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PDBsum entry 3rh5

Go to PDB code: 
protein dna_rna ligands metals links
Transferase/DNA PDB id
3rh5
Jmol PyMol
Contents
Protein chain
326 a.a.
DNA/RNA
Ligands
DCP ×2
Metals
_CL ×5
_MN ×7
_NA ×2
Waters ×286
PDB id:
3rh5
Name: Transferase/DNA
Title: DNA polymerase beta mutant (y271) with a dideoxy-terminated with an incoming deoxynucleotide (dctp)
Structure: DNA polymerase beta. Chain: a. Engineered: yes. Mutation: yes. 5'-d( Cp Cp Gp Ap Cp Gp Cp Cp Gp Cp Ap Tp Cp Ap G chain: t. Engineered: yes. 5'-d( Gp Cp Tp Gp Ap Tp Gp Cp Gp (Ddg))-3'. Chain: p.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: polb. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes
Resolution:
2.10Å     R-factor:   0.215     R-free:   0.281
Authors: N.A.Cavanaugh,W.A.Beard,V.K.Batra,L.Perera,L.G.Pedersen,S.H.
Key ref: N.A.Cavanaugh et al. (2011). Molecular insights into DNA polymerase deterrents for ribonucleotide insertion. J Biol Chem, 286, 31650-31660. PubMed id: 21733843 DOI: 10.1074/jbc.M111.253401
Date:
11-Apr-11     Release date:   06-Jul-11    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06746  (DPOLB_HUMAN) -  DNA polymerase beta
Seq:
Struc:
335 a.a.
326 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.7.7.7  - DNA-directed Dna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Deoxynucleoside triphosphate
Bound ligand (Het Group name = DCP)
matches with 68.97% similarity
+ 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!
  Cellular component     protein complex   6 terms 
  Biological process     immunoglobulin heavy chain V-D-J recombination   27 terms 
  Biochemical function     protein binding     12 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M111.253401 J Biol Chem 286:31650-31660 (2011)
PubMed id: 21733843  
 
 
Molecular insights into DNA polymerase deterrents for ribonucleotide insertion.
N.A.Cavanaugh, W.A.Beard, V.K.Batra, L.Perera, L.G.Pedersen, S.H.Wilson.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22139012 Y.Shen, K.D.Koh, B.Weiss, and F.Storici (2012).
Mispaired rNMPs in DNA are mutagenic and are targets of mismatch repair and RNases H.
  Nat Struct Mol Biol, 19, 98.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.

 

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