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(-) Description

Title :  STRUCTURE OF THE HIGH FIDELITY DNA POLYMERASE I WITH EXTENDING FROM AN OXIDATIVE FORMAMIDOPYRIMIDINE-DG DNA LESION -DA BASEPAIR.
 
Authors :  T. H. Gehrke, U. Lischke, S. Arnold, S. Schneider, T. Carell
Date :  06 Sep 12  (Deposition) - 17 Apr 13  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Transferase-Dna Complex, Dna Polymerase, Oxidative Dna Lesion, Dna Damage, Translesion Dna Synthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. H. Gehrke, U. Lischke, K. L. Gasteiger, S. Schneider, S. Arnold, H. C. Muller, D. S. Stephenson, H. Zipse, T. Carell
Unexpected Non-Hoogsteen-Based Mutagenicity Mechanism Of Fapy-Dna Lesions.
Nat. Chem. Biol. V. 9 455 2013
PubMed-ID: 23685671  |  Reference-DOI: 10.1038/NCHEMBIO.1254

(-) Compounds

Molecule 1 - DNA POLYMERASE
    ChainsA
    EC Number2.7.7.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VectorPDEST007
    Expression System Vector TypePLASMID
    Organism ScientificGEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid1422
    Other DetailsGERMAN COLLECTION OF MICROORGANISMS DSM NO. 22
    SynonymDNA POLYMERASE I
 
Molecule 2 - 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*TP*AP*AP)-3'
    ChainsB
    Organism ScientificGEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid1422
    Other DetailsOXIDATIVE DNA LESION FAPYG AT C4
    SyntheticYES
 
Molecule 3 - 5'-D(*CP*AP*TP*FOXP*AP*GP*AP*GP*TP*CP*AP*GP*GP*CP*TP)-3'
    ChainsC
    Organism ScientificGEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid1422
    Other DetailsOXIDATIVE DNA LESION FAPYG AT C4
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1FOX1Mod. Nucleotide((1R,2S,4R)-4-{[2-AMINO-5-(FORMYLAMINO)-6-OXO-3,6-DIHYDROPYRIMIDIN-4-YL]AMINO}-2-HYDROXYCYCLOPENTYL)METHYL 5'-PHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3SO46Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:682 , ARG A:702 , LYS A:706 , HOH A:2123BINDING SITE FOR RESIDUE SO4 A1877
2AC2SOFTWAREMET A:299 , ALA A:300 , ARG A:343 , ARG A:677BINDING SITE FOR RESIDUE SO4 A1878
3AC3SOFTWAREGLU A:321 , VAL A:322 , ASP A:425 , TYR A:429BINDING SITE FOR RESIDUE SO4 A1879
4AC4SOFTWAREGLU A:667 , ASP A:668 , ASP A:669 , GLY A:745 , ARG A:748 , HOH A:2128BINDING SITE FOR RESIDUE SO4 A1880
5AC5SOFTWAREHIS A:568 , ARG A:779 , ARG A:819BINDING SITE FOR RESIDUE SO4 A1881
6AC6SOFTWARESER A:655 , GLN A:656 , MG A:1883 , HOH A:2118BINDING SITE FOR RESIDUE SO4 A1882
7AC7SOFTWAREASP A:653 , TYR A:654 , ASP A:830 , SO4 A:1882BINDING SITE FOR RESIDUE MG A1883

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B9V)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:620 -Pro A:621

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B9V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4B9V)

(-) Exons   (0, 0)

(no "Exon" information available for 4B9V)

(-) 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:579
 aligned with E1C9K5_GEOSE | E1C9K5 from UniProtKB/TrEMBL  Length:580

