDB=1taq | SIZE=350| SCENE=DNA_polymerase/Cv/1 |right|CAPTION=DNA polymerase complex with octylglucoside [[1taq]] }}
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[[DNA polymerase]] '''(Dpo)''' reads a [[DNA|DNA strand]] and catalyzes the synthesis of its complementary strand. Dpo sliding clamp is made of the complex of Dpo and [[Proliferating Cell Nuclear Antigen]] (PCNA) which encircles it. The BRCT domain in Dpo is the C-terminal domain of breast [[cancer]] susceptibility protein. The Klenow fragment is a large Dpo fragment produced upon cleavage of Dpo by [[Subtilisin|subtilisin]]. In the ''E. coli'', the EcDpo III subunits β, γ, δ, δ' are named clamp loader. This complex assembles the β subunit sliding clamp unto the DNA. '''Rev1''' is a '''Dpo''' involved in replication over DNA lesions. '''Terminal deoxynucleotidyl transferase (TdT)''' is a Dpo expressed in immature lymphoid cells. TdT adds nucleotides to exons during antibody gene recombination. For more details see<br />
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[[DNA polymerase]] '''(Dpo)''' reads a [[DNA|DNA strand]] and catalyzes the synthesis of its complementary strand. Dpo's are divided into 7 families according to their sequence homology and 3D structure similarities. The families are:<br />
 +
* Family A - replicative or repair Dpo.<br />
 +
* Family B - replicative Dpo involved in processing DNA replication during cell division (includes eukaryotic Dpo α,δ,ε).<br />
 +
* Family C - major replicative Dpo in bacteria (includes Dpo II, III, IV).<br />
 +
* Family D - replicative. Present in archaea.<br />
 +
* Family X - eukaryotic repair Dpo (includes Dpo β,λ,σ,μ and terminal deoxynucleotidyl transferase).<br />
 +
* Family Y - replicative of damaged DNA (includes eukaryotic η,ι,κ).<br />
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* Family RT - reverse transcriptase. See [[Reverse transcriptase]].<br />
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Some Dpo terminology:<br />
 +
Dpo '''sliding clamp''' is made of the complex of Dpo and [[Proliferating Cell Nuclear Antigen]] (PCNA) which encircles it.<br />
 +
The '''BRCT domain''' in Dpo is the C-terminal domain of breast [[cancer]] susceptibility protein.<br />
 +
'''Klenow fragment''' is a large Dpo fragment produced upon cleavage of Dpo by [[Subtilisin|subtilisin]].<br />
 +
In the ''E. coli'', the EcDpo III subunits β, γ, δ, δ' are named '''clamp loader'''. This complex assembles the β subunit sliding clamp unto the DNA.<br />
 +
'''Rev1''' is a '''Dpo''' involved in replication over DNA lesions. <br />
 +
'''Terminal deoxynucleotidyl transferase (TdT)''' is a family X Dpo expressed in immature lymphoid cells. TdT adds nucleotides to exons during antibody gene recombination.<br />
 +
For more details see<br />
* [[DNA Polymerase I]]<br />
* [[DNA Polymerase I]]<br />
* [[Polymerase III homoenzyme beta subunit]]<br />
* [[Polymerase III homoenzyme beta subunit]]<br />
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{{#tree:id=OrganizedByTopic|openlevels=0|
{{#tree:id=OrganizedByTopic|openlevels=0|
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*Family A – replicative and repair Dpo
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*Family A
**[[2ajq]] – T7Dpo (mutant) + thioredoxin (mutant) + DNA - Enterobacteria phage T7<br />
**[[2ajq]] – T7Dpo (mutant) + thioredoxin (mutant) + DNA - Enterobacteria phage T7<br />
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**[[4p4m]], [[4p4o]], [[4p4p]] - Dpo β + DNA + nucleotide – ''Leishmania infantum''<br />
**[[4p4m]], [[4p4o]], [[4p4p]] - Dpo β + DNA + nucleotide – ''Leishmania infantum''<br />
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*Family B – 3’-5’ exonuclease activity (includes eukaryotic α,δ,ε)
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*Family B
**[[1ih7]] – EpDpo - Enterobacteria phage RB69<br />
**[[1ih7]] – EpDpo - Enterobacteria phage RB69<br />
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**[[4flt]], [[4flu]], [[4flv]], [[4flw]], [[4flx]], [[4fly]], [[4flz]], [[4fm0]], [[4fm1]], [[4fm2]] – Dpo + DNA – ''Pyrococcus abyssi''
**[[4flt]], [[4flu]], [[4flv]], [[4flw]], [[4flx]], [[4fly]], [[4flz]], [[4fm0]], [[4fm1]], [[4fm2]] – Dpo + DNA – ''Pyrococcus abyssi''
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*Family C – bacterial chromosomal replicative Dpo (Pol III)
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*Family C
**[[2hnh]], [[2hqa]] - EcDpo III subunit α catalytic fragment<br />
**[[2hnh]], [[2hqa]] - EcDpo III subunit α catalytic fragment<br />
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**[[1bgx]] – TaDpo + TP7 MAB<br />
**[[1bgx]] – TaDpo + TP7 MAB<br />
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*Family X – eukaryotic Dpo (β,λ,σ,μ) involved in base excision repair, non-homologous end-joining and V(D)J recombination
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*Family X
**[[3q8p]], [[3q8q]], [[3lk9]], [[3mby]], [[3isb]], [[3isc]], [[1zjm]], [[1tv9]], [[1tva]], [[1bpx]], [[1bpz]], [[1zqa]], [[1zqb]], [[1zqc]], [[1zqd]], [[1zqf]], [[1zqg]], [[1zqh]], [[1zqi]], [[1zaj]], [[1zqk]], [[1zql]], [[1zqm]], [[1zqn]], [[1zqo]], [[1zqp]], [[1zqq]], [[1zqr]], [[1zqs]], [[1zqt]], [[1zqu]], [[1zqv]], [[1zqw]], [[1zqx]], [[1zqy]], [[1zqz]], [[7ice]], [[7icf]], [[7ici]], [[7icj]], [[7icl]], [[7icm]], [[7icp]], [[7icr]], [[7ict]], [[7icu]], [[7icv]], [[8icb]], [[8icc]], [[9icj]], [[9ick]], [[9icl]], [[9icm]], [[9icp]], [[9icw]], [[9icx]], [[9icy]], [[7icg]], [[7ich]], [[7ick]], [[7icn]], [[7ico]], [[7icq]], [[7ics]], [[1zqe]], [[4gxi]], [[4gxj]], [[4gxk]], [[4kld]], [[4kle]], [[4klf]], [[4klg]], [[4klh]], [[4kli]], [[4klj]], [[4kll]], [[4klm]], [[4klo]], [[4klp]], [[4klq]], [[4kls]], [[4klt]], [[4klu]], [[1zqj]], [[4lvs]], [[4m2y]], [[4m47]], [[4nlk]], [[4nln]], [[4nlz]], [[4nm1]], [[4nm2]], [[3gdx]], [[3rh4]], [[3rh5]], [[3rh6]] - hDpo β + DNA<br />
**[[3q8p]], [[3q8q]], [[3lk9]], [[3mby]], [[3isb]], [[3isc]], [[1zjm]], [[1tv9]], [[1tva]], [[1bpx]], [[1bpz]], [[1zqa]], [[1zqb]], [[1zqc]], [[1zqd]], [[1zqf]], [[1zqg]], [[1zqh]], [[1zqi]], [[1zaj]], [[1zqk]], [[1zql]], [[1zqm]], [[1zqn]], [[1zqo]], [[1zqp]], [[1zqq]], [[1zqr]], [[1zqs]], [[1zqt]], [[1zqu]], [[1zqv]], [[1zqw]], [[1zqx]], [[1zqy]], [[1zqz]], [[7ice]], [[7icf]], [[7ici]], [[7icj]], [[7icl]], [[7icm]], [[7icp]], [[7icr]], [[7ict]], [[7icu]], [[7icv]], [[8icb]], [[8icc]], [[9icj]], [[9ick]], [[9icl]], [[9icm]], [[9icp]], [[9icw]], [[9icx]], [[9icy]], [[7icg]], [[7ich]], [[7ick]], [[7icn]], [[7ico]], [[7icq]], [[7ics]], [[1zqe]], [[4gxi]], [[4gxj]], [[4gxk]], [[4kld]], [[4kle]], [[4klf]], [[4klg]], [[4klh]], [[4kli]], [[4klj]], [[4kll]], [[4klm]], [[4klo]], [[4klp]], [[4klq]], [[4kls]], [[4klt]], [[4klu]], [[1zqj]], [[4lvs]], [[4m2y]], [[4m47]], [[4nlk]], [[4nln]], [[4nlz]], [[4nm1]], [[4nm2]], [[3gdx]], [[3rh4]], [[3rh5]], [[3rh6]] - hDpo β + DNA<br />
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**[[4i2g]] – mTdT catalytic domain + Mg + Co + DNA<br / >
**[[4i2g]] – mTdT catalytic domain + Mg + Co + DNA<br / >
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*Family Y – translesion Dpo (includes eukaryotic η,ι,κ)
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*Family Y
**[[2i5o]] - hDpo η ubiquitin-binding zinc finger - NMR<br />
**[[2i5o]] - hDpo η ubiquitin-binding zinc finger - NMR<br />

