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(-) Description

Title :  CRYSTAL STRUCTURE OF E.COLI POL II-ABASIC DNA-DDGTP LT(-2, 2) TERNARY COMPLEX
 
Authors :  W. Yang, F. Wang
Date :  07 Oct 09  (Deposition) - 02 Feb 10  (Release) - 02 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym./Biol. Unit :  A,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
    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(*AP*GP*TP*CP*CP*TP*GP*(3DR) P*AP*CP*GP*CP*TP*AP*GP*GP*CP*AP*CP*A)-3')
    Chains: T
    Engineered: YES
    Other Details: ABASIC LT(-2, 2) 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

  123
Asymmetric/Biological Unit : APT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
13DR1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2CA2Ligand/IonCALCIUM ION
3DG31Ligand/Ion2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:419 , TYR A:420 , LYS A:421 , SER A:422 , LEU A:423 , ARG A:477 , LYS A:493 , ASN A:497 , TYR A:500 , ASP A:547 , HOH A:826 , HOH A:865 , HOH A:930 , HOH A:957 , CA A:1001 , CA A:1002 , HOH A:1115 , DG P:913 , DC T:802 , DC T:803BINDING SITE FOR RESIDUE DG3 A 914
2AC2SOFTWAREASP A:419 , TYR A:420 , ASP A:547 , DG3 A:914BINDING SITE FOR RESIDUE CA A 1001
3AC3SOFTWAREASP A:419 , ASP A:547 , DG3 A:914 , DG P:913BINDING SITE FOR RESIDUE CA A 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K5M)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:182 -Pro A:183

 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, 1)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3K5M)

(-) 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:768
 aligned with DPO2_ECOLI | P21189 from UniProtKB/Swiss-Prot  Length:783

    Alignment length:772
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768  
           DPO2_ECOLI     - --MAQAGFILTRHWRDTPQGTEVSFWLATDNGPLQVTLAPQESVAFIPADQVPRAQHILQGEQGFRLTPLALKDFHRQPVYGLYCRAHRQLMNYEKRLREGGVTVYEADVRPPERYLMERFITSPVWVEGDMHNGTIVNARLKPHPDYRPPLKWVSIDIETTRHGELYCIGLEGCGQRIVYMLGPENGDASSLDFELEYVASRPQLLEKLNAWFANYDPDVIIGWNVVQFDLRMLQKHAERYRLPLRLGRDNSELEWREHGFKNGVFFAQAKGRLIIDGIEALKSAFWNFSSFSLETVAQELLGEGKSIDNPWDRMDEIDRRFAEDKPALATYNLKDCELVTQIFHKTEIMPFLLERATVNGLPVDRHGGSVAAFGHLYFPRMHRAGYVAPNLGEVPPHASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPVGLVEGMAQPDPEHSTEGFLDAWFSREKHCLPEIVTNIWHGRDEAKRQGNKPLSQALKIIMNAFYGVLGTTACRFFDPRLASSITMRGHQIMRQTKALIEAQGYDVIYGDTDSTFVWLKGAHSEEEAAKIGRALVQHVNAWWAETLQKQRLTSALELEYETHFCRFLMPTIRGADTGSKKRYAGLIQEGDKQRMVFKGLETVRTDWTPLAQQFQQELYLRIFRNEPYQEYVRETIDKLMAGELDARLVYRKRLRRPLSEYQRNVPPHVRAARLADEENQKRGRPLQYQNRGTIKYVWTTNGPEPLDYQRSPLDYEHYLTRQLQPVAEGILPFIED 770
               SCOP domains d3k5ma1 A:-1-389 automated matches                                                                                                                                                                                                                                                                                                                                                                     d3k5ma2 A:390-770 automated matches                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------DNA_pol_B_exo1-3k5mA03 A:49-296                                                                                                                                                                                                                         -------- ------------------------------------------------------------------------------------------------------------------------------------------DNA_pol_B-3k5mA01 A:444-770                                                                                                                                                                                                                                                                                                             Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_pol_B-3k5mA02 A:444-770                                                                                                                                                                                                                                                                                                             Pfam domains (2)
         Sec.struct. author .eeeeeeeeeeeeee......eeeeeeee..eeeeeee....eeeeee..hhhhhhhhh.....eeeeeeeee.....eeeeeee.hhhhhhhhhhhhhhh.........hhhhhhhhhh....eeeeeeeee..eeeeeeeee.........eeeeeeee.....eeeeeeee..eeeeeee............eeeee.hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh............eee..--...-.eee....eeeehhhhhhhh.......hhhhhhhhhhh..-...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.........................eeeeeeeeeee.hhhhhhhhhhh.hhhhhhhhhhh.....eee.....eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeeeee.............eeeeee....eeeeee.hhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhh.eeeee..hhhhh....hhhhhhhhhhhhhhhhhh........eeeeeeee..eeee........hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYM--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k5m A  -1 PHMAQAGFILTRHWRDTPQGTEVSFWLATDNGPLQVTLAPQESVAFIPADQVPRAQHILQGEQGFRLTPLALKDFHRQPVYGLYCRAHRQLMNYEKRLREGGVTVYEADVRPPERYLMERFITSPVWVEGDMHNGTIVNARLKPHPDYRPPLKWVSIDIETTRHGELYCIGLEGCGQRIVYMLGPENGDASSLDFELEYVASRPQLLEKLNAWFANYDPDVIIGWNVVQFDLRMLQKHAERYRLPLRLGRDNSELEWREH--KNG-FFAQAKGRLIIDGIEALKSAFWNFSSFSLETVAQELLGEG-SIDNPWDRMDEIDRRFAEDKPALATYNLKNCELVTQIFHKTEIMPFLLERATVNGLPVDRHGGSVAAFGHLYFPRMHRAGYVAPNLGEVPPHASPGGYVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPVGLVEGMAQPDPEHSTEGFLDAWFSREKHCLPEIVTNIWHGRDEAKRQGNKPLSQALKIIMNAFYGVLGTTACRFFDPRLASSITMRGHQIMRQTKALIEAQGYDVIYGDTDSTFVWLKGAHSEEEAAKIGRALVQHVNAWWAETLQKQRLTSALELEYETHFCRFLMPTIRGADTGSKKRYAGLIQEGDKQRMVFKGLETVRTDWTPLAQQFQQELYLRIFRNEPYQEYVRETIDKLMAGELDARLVYRKRLRRPLSEYQRNVPPHVRAARLADEENQKRGRPLQYQNRGTIKYVWTTNGPEPLDYQRSPLDYEHYLTRQLQPVAEGILPFIED 770
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258  | | |268       278       288       298     | 308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768  
                                                                                                                                                                                                                                                                                             258  | | |                                    304 |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
                                                                                                                                                                                                                                                                                                261 | |                                      306                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
                                                                                                                                                                                                                                                                                                  263 |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
                                                                                                                                                                                                                                                                                                    265                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         


Chain P from PDB  Type:DNA  Length:13
                                             
                 3k5m P 901 GTGCCTAGCGTAG 913
                                   910   


Chain T from PDB  Type:DNA  Length:20
                                                    
                 3k5m T 799 AGTCCTGxACGCTAGGCACA 818
                                   808       818
                                 806-3DR
   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, 2)

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 3K5M)

(-) Pfam Domains  (2, 3)

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   (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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  3k5m
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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 3k5n 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
3k5n CRYSTAL STRUCTURE OF E.COLI POL II-ABASIC DNA BINARY COMPLEX
3k5o CRYSTAL STRUCTURE OF E.COLI POL II