    Alignment length:579
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571         
         E1C9K5_GEOSE     2 KMAFTLADRVTEEMLADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLAAYLLDPAQGVDDVAAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWALERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDTKRLEQMGEELAEQLRTVEQRIYELAGQEFNINSPKQLGVILFEKLQLPVLKKSKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEVTPNMRRQAKAVNFGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVKRYMENIVQEAKQKGYVTTLLHRRRYLPDITSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARLKEERLQARLLLQVHDELILEAPKEEMERLCRLVPEVMEQAVTLRVPLKVDYHYGSTWYDAK 580
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...hhhhhh.eeeeeee............eeeeee..eeeeehhhhhh.hhhhhhhhhh...eeee.hhhhhhhhhhh.......eeeehhhhhhhhhhhhh..hhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......ee..eee.........eee..........hhhhhhhhh.ee.....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.....eee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...eeeeeee..hhhhhhhhhhhhhhh.........eeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b9v A 298 KMAFTLADRVTEEMLADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLAAYLLDPAQGVDDVAAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWALERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDTKRLEQMGEELAEQLRTVEQRIYELAGQEFNINSPKQLGVILFEKLQLPVLKKSKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEVTPNMRRQAKAVNFGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVKRYMENIVQEAKQKGYVTTLLHRRRYLPDITSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARLKEERLQARLLLQVHDELILEAPKEEMERLCRLVPEVMEQAVTLRVPLKVDYHYGSTWYDAK 876
                                   307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867         

Chain B from PDB  Type:DNA  Length:11
                                           
                 4b9v B   1 CCTGACTCTAA  11
                                    10 

Chain C from PDB  Type:DNA  Length:12
                                            
                 4b9v C   4 TgAGAGTCAGGC  15
                             |      13  
                             5-FOX      

   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  (0, 0)

(no "SCOP Domain" information available for 4B9V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B9V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B9V)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (E1C9K5_GEOSE | E1C9K5)
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: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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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: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:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.

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 Related Entries

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

UniProtKB/TrEMBL
        E1C9K5_GEOSE | E1C9K52xo7 2xy5 2xy6 2xy7 2y1i 2y1j 4b9l 4b9m 4b9n 4b9s 4b9t 4b9u 4dsi 4dsj 4dsk 4dsl 4dwi 4uqg 4yfu

(-) Related Entries Specified in the PDB File

2xo7 CRYSTAL STRUCTURE OF A DA:O-ALLYLHYDROXYLAMINE-DC BASEPAIR IN COMPLEX WITH FRAGMENT DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS
2xy5 CRYSTAL STRUCTURE OF AN ARTIFICIAL SALEN-COPPER BASEPAIR IN COMPLEX WITH FRAGMENT DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS
2xy6 CRYSTAL STRUCTURE OF A SALICYLIC ALDEHYDE BASEPAIR IN COMPLEX WITH FRAGMENT DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS
2xy7 CRYSTAL STRUCTURE OF A SALICYLIC ALDEHYDE BASE IN THE PRE-INSERTION SITE OF FRAGMENT DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS
2y1i CRYSTAL STRUCTURE OF A S-DIASTEREOMER ANALOGUE OF THE SPORE PHOTOPRODUCT IN COMPLEX WITH FRAGMENT DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS
2y1j CRYSTAL STRUCTURE OF A R-DIASTEREOMER ANALOGUE OF THE SPORE PHOTOPRODUCT IN COMPLEX WITH FRAGMENT DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS
4b9l STRUCTURE OF THE HIGH FIDELITY DNA POLYMERASE I WITH THE OXIDATIVE FORMAMIDOPYRIMIDINE-DA DNA LESION IN THE PRE-INSERTION SITE.
4b9m STRUCTURE OF THE HIGH FIDELITY DNA POLYMERASE I WITH AN OXIDATIVE FORMAMIDOPYRIMIDINE-DA DNA LESION -THYMINE BASEPAIR IN THE POST-INSERTION SITE.
4b9n STRUCTURE OF THE HIGH FIDELITY DNA POLYMERASE I CORRECTLY BYPASSING THE OXIDATIVE FORMAMIDOPYRIMIDINE-DA DNA LESION.
4b9s STRUCTURE OF THE HIGH FIDELITY DNA POLYMERASE I WITH AN OXIDATIVE FORMAMIDOPYRIMIDINE-DG DNA LESION OUTSIDE OF THE PRE-INSERTION SITE.
4b9t STRUCTURE OF THE HIGH FIDELITY DNA POLYMERASE I WITH AN OXIDATIVE FORMAMIDOPYRIMIDINE-DG DNA LESION -DC BASEPAIR IN THE POST-INSERTION SITE.
4b9u STRUCTURE OF THE HIGH FIDELITY DNA POLYMERASE I WITH AN OXIDATIVE FORMAMIDOPYRIMIDINE-DG DNA LESION -DA BASEPAIR IN THE POST-INSERTION SITE.