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(-) Description

Title :  PRE-INSERTION BINARY COMPLEX OF DBH DNA POLYMERASE
 
Authors :  J. D. Pata, R. C. Wilson
Date :  19 Dec 07  (Deposition) - 08 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,P,T
Keywords :  Dna Polymerase, Y-Family, Lesion Bypass, Single-Base Deletion, -1 Frameshift, Dna Damage, Dna Repair, Dna Replication, Dna-Binding, Dna-Directed Dna Polymerase, Magnesium, Metal-Binding, Mutator Protein, Nucleotidyltransferase, Transferase, Transferase/Dna, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. C. Wilson, J. D. Pata
Structural Insights Into The Generation Of Single-Base Deletions By The Y Family Dna Polymerase Dbh.
Mol. Cell V. 29 767 2008
PubMed-ID: 18374650  |  Reference-DOI: 10.1016/J.MOLCEL.2008.01.014

(-) Compounds

Molecule 1 - DNA POLYMERASE IV
    ChainsA
    EC Number2.7.7.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPKKT7
    Expression System StrainBLR(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneDBH
    Organism ScientificSULFOLOBUS ACIDOCALDARIUS
    Organism Taxid2285
    SynonymPOL IV, DBH
 
Molecule 2 - DNA (5'-D(*DGP*DAP*DAP*DGP*DCP*DCP*DGP*DGP*DCP*DG)-3')
    ChainsP
    EngineeredYES
    Other DetailsPRIMER
    SyntheticYES
 
Molecule 3 - DNA (5'- D(*DT*DTP*DCP*DCP*DGP*DCP*DCP*DCP*DGP*DGP*DCP*DTP*DTP*DCP*DC)-3')
    ChainsT
    EngineeredYES
    Other DetailsTEMPLATE
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit APT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH P:11BINDING SITE FOR RESIDUE CA A 355

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BQ0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:160 -Pro A:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BQ0)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UMUCPS50173 UmuC domain profile.DPO4_SULAC3-188  1A:3-188

(-) Exons   (0, 0)

(no "Exon" information available for 3BQ0)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:341
 aligned with DPO4_SULAC | Q4JB80 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:344
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340    
           DPO4_SULAC     1 MIVIFVDFDYFFAQVEEVLNPQYKGKPLVVCVYSGRTKTSGAVATANYEARKLGVKAGMPIIKAMQIAPSAIYVPMRKPIYEAFSNRIMNLLNKHADKIEVASIDEAYLDVTNKVEGNFENGIELARKIKQEILEKEKITVTVGVAPNKILAKIIADKSKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEKITGKAKALYLLKLAQNKYSEPVENKSKIPHGRYLTLPYNTRDVKVILPYLKKAINEAYNKVNGIPMRITVIAIMEDLDILSKGKKFKHGISIDNAYKVAEDLLRELLVRDKRRNVRRIGVKLDNIIIN 344
               SCOP domains d3bq0a2 A:1-241 DinB homolog (DBH)                                                                                                                                                                                                               d3bq0a1 A:242-344 DinB homolog (DBH)                                                                    SCOP domains
               CATH domains -3bq0A01  -------------------------------------------------------------------3bq0A01 A:2-10,A:78-166  [code=3.30.70.270, no name defined]                             3bq0A03 A:167-233 5' to 3' exonuclease, C-terminal subdomain       ----------3bq0A04 A:244-341  [code=3.30.1490.100, no name defined]                                          --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhh...eeeee...---...eeeeehhhhhhh......hhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh...eeeeee..eeeee.......hhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh.....eee.hhhhhhhhhhhh........hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........ee...eeeeeeeeeee.hhhhhhhhhhhhhhhhhh....eeeeeeeeeee....eeeeeee.....hhhhhhhhhhhhhhhhh.......eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --UMUC  PDB: A:3-188 UniProt: 3-188                                                                                                                                                         ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bq0 A   1 MIVIFVDFDYFFAQVEEVLNPQYKGKPLVVCVYSG---TSGAVATANYEARKLGVKAGMPIIKAMQIAPSAIYVPMRKPIYEAFSNRIMNLLNKHADKIEVASIDEAYLDVTNKVEGNFENGIELARKIKQEILEKEKITVTVGVAPNKILAKIIADKSKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEKITGKAKALYLLKLAQNKYSEPVENKSKIPHGRYLTLPYNTRDVKVILPYLKKAINEAYNKVNGIPMRITVIAIMEDLDILSKGKKFKHGISIDNAYKVAEDLLRELLVRDKRRNVRRIGVKLDNIIIN 344
                                    10        20        30    |   40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340    
                                                             35  39                                                                                                                                                                                                                                                                                                                 

Chain P from PDB  Type:DNA  Length:10
                                          
                 3bq0 P   1 GAAGCCGGCG  10
                                    10

Chain T from PDB  Type:DNA  Length:13
                                             
                 3bq0 T   2 TCCGCCCGGCTTC  14
                                    11   

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BQ0)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DPO4_SULAC | Q4JB80)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0006261    DNA-dependent DNA replication    A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DPO4_SULAC | Q4JB803bq1 3bq2 4f4w 4f4x 4f4y 4f4z 4f50 4hyk 4nlg

(-) Related Entries Specified in the PDB File

3bq1 INSERTION TERNARY COMPLEX OF DBH
3bq2 POST-INSERTION BINARY COMPLEX OF DBH