DNA polymerase: Difference between revisions

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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]] }}


[[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 />
[[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 />
* Family RT - reverse transcriptase.  See [[Reverse transcriptase]].<br />
 
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|


*Family A – replicative and repair Dpo
*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 />


*Family B – 3’-5’ exonuclease activity (includes eukaryotic α,δ,ε)
*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''


*Family C – bacterial chromosomal replicative Dpo (Pol III)
*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 />


*Family X – eukaryotic Dpo (β,λ,σ,μ) involved in base excision repair, non-homologous end-joining and V(D)J recombination
*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 / >


*Family Y – translesion Dpo (includes eukaryotic η,ι,κ)
*Family Y  


**[[2i5o]] - hDpo η ubiquitin-binding zinc finger - NMR<br />
**[[2i5o]] - hDpo η ubiquitin-binding zinc finger - NMR<br />

Revision as of 11:30, 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 polymerase3D Structures of DNA polymerase

Updated on 14-October-2015

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Alexander Berchansky, David Canner, Michal Harel, Joel L. Sussman, Cori Damron, Emily Bray, Jaime Prilusky
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