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(-) Description

Title :  CRYSTAL STRUCTURE OF E.COLI POL II-ABASIC DNA BINARY COMPLEX
 
Authors :  W. Yang, F. Wang
Date :  07 Oct 09  (Deposition) - 02 Feb 10  (Release) - 02 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.15
Chains :  Asym./Biol. Unit :  A,B,P,T
Keywords :  Dna Damage, Dna Repair, Dna-Binding, Dna-Directed Dna Polymerase, Nucleotidyltransferase, Sos Response, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Wang, W. Yang
Structural Insight Into Translesion Synthesis By Dna Pol Ii.
Cell(Cambridge, Mass. ) V. 139 1279 2009
PubMed-ID: 20064374  |  Reference-DOI: 10.1016/J.CELL.2009.11.043

(-) Compounds

Molecule 1 - DNA POLYMERASE II
    Chains: A, B
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: B0060, DINA, JW0059, POLB
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: K-12
    Synonym: POL II
 
Molecule 2 - DNA (5'-D(*GP*TP*CP*CP*TP*GP*(3DR) *TP*AP*CP*GP*CP*TP*AP*GP*GP*CP*AP*CP*A)-3')
    Chains: T
    Engineered: YES
    Other Details: ABASIC TEMPLATE
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*GP*TP*GP*CP*CP*TP*AP*GP*CP*GP*TP*AP*G)-3')
    Chains: P
    Engineered: YES
    Other Details: PRIMER
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABPT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3K5N)

(-) Sites  (0, 0)

(no "Site" information available for 3K5N)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K5N)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Gly A:182 -Pro A:183
2Phe A:772 -Ala A:773
3Gly B:182 -Pro B:183
4Asp B:413 -Ser B:414
5Gly B:484 -Asn B:485

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_DPO2_ECOLI_001 *G401DDPO2_ECOLI  ---  ---AG401D
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNA_POLYMERASE_BPS00116 DNA polymerase family B signature.DPO2_ECOLI543-551
 		  2A:543-551
B:543-551

(-) Exons   (0, 0)

(no "Exon" information available for 3K5N)

(-) 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:759
 aligned with DPO2_ECOLI | P21189 from UniProtKB/Swiss-Prot  Length:783

    Alignment length:783
                                    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       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780   
           DPO2_ECOLI     1 MAQAGFILTRHWRDTPQGTEVSFWLATDNGPLQVTLAPQESVAFIPADQVPRAQHILQGEQGFRLTPLALKDFHRQPVYGLYCRAHRQLMNYEKRLREGGVTVYEADVRPPERYLMERFITSPVWVEGDMHNGTIVNARLKPHPDYRPPLKWVSIDIETTRHGELYCIGLEGCGQRIVYMLGPENGDASSLDFELEYVASRPQLLEKLNAWFANYDPDVIIGWNVVQFDLRMLQKHAERYRLPLRLGRDNSELEWREHGFKNGVFFAQAKGRLIIDGIEALKSAFWNFSSFSLETVAQELLGEGKSIDNPWDRMDEIDRRFAEDKPALATYNLKDCELVTQIFHKTEIMPFLLERATVNGLPVDRHGGSVAAFGHLYFPRMHRAGYVAPNLGEVPPHASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPVGLVEGMAQPDPEHSTEGFLDAWFSREKHCLPEIVTNIWHGRDEAKRQGNKPLSQALKIIMNAFYGVLGTTACRFFDPRLASSITMRGHQIMRQTKALIEAQGYDVIYGDTDSTFVWLKGAHSEEEAAKIGRALVQHVNAWWAETLQKQRLTSALELEYETHFCRFLMPTIRGADTGSKKRYAGLIQEGDKQRMVFKGLETVRTDWTPLAQQFQQELYLRIFRNEPYQEYVRETIDKLMAGELDARLVYRKRLRRPLSEYQRNVPPHVRAARLADEENQKRGRPLQYQNRGTIKYVWTTNGPEPLDYQRSPLDYEHYLTRQLQPVAEGILPFIEDNFATLMTGQLGLF 783
               SCOP domains d3k5na1 A:1-389 automated matches                                                                                                                                                                                                                                                                                                                                                                    d3k5na2 A:390-783 automated matches                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee..eeeeeeeee....eeeeee....eeeeee.hhhhhhhhhh.....eeeeeeeee.....eeeeeee.hhhhhhhhhhhhhhh.........hhhhhhhhhh....eeeeeeeee..eeeeeeeee.........eeeeeeee.....eeeeeeee..eeeeeee............eeeee.hhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhh...............---------........ee.hhhhhhhhh.......hhhhhhhhhh...------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh..........................eeeeeeeeeee.hhhhhhhhhhh.hhhhhhhhh.......eee.....eee....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...eeeee.....hhhhhhhhhhhhhhhhhhhhhhhh..........eeeeeeeeeeee..---------..eeeeeee..eeeeeee.........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.........ee...hhhhh....hhhhhhhhhhhhh..............ee.eeee..eeee........hhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYM---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k5n A   1 MAQAGFILTRHWRDTPQGTEVSFWLATDNGPLQVTLAPQESVAFIPADQVPRAQHILQGEQGFRLTPLALKDFHRQPVYGLYCRAHRQLMNYEKRLREGGVTVYEADVRPPERYLMERFITSPVWVEGDMHNGTIVNARLKPHPDYRPPLKWVSIDIETTRHGELYCIGLEGCGQRIVYMLGPENGDASSLDFELEYVASRPQLLEKLNAWFANYDPDVIIGWNVVQFDLRMLQKHAERYRLPLRLGRDNSELEW---------FFAQAKGRLIIDGIEALKSAFWNFSSFSLETVAQELLGEG------WDRMDEIDRRFAEDKPALATYNLKNCELVTQIFHKTEIMPFLLERATVNGLPVDRHGGSVAAFGHLYFPRMHRAGYVAPNLGEVPPHASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPVGLVEGMAQPDPEHSTEGFLDAWFSREKHCLPEIVTNIWHGRDEAKRQGNKPLSQALKIIMNAFYGVLGTTACRFFDPRLASSITMRGHQIMRQTKALIEAQGYDVIYGDTDSTFVWLKGAHSEEEAAKIGRALVQHVNAWWAETLQKQRLTSALELEYETHFCRFLMPT---------KRYAGLIQEGDKQRMVFKGLETVRTDWTPLAQQFQQELYLRIFRNEPYQEYVRETIDKLMAGELDARLVYRKRLRRPLSEYQRNVPPHVRAARLADEENQKRGRPLQYQNRGTIKYVWTTNGPEPLDYQRSPLDYEHYLTRQLQPVAEGILPFIEDNFATLMTGQLGLF 783
                                    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    |    -    |  270       280       290       300   |     -|      320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600    |    -    |  620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780   
                                                                                                                                                                                                                                                                                        255       265                                    304    311                                                                                                                                                                                                                                                                                                   605       615                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:738
 aligned with DPO2_ECOLI | P21189 from UniProtKB/Swiss-Prot  Length:783

