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PDBsum entry 2rdi
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protein ligands links
Transferase PDB id
2rdi

 

 

 

 

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JSmol PyMol  
Contents
Protein chain
336 a.a. *
Ligands
PEG
GOL
Waters ×235
* Residue conservation analysis
PDB id:
2rdi
Name: Transferase
Title: Snapshots of a y-family DNA polymerase in replication: dpo4 in apo and binary/ternary complex forms
Structure: DNA polymerase iv. Chain: a. Synonym: pol iv. Engineered: yes
Source: Sulfolobus solfataricus. Strain: p2. Gene: dbh, dpo4. Expressed in: escherichia coli.
Resolution:
1.92Å     R-factor:   0.207     R-free:   0.247
Authors: J.H.Y.Wong,H.Ling
Key ref: J.H.Wong et al. (2008). Snapshots of a Y-family DNA polymerase in replication: substrate-induced conformational transitions and implications for fidelity of Dpo4. J Mol Biol, 379, 317-330. PubMed id: 18448122
Date:
24-Sep-07     Release date:   24-Jun-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q97W02  (DPO4_SULSO) -  DNA polymerase IV from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
Seq:
Struc: 		352 a.a.
336 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: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
DNA(n)
 + 2'-deoxyribonucleoside 5'-triphosphate
 = DNA(n+1)
 + diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
J Mol Biol 379:317-330 (2008)
PubMed id: 18448122  
 
 
Snapshots of a Y-family DNA polymerase in replication: substrate-induced conformational transitions and implications for fidelity of Dpo4.
J.H.Wong, K.A.Fiala, Z.Suo, H.Ling.
 
  ABSTRACT  
 
Y-family DNA polymerases catalyze translesion DNA synthesis over damaged DNA. Each Y-family polymerase has a polymerase core consisting of a palm, finger and thumb domain in addition to a fourth domain known as a little finger domain. It is unclear how each domain moves during nucleotide incorporation and what type of conformational changes corresponds to the rate-limiting step previously reported in kinetic studies. Here, we present three crystal structures of the prototype Y-family polymerase: apo-Dpo4 at 1.9 A resolution, Dpo4-DNA binary complex and Dpo4-DNA-dTMP ternary complex at 2.2 A resolution. Dpo4 undergoes dramatic conformational changes from the apo to the binary structures with a 131 degrees rotation of the little finger domain relative to the polymerase core upon DNA binding. This DNA-induced conformational change is verified in solution by our tryptophan fluorescence studies. In contrast, the polymerase core retains the same conformation in all three conformationally distinct states. Particularly, the finger domain which is responsible for checking base pairing between the template base and an incoming nucleotide retains a rigid conformation. The inflexibility of the polymerase core likely contributes to the low fidelity of Dpo4, in addition to its loose and solvent-accessible active site. Interestingly, while the binary and ternary complexes of Dpo4 retain an identical global conformation, the aromatic side chains of two conserved tyrosines at the nucleotide-binding site change orientations between the binary and ternary structures. Such local conformational changes may correspond to the rate-limiting step in the mechanism of nucleotide incorporation. Together, the global and local conformational transitions observed in our study provide a structural basis for the distinct kinetic steps of a catalytic cycle of DNA polymerization performed by a Y-family polymerase.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21300901 K.N.Kirouac, and H.Ling (2011).
Unique active site promotes error-free replication opposite an 8-oxo-guanine lesion by human DNA polymerase iota.
  Proc Natl Acad Sci U S A, 108, 3210-3215.
PDB codes: 3q8p 3q8q 3q8r
20609084 D.I.Andersson, S.Koskiniemi, and D.Hughes (2010).
Biological roles of translesion synthesis DNA polymerases in eubacteria.
  Mol Microbiol, 77, 540-548.  
20582735 D.Ma, J.D.Fowler, C.Yuan, and Z.Suo (2010).
Backbone assignment of the catalytic core of a Y-family DNA polymerase.
  Biomol NMR Assign, 4, 207-209.  
  20798853 J.A.Brown, L.Zhang, S.M.Sherrer, J.S.Taylor, P.M.Burgers, and Z.Suo (2010).
Pre-Steady-State Kinetic Analysis of Truncated and Full-Length Saccharomyces cerevisiae DNA Polymerase Eta.
  J Nucleic Acids, 2010, 0.  
20123134 J.D.Pata (2010).
Structural diversity of the Y-family DNA polymerases.
  Biochim Biophys Acta, 1804, 1124-1135.  
  20936174 S.Chandani, C.Jacobs, and E.L.Loechler (2010).
Architecture of y-family DNA polymerases relevant to translesion DNA synthesis as revealed in structural and molecular modeling studies.
  J Nucleic Acids, 2010, 0.  
19859523 C.Xu, B.A.Maxwell, J.A.Brown, L.Zhang, and Z.Suo (2009).
Global conformational dynamics of a Y-family DNA polymerase during catalysis.
  PLoS Biol, 7, e1000225.  
19440206 K.N.Kirouac, and H.Ling (2009).
Structural basis of error-prone replication and stalling at a thymine base by human DNA polymerase iota.
  EMBO J, 28, 1644-1654.
PDB codes: 3gv5 3gv7 3gv8
19607844 K.Y.Seo, J.Yin, P.Donthamsetti, S.Chandani, C.H.Lee, and E.L.Loechler (2009).
Amino acid architecture that influences dNTP insertion efficiency in Y-family DNA polymerase V of E. coli.
  J Mol Biol, 392, 270-282.  
19515847 R.L.Eoff, R.Sanchez-Ponce, and F.P.Guengerich (2009).
Conformational Changes during Nucleotide Selection by Sulfolobus solfataricus DNA Polymerase Dpo4.
  J Biol Chem, 284, 21090-21099.  
19188081 S.Chandani, and E.L.Loechler (2009).
Y-Family DNA polymerases may use two different dNTP shapes for insertion: a hypothesis and its implications.
  J Mol Graph Model, 27, 759-769.  
19124465 S.M.Sherrer, J.A.Brown, L.R.Pack, V.P.Jasti, J.D.Fowler, A.K.Basu, and Z.Suo (2009).
Mechanistic studies of the bypass of a bulky single-base lesion catalyzed by a Y-family DNA polymerase.
  J Biol Chem, 284, 6379-6388.  
18984592 J.W.Beckman, Q.Wang, and F.P.Guengerich (2008).
Kinetic Analysis of Correct Nucleotide Insertion by a Y-family DNA Polymerase Reveals Conformational Changes Both Prior to and following Phosphodiester Bond Formation as Detected by Tryptophan Fluorescence.
  J Biol Chem, 283, 36711-36723.  
18931375 L.Jia, N.E.Geacintov, and S.Broyde (2008).
The N-clasp of human DNA polymerase kappa promotes blockage or error-free bypass of adenine- or guanine-benzo[a]pyrenyl lesions.
  Nucleic Acids Res, 36, 6571-6584.  
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. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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