2UVU Transferase date Mar 14, 2007
title Crystal Structures Of Mutant Dpo4 Dna Polymerases With 8- Oxog Containing Dna Template-Primer Constructs
authors A.Irimia, M.Egli
compound source
Molecule: Dna Polymerase Iv
Chain: A
Synonym: Pol Iv
Ec: 2.7.7.7
Engineered: Yes
Mutation: Yes
Other_details: R332a Mutant Of Dpo4
Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 273057
Strain: P2
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22bdpo4-Nhis
Other_details: Gene Dpo4

Molecule: 5'-D(Gpgpgpgpgpapapgpgpap Tptpcpa)-3';
Chain: P
Synonym: 14-Mer Primer
Other_details: Ggg Gga Agg Att Ca

Synthetic: Yes

Molecule: 5'-D(Tpcpapcp8ogpgpapaptpcp Cptptpcpcpcpcpc)-3';
Chain: T
Synonym: 18-Mer Template
Other_details: T C A C 8og G A A T C C T T C C C C C

Synthetic: Yes
symmetry Space Group: P 21 21 2
R_factor 0.216 R_Free 0.270
crystal
cell
length a length b length c angle alpha angle beta angle gamma
95.131 104.124 52.941 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand 8OG, CA, DGT enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceHydrogen bonding of 7,8-dihydro-8-oxodeoxyguanosine with a charged residue in the little finger domain determines miscoding events in Sulfolobus solfataricus DNA polymerase Dpo4., Eoff RL, Irimia A, Angel KC, Egli M, Guengerich FP, J Biol Chem. 2007 Jul 6;282(27):19831-43. Epub 2007 Apr 27. PMID:17468100
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (2uvu.pdb1.gz) 73 Kb
  • LPC: Ligand-Protein Contacts for 2UVU
  • CSU: Contacts of Structural Units for 2UVU
  • Likely Quarternary Molecular Structure file(s) for 2UVU
  • Structure Factors (104 Kb)
  • Retrieve 2UVU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2UVU from S2C, [Save to disk]
  • Re-refined 2uvu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2UVU in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2UVU
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2UVU, from MSDmotif at EBI
  • Fold representative 2uvu from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2uvu] [2uvu_P] [2uvu_T] [2uvu_A]
  • SWISS-PROT database: [Q97W02]
  • Domain organization of [DPO42_SULSO] by SWISSPFAM
  • Other resources with information on 2UVU
  • Community annotation for 2UVU at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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