NON-PRODUCTIVE COMPLEX OF THE Y-FAMILY DNA POLYMERASE DPO4 WITH DGTP SKIPPING THE M1DG ADDUCT TO PAIR WITH THE NEXT TEMPLATE CYTOSINE DOI:10.2210/pdb2v4r/pdb   NDB ID: 2V4R

2V4R   Display Files  close FASTA Sequence PDB File PDB File (Header) mmCIF File mmCIF File (Header) PDBML/XML File PDBML/XML File (Header)   Download Files  close FASTA Sequence PDB File (Text) PDB File (gz) mmCIF File mmCIF File (gz) PDBML/XML File PDBML/XML File (gz) Structure Factor (Text) Structure Factor (gz) Biological Assembly (gz) (A+S)   Share this Page  close Facebook Twitter LinkedIn Email Link this Page

Primary Citation       Related Citations in PDB Entry (REMARK 1) Hide     Molecular Description Hide Classification: Transferase Structure Weight: 51219.88 Molecule: DNA POLYMERASE IV Polymer: 1 Type: protein Length: 358 Chains: A EC#: 2.7.7.7    Details: Y-FAMILY DNA POLYMERASE FROM SULFOLOBUS SOLFATARICUS Organism Sulfolobus solfataricus P2 Gene Names dbh dpo4 SSO2448 UniProtKB:   Protein Feature View | Search PDB | Q97W02     Molecule: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3' Polymer: 2 Type: dna Length: 13 Chains: P Details: 13 BASE PRIMER DNA 5'-GGG GGA AGG ATT C-3' Molecule: 5'-D(*TP*CP*AP*CP*M1GP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3' Polymer: 3 Type: dna Length: 18 Chains: T Details: 18 BASE TEMPLATE DNA 5'-TCA C(M1G)G AAT CCT TCC CCC-3'     Source Hide Polymer: 1 Scientific Name: Sulfolobus solfataricus   Taxonomy   Expression System: Escherichia coli   Polymer: 2 Scientific Name: Synthetic construct   Taxonomy     Polymer: 3 Scientific Name: Synthetic construct   Taxonomy         Related PDB Entries Hide Identifier Details 1JX4  CRYSTAL STRUCTURE OF A Y-FAMILY DNA POLYMERASE IN A TERNARYCOMPLEX WITH DNA SUBSTRATES AND AN INCOMING NUCLEOTIDE  1JXL  CRYSTAL STRUCTURE OF A Y-FAMILY DNA POLYMERASE IN A TERNARYCOMPLEX WITH DNA SUBSTRATES AND AN INCOMING NUCLEOTIDE  1N48  Y-FAMILY DNA POLYMERASE DPO4 IN COMPLEX WITH DNA CONTAININGABASIC LESION  1N56  Y-FAMILY DNA POLYMERASE DPO4 IN COMPLEX WITH DNA CONTAININGABASIC LESION  1RYR  REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION  1RYS  REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION  1S0M  CRYSTAL STRUCTURE OF A BENZO[A]PYRENE DIOL EPOXIDE ADDUCTIN A TERNARY COMPLEX WITH A DNA POLYMERASE  1S0N  SNAPSHOTS OF REPLICATION THROUGH AN ABASIC LESION:STRUCTURAL BASIS FOR BASE SUBSTITUTION AND FRAMESHIFT  1S0O  SNAPSHOTS OF REPLICATION THROUGH AN ABASIC LESION:STRUCTURAL BASIS FOR BASE SUBSTITUTION AND FRAMESHIFT  1S10  SNAPSHOTS OF REPLICATION THROUGH AN ABASIC LESION:STRUCTURAL BASIS FOR BASE SUBSTITUTION AND FRAMESHIFT  1S97  DPO4 WITH GT MISMATCH  1S9F  DPO WITH AT MATCHED  2AGO  FIDELITY OF DPO4: EFFECT OF METAL IONS, NUCLEOTIDESELECTION AND PYROPHOSPHOROLYSIS  2AGP  FIDELITY OF DPO4: EFFECT OF METAL IONS, NUCLEOTIDESELECTION AND PYROPHOSPHOROLYSIS  2AGQ  FIDELITY OF DPO4: EFFECT OF METAL IONS, NUCLEOTIDESELECTION AND PYROPHOSPHOROLYSIS  2ASD  OXOG-MODIFIED INSERTION TERNARY COMPLEX  2ASJ  OXOG-MODIFIED PREINSERTION BINARY COMPLEX  2ASL  OXOG-MODIFIED POSTINSERTION BINARY COMPLEX  2ATL  UNMODIFIED INSERTION TERNARY COMPLEX  2AU0  UNMODIFIED PREINSERTION BINARY COMPLEX  2BQ3  DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4. ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1 ,N2-ETHENOGUANINE  2BQR  DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4. ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1 ,N2-ETHENOGUANINE  2BQU  DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4. ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1 ,N2-ETHENOGUANINE  2BR0  DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4. ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1 ,N2-ETHENOGUANINE  2C22  EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8-DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4  2C28  EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8-DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4  2C2D  EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8-DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4  2C2E  EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8-DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4  2C2R  EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8-DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4  2J6S  TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6-METHYLGUANINE MODIFIED DNA, AND DATP.  2J6T  TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6-METHYLGUANINE MODIFIED DNA, AND DATP.  2J6U  TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6-METHYLGUANINE MODIFIED DNA, AND DGTP.  2JEF  THE MOLECULAR BASIS OF SELECTIVITY OF NUCLEOTIDE TRIPHOSPHATE INCORPORATION OPPOSITE O6-BENZYLGUANINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE IV: STEADY-STATE AND PRE- STEADY-STATE AND X-RAY CRYSTALLOGRAPHY OF CORRECT AND INCORRECT PAIRING  2JEG  THE MOLECULAR BASIS OF SELECTIVITY OF NUCLEOSIDE TRIPHOSPHATE INCORPORATION OPPOSITE O6-BENZYLGUANINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE IV: STEADY-STATE AND PRE- STEADY-STATE KINETICS AND X-RAY CRYSTALLOGRAPHY OF CORRECT AND INCORRECT PAIRING  2JEI  THE MOLECULAR BASIS OF SELECTIVITY OF NUCLEOSIDE TRIPHOSPHATE INCORPORATION OPPOSITE O6-BENZYLGUANINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE IV: STEADY-STATE AND PRE- STEADY-STATE KINETICS AND X-RAY CRYSTALLOGRAPHY OF CORRECT AND INCORRECT PAIRING  2JEJ  THE MOLECULAR BASIS OF SELECTIVITY OF NUCLEOSIDE TRIPHOSPHATE INCORPORATION OPPOSITE O6-BENZYLGUANINE BY SULFOLOBUS SOLFATARICUS DNA POLYMERASE IV: STEADY-STATE AND PRE- STEADY-STATE KINETICS AND X-RAY CRYSTALLOGRAPHY OF CORRECT AND INCORRECT PAIRING  2UVR  CRYSTAL STRUCTURES OF MUTANT DPO4 DNA POLYMERASES WITH 8-OXOG CONTAINING DNA TEMPLATE-PRIMER CONSTRUCTS  2UVU  CRYSTAL STRUCTURES OF MUTANT DPO4 DNA POLYMERASES WITH 8-OXOG CONTAINING DNA TEMPLATE-PRIMER CONSTRUCTS  2UVV  CRYSTAL STRUCTURES OF MUTANT DPO4 DNA POLYMERASES WITH 8-OXOG CONTAINING DNA TEMPLATE-PRIMER CONSTRUCTS  2UVW  CRYSTAL STRUCTURES OF MUTANT DPO4 DNA POLYMERASES WITH 8-OXOG CONTAINING DNA TEMPLATE-PRIMER CONSTRUCTS  2V4Q  POST-INSERTION COMPLEX OF THE Y-FAMILY DNA POLYMERASE DPO4 WITH M1DG CONTAINING TEMPLATE DNA  2V4S  Y-FAMILY DNA POLYMERASE DPO4 BYPASSING N2- NAPHTHYL-GUANINE ADDUCT IN SYN ORIENTATION  2V4T  Y-FAMILY DNA POLYMERASE DPO4 BYPASSING N2- NAPHTHYL-GUANINE ADDUCT IN ANTI ORIENTATION  2V9W  COMPLEX STRUCTURE OF SULFOLOBUS SOLFATARICUS DPO4 AND DNA DUPLEX CONTAINING A HYDROPHOBIC THYMINE ISOSTERE 2,4-DIFLUOROTOLUENE NUCLEOTIDE IN THE TEMPLATE STRAND  2VA2  COMPLEX STRUCTURE OF SULFOLOBUS SOLFATARICUS DPO4 AND DNA DUPLEX CONTAINING A HYDROPHOBIC THYMINE ISOSTERE 2,4-DIFLUOROTOLUENE NUCLEOTIDE IN THE TEMPLATE STRAND  2VA3  COMPLEX STRUCTURE OF SULFOLOBUS SOLFATARICUS DPO4 AND DNA DUPLEX CONTAINING A HYDROPHOBIC THYMINE ISOSTERE 2,4-DIFLUOROTOLUENE NUCLEOTIDE IN THE TEMPLATE STRAND      Ligand Chemical Component Hide Identifier Formula Name Interactions CA Search  Download  Ca CALCIUM ION   Ligand Explorer DGT Search  Download  C10 H16 N5 O13 P3 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE   Ligand Explorer     Modified Residues Hide Identifier Formula Parent Type M1G Search  C13 H14 N5 O7 P DG dnaLinking     External Domain Annotations Hide Pfam Classification: 3 Domains - data from Pfam   GO Terms: 12 Terms - data from GO      Structural Biology Knowledgebase Data Hide   Nucleic Acid Database Hide View the NDB ID associated with this structure: 2V4R     Data in orange boxes are gathered from external resources (when available). 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Biological Assembly            View in 3D More Images... Biological assembly 1 assigned by authors and generated by PISA (software) Downloadable viewers: Simple Viewer Protein Workshop Ligand Explorer Kiosk Viewer Other Viewers  KiNG WebMol QuickPDB FirstGlance         MyPDB Personal Annotations Hide     Deposition Summary Hide Authors:   Eoff, R.L.,  Stafford, J.B.,  Szekely, J.,  Rizzo, C.J.,  Egli, M.,  Guengerich, F.P.,  Marnett, L.J. Deposition:   2008-09-26 Release:   2009-06-16 Last Modified (REVDAT):   2011-06-01     Revision History    Hide Mouse over text for details 2011-07-13 Version format compliance     Experimental Details Hide Method:   X-RAY DIFFRACTION Exp. Data:   Structure Factors EDS   Resolution[Å]:   2.50 R-Value: 0.218 (obs.) R-Free: 0.273 Space Group: P 21 21 2 Unit Cell:   Length [Å] Angles [°] a = 93.54 α = 90.00  b = 102.54 β = 90.00  c = 52.18 γ = 90.00      Molecule of the Month Hide Thymine Dimers