Revision as of 08:30, 14 October 2015

Template:STRUCTURE 1taq

DNA polymerase (Dpo) reads a DNA strand and catalyzes the synthesis of its complementary strand. Dpo's are divided into 7 families according to their sequence homology and 3D structure similarities. The families are:

  • Family A - replicative or repair Dpo.
  • Family B - replicative Dpo involved in processing DNA replication during cell division (includes eukaryotic Dpo α,δ,ε).
  • Family C - major replicative Dpo in bacteria (includes Dpo II, III, IV).
  • Family D - replicative. Present in archaea.
  • Family X - eukaryotic repair Dpo (includes Dpo β,λ,σ,μ and terminal deoxynucleotidyl transferase).
  • Family Y - replicative of damaged DNA (includes eukaryotic η,ι,κ).
  • Family RT - reverse transcriptase. See Reverse transcriptase.

Some Dpo terminology:
Dpo sliding clamp is made of the complex of Dpo and Proliferating Cell Nuclear Antigen (PCNA) which encircles it.
The BRCT domain in Dpo is the C-terminal domain of breast cancer susceptibility protein.
Klenow fragment is a large Dpo fragment produced upon cleavage of Dpo by subtilisin.
In the E. coli, the EcDpo III subunits β, γ, δ, δ' are named clamp loader. This complex assembles the β subunit sliding clamp unto the DNA.
Rev1 is a Dpo involved in replication over DNA lesions.
Terminal deoxynucleotidyl transferase (TdT) is a family X Dpo expressed in immature lymphoid cells. TdT adds nucleotides to exons during antibody gene recombination.
For more details see

3D Structures of DNA polymerase

Updated on 14-October-2015

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