PDBsum entry 3flo

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
Protein chains
433 a.a. *
180 a.a. *
SO4 ×65
_ZN ×8
Waters ×571
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Crystal structure of the carboxyl-terminal domain of yeast d polymerase alpha in complex with its b subunit
Structure: DNA polymerase alpha subunit b. Chain: a, c, e, g. Fragment: unp residues 246-705. Synonym: DNA polymerase i subunit b, DNA polymerase alpha:p complex p86 subunit, pol alpha-primase complex p86 subunit, polymerase-primase complex p74 subunit. Engineered: yes. DNA polymerase alpha catalytic subunit a. Chain: i, j, k, l.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: pol12. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: pol1, cdc17.
2.50Å     R-factor:   0.192     R-free:   0.218
Authors: S.N.Klinge,L.Pellegrini
Key ref: S.Klinge et al. (2009). 3D architecture of DNA Pol alpha reveals the functional core of multi-subunit replicative polymerases. EMBO J, 28, 1978-1987. PubMed id: 19494830
19-Dec-08     Release date:   09-Jun-09    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P38121  (DPOA2_YEAST) -  DNA polymerase alpha subunit B
705 a.a.
433 a.a.
Protein chains
Pfam   ArchSchema ?
P13382  (DPOA_YEAST) -  DNA polymerase alpha catalytic subunit A
1468 a.a.
180 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains B, D, F, H: E.C.  - DNA-directed Dna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Deoxynucleoside triphosphate
+ DNA(n)
= diphosphate
+ DNA(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA replication   2 terms 
  Biochemical function     nucleoside binding     3 terms  


EMBO J 28:1978-1987 (2009)
PubMed id: 19494830  
3D architecture of DNA Pol alpha reveals the functional core of multi-subunit replicative polymerases.
S.Klinge, R.Núñez-Ramírez, O.Llorca, L.Pellegrini.
Eukaryotic DNA replication requires the coordinated activity of the multi-subunit DNA polymerases: Pol alpha, Pol delta and Pol epsilon. The conserved catalytic and regulatory B subunits associate in a constitutive heterodimer that represents the functional core of all three replicative polymerases. Here, we combine X-ray crystallography and electron microscopy (EM) to describe subunit interaction and 3D architecture of heterodimeric yeast Pol alpha. The crystal structure of the C-terminal domain (CTD) of the catalytic subunit bound to the B subunit illustrates a conserved mechanism of accessory factor recruitment by replicative polymerases. The EM reconstructions of Pol alpha reveal a bilobal shape with separate catalytic and regulatory modules. Docking of the B-CTD complex in the EM reconstruction shows that the B subunit is tethered to the polymerase domain through a structured but flexible linker. Our combined findings provide a structural template for the common functional architecture of the three major replicative DNA polymerases.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20163964 E.Johansson, and S.A.Macneill (2010).
The eukaryotic replicative DNA polymerases take shape.
  Trends Biochem Sci, 35, 339-347.  
19682465 Y.I.Pavlov, and P.V.Shcherbakova (2010).
DNA polymerases at the eukaryotic fork-20 years later.
  Mutat Res, 685, 45-53.  
19686603 J.Sanchez Garcia, A.G.Baranovskiy, E.V.Knatko, F.C.Gray, T.H.Tahirov, and S.A.MacNeill (2009).
Functional mapping of the fission yeast DNA polymerase delta B-subunit Cdc1 by site-directed and random pentapeptide insertion mutagenesis.
  BMC Mol Biol, 10, 82.  
19818796 R.Jain, M.Hammel, R.E.Johnson, L.Prakash, S.Prakash, and A.K.Aggarwal (2009).
Structural insights into yeast DNA polymerase delta by small angle X-ray scattering.
  J Mol Biol, 394, 377-382.  
19747370 R.Ohsawa, M.Adkins, and J.K.Tyler (2009).
Epigenetic inheritance of an inducibly nucleosome-depleted promoter and its associated transcriptional state in the apparent absence of transcriptional activators.
  Epigenetics Chromatin, 2, 11.  
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