    Alignment length:770
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769
           DPO2_ECOLI     - -MAQAGFILTRHWRDTPQGTEVSFWLATDNGPLQVTLAPQESVAFIPADQVPRAQHILQGEQGFRLTPLALKDFHRQPVYGLYCRAHRQLMNYEKRLREGGVTVYEADVRPPERYLMERFITSPVWVEGDMHNGTIVNARLKPHPDYRPPLKWVSIDIETTRHGELYCIGLEGCGQRIVYMLGPENGDASSLDFELEYVASRPQLLEKLNAWFANYDPDVIIGWNVVQFDLRMLQKHAERYRLPLRLGRDNSELEWREHGFKNGVFFAQAKGRLIIDGIEALKSAFWNFSSFSLETVAQELLGEGKSIDNPWDRMDEIDRRFAEDKPALATYNLKDCELVTQIFHKTEIMPFLLERATVNGLPVDRHGGSVAAFGHLYFPRMHRAGYVAPNLGEVPPHASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPVGLVEGMAQPDPEHSTEGFLDAWFSREKHCLPEIVTNIWHGRDEAKRQGNKPLSQALKIIMNAFYGVLGTTACRFFDPRLASSITMRGHQIMRQTKALIEAQGYDVIYGDTDSTFVWLKGAHSEEEAAKIGRALVQHVNAWWAETLQKQRLTSALELEYETHFCRFLMPTIRGADTGSKKRYAGLIQEGDKQRMVFKGLETVRTDWTPLAQQFQQELYLRIFRNEPYQEYVRETIDKLMAGELDARLVYRKRLRRPLSEYQRNVPPHVRAARLADEENQKRGRPLQYQNRGTIKYVWTTNGPEPLDYQRSPLDYEHYLTRQLQPVAEGILPFIE 769
               SCOP domains d3k5nb1 B:0-389 automated matches                                                                                                                                                                                                                                                                                                                                                                     d3k5nb2         B:390-769 automated matches                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------DNA_pol_B_exo1-3k5nB05 B:49-296                                                                                                                                                                                                                         -------         -------------------------------------------------------------------------------------        --------------------------------------DNA_pol_B-3k5nB01 B:444-769                                                                                                                                                                                                                                                                                                            Pfam domains (1)
           Pfam domains (2) -------------------------------------------------DNA_pol_B_exo1-3k5nB06 B:49-296                                                                                                                                                                                                                         -------         -------------------------------------------------------------------------------------        --------------------------------------DNA_pol_B-3k5nB02 B:444-769                                                                                                                                                                                                                                                                                                            Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------    ------------------------------------------         -------------------------------------------------------------------------------------        --------------------------------------DNA_pol_B-3k5nB03 B:444-769                                                                                                                                                                                                                                                                                                            Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------    ------------------------------------------         -------------------------------------------------------------------------------------        --------------------------------------DNA_pol_B-3k5nB04 B:444-769                                                                                                                                                                                                                                                                                                            Pfam domains (4)
         Sec.struct. author ..eeeeeeeeeeeeee..eeeeeeeeee..eeeeeee....eeeeee..hhhhhhhhh.....eeeeeeeee.....eeeeeee.hhhhhhhhhhhhhhh.........hhhhhhhhh.....eeeeeeeee..eeeeeeeee.........eeeeeeee.....eeeeeeee..eeeeeee..............eee.hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh............eee.----....eee....eeeehhhhhhh........hhhhhhhhhhh.---------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh..............--------....eee..eeeeee.hhhhhhhhhh..hhhhhhhhh...hhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee..eee.-----------..eeeeee..eeeeee..hhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhheeeeeeee........hhhhhhhhhhhhhhhhh.......eeeeeeeee....eee........hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYM-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k5n B   0 HMAQAGFILTRHWRDTPQGTEVSFWLATDNGPLQVTLAPQESVAFIPADQVPRAQHILQGEQGFRLTPLALKDFHRQPVYGLYCRAHRQLMNYEKRLREGGVTVYEADVRPPERYLMERFITSPVWVEGDMHNGTIVNARLKPHPDYRPPLKWVSIDIETTRHGELYCIGLEGCGQRIVYMLGPENGDASSLDFELEYVASRPQLLEKLNAWFANYDPDVIIGWNVVQFDLRMLQKHAERYRLPLRLGRDNSELEWRE----NGVFFAQAKGRLIIDGIEALKSAFWNFSSFSLETVAQELLGE---------RMDEIDRRFAEDKPALATYNLKNCELVTQIFHKTEIMPFLLERATVNGLPVDRHGGSVAAFGHLYFPRMHRAGYVAPNLGEVPPH--------DSRPGLYDSVLVLDYKSLYPSIIRTFLIDPVGLVEGMAQPDPEHSTEGFLDAWFSREKHCLPEIVTNIWHGRDEAKRQGNKPLSQALKIIMNAFYGVLGTTACRFFDPRLASSITMRGHQIMRQTKALIEAQGYDVIYGDTDSTFVWLKGAHSEEEAAKIGRALVQHVNAWWAETLQKQRLTSALELEYETHFCRFLMP-----------RYAGLIQEGDKQRMVFKGLETVRTDWTPLAQQFQQELYLRIFRNEPYQEYVRETIDKLMAGELDARLVYRKRLRRPLSEYQRNVPPHVRAARLADEENQKRGRPLQYQNRGTIKYVWTTNGPEPLDYQRSPLDYEHYLTRQLQPVAEGILPFIE 769
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       | -  |    269       279       289       299   |     -   |   319       329       339       349       359       369       379       389       | -      |409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599    |    -      |619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769
                                                                                                                                                                                                                                                                                           257  262                                      303       313                                                                                 397      406                                                                                                                                                                                                   604         616                                                                                                                                                         


