2IA6 Transferase Dna date Sep 07, 2006
title Bypass Of Major Benzopyrene-Dg Adduct By Y-Family Dna Polyme Unique Structural Gap
authors J.Bauer, H.Ling, J.M.Sayer, G.Xing, H.Yagi, D.M.Jerina
compound source
Molecule: Dna Polymerase Iv
Chain: A, B
Synonym: Pol Iv
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 273057
Strain: P2
Gene: Dbh, Dpo4
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b

Molecule: 5'-D(Gpgpgpgpgpapapgpgpaptptpa)-3'
Chain: C, E
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Tpcpaptpgpapaptpcpcptptpcpcpc 3';
Chain: D, F
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.216 R_Free 0.247
crystal
cell
length a length b length c angle alpha angle beta angle gamma
98.217 102.580 106.147 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand ATP, BAP, CA, EDO, GOL, PO4 enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceA structural gap in Dpo4 supports mutagenic bypass of a major benzo[a]pyrene dG adduct in DNA through template misalignment., Bauer J, Xing G, Yagi H, Sayer JM, Jerina DM, Ling H, Proc Natl Acad Sci U S A. 2007 Sep 18;104(38):14905-10. Epub 2007 Sep 11. PMID:17848527
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (155 Kb) [Save to disk]
  • Biological Unit Coordinates (2ia6.pdb1.gz) 75 Kb
  • Biological Unit Coordinates (2ia6.pdb2.gz) 76 Kb
  • LPC: Ligand-Protein Contacts for 2IA6
  • CSU: Contacts of Structural Units for 2IA6
  • Likely Quarternary Molecular Structure file(s) for 2IA6
  • Structure Factors (282 Kb)
  • Retrieve 2IA6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2IA6 from S2C, [Save to disk]
  • Re-refined 2ia6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2IA6 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 2IA6
  • 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 2IA6, from MSDmotif at EBI
  • Fold representative 2ia6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ia6] [2ia6_F] [2ia6_A] [2ia6_E] [2ia6_B] [2ia6_C] [2ia6_D]
  • SWISS-PROT database: [Q97W02]
  • Domain organization of [DPO42_SULSO] by SWISSPFAM
  • Other resources with information on 2IA6
  • Community annotation for 2IA6 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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