Chain P from PDB  Type:DNA  Length:13
                                             
                 3k5n P 901 GTGCCTAGCGTAG 913
                                   910   


Chain T from PDB  Type:DNA  Length:13
                                             
                 3k5n T 808 TACGCTAGGCACA 820
                                   817
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K5N)

(-) Pfam Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Clan: DNA_pol_B-like (44)
(-)
Clan: RNase_H (288)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DPO2_ECOLI | P21189)
molecular function
    GO:0008408    3'-5' exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
    GO:0008296    3'-5'-exodeoxyribonuclease activity    Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a DNA molecule.
    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:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0045004    DNA replication proofreading    Correction of replication errors by DNA polymerase using a 3'-5' exonuclease activity.
    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:0009432    SOS response    An error-prone process for repairing damaged microbial DNA.
    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.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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  Cis Peptide Bonds
    Asp B:413 - Ser B:414   [ RasMol ]  
    Gly A:182 - Pro A:183   [ RasMol ]  
    Gly B:182 - Pro B:183   [ RasMol ]  
    Gly B:484 - Asn B:485   [ RasMol ]  
    Phe A:772 - Ala A:773   [ RasMol ]  
 

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  3k5n
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  DPO2_ECOLI | P21189
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  2.7.7.7
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 Related Entries

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

UniProtKB/Swiss-Prot
        DPO2_ECOLI | P21189: 1q8i 3k57 3k58 3k59 3k5l 3k5m 3k5o 3maq

(-) Related Entries Specified in the PDB File

3k57 CRYSTAL STRUCTURE OF E.COLI POL II-NORMAL DNA-DATP TERNARY COMPLEX
3k58 CRYSTAL STRUCTURE OF E.COLI POL II-NORMAL DNA-DTTP TERNARY COMPLEX
3k59 CRYSTAL STRUCTURE OF E.COLI POL II-NORMAL DNA-DCTP TERNARY COMPLEX
3k5a CRYSTAL STRUCTURE OF E.COLI POL II-NORMAL DNA-DGTP TERNARY COMPLEX
3k5l CRYSTAL STRUCTURE OF E.COLI POL II-ABASIC DNA-DATP LT(0, 3) TERNARY COMPLEX
3k5m CRYSTAL STRUCTURE OF E.COLI POL II-ABASIC DNA-DDGTP LT(-2, 2) TERNARY COMPLEX
3k5o CRYSTAL STRUCTURE OF E.COLI POL II