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(-) Description

Title :  BYPASS OF MAJOR BENZOPYRENE-DG ADDUCT BY Y-FAMILY DNA POLYMERASE WITH UNIQUE STRUCTURAL GAP
 
Authors :  J. Bauer, H. Ling, J. M. Sayer, G. Xing, H. Yagi, D. M. Jerina
Date :  11 Sep 06  (Deposition) - 11 Sep 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,D,E
Keywords :  Benzo Pyrene, Carcinogen, Lesion Bypass, Polymerase, Translesion Synthesis, Dpo4, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Bauer, G. Xing, H. Yagi, J. M. Sayer, D. M. Jerina, H. Ling
A Structural Gap In Dpo4 Supports Mutagenic Bypass Of A Major Benzo[A]Pyrene Dg Adduct In Dna Through Template Misalignment.
Proc. Natl. Acad. Sci. Usa V. 104 14905 2007
PubMed-ID: 17848527  |  Reference-DOI: 10.1073/PNAS.0700717104

(-) Compounds

Molecule 1 - DNA POLYMERASE IV
    ChainsA
    EC Number2.7.7.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET22B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneDBH, DPO4
    Organism ScientificSULFOLOBUS SOLFATARICUS
    Organism Taxid273057
    StrainP2
    SynonymPOL IV
 
Molecule 2 - 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*AP*T)-3'
    ChainsD
    EngineeredYES
    SyntheticYES
 
Molecule 3 - 5'-D(*TP*CP*AP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)- 3'
    ChainsE
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ADE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
1BAP1Ligand/Ion1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE
2CA2Ligand/IonCALCIUM ION
3EDO3Ligand/Ion1,2-ETHANEDIOL
4GOL1Ligand/IonGLYCEROL
5POP1Ligand/IonPYROPHOSPHATE 2-

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:7 , PHE A:8 , ASP A:105 , POP A:405 , HOH A:492BINDING SITE FOR RESIDUE CA A 401
2AC2SOFTWAREASP A:105 , GLU A:106 , POP A:405 , HOH A:465 , HOH A:492 , HOH A:500 , DT D:14BINDING SITE FOR RESIDUE CA A 402
3AC3SOFTWARELYS A:78 , GLU A:79 , ARG A:247 , GLU A:271 , TYR A:274 , LYS A:275 , DG E:106 , GOL E:409 , HOH E:1108 , HOH E:1114BINDING SITE FOR RESIDUE BAP E 1106
4AC4SOFTWAREDT E:113 , DC E:114BINDING SITE FOR RESIDUE EDO E 406
5AC5SOFTWARESER A:338 , LYS A:339 , HOH A:534 , HOH A:539BINDING SITE FOR RESIDUE EDO A 407
6AC6SOFTWARETYR A:274 , HOH A:541 , GOL E:409BINDING SITE FOR RESIDUE EDO A 408
7AC7SOFTWAREASP A:7 , PHE A:8 , ASP A:9 , TYR A:10 , PHE A:11 , THR A:45 , TYR A:48 , ARG A:51 , ASP A:105 , LYS A:159 , CA A:401 , CA A:402 , HOH A:415 , HOH A:420 , HOH A:500 , HOH A:538BINDING SITE FOR RESIDUE POP A 405
8AC8SOFTWAREGLU A:79 , EDO A:408 , DG E:106 , BAP E:1106BINDING SITE FOR RESIDUE GOL E 409

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2IBK)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:159 -Pro A:160

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2IBK)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UMUCPS50173 UmuC domain profile.DPO4_SULSO3-187  1A:3-187

(-) Exons   (0, 0)

(no "Exon" information available for 2IBK)

(-) 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_SULSO | Q97W02 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:341
                                    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_SULSO     1 MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI 341
               SCOP domains d2ibka2 A:1-240 DinB homolog (DBH)                                                                                                                                                                                                              d2ibka1 A:241-341 DinB homolog (DBH)                                                                  SCOP domains
               CATH domains -2ibkA01  -------------------------------------------------------------------2ibkA01 A:2-10,A:78-166  [code=3.30.70.270, no name defined]                             2ibkA03 A:167-233 5' to 3' exonuclease, C-terminal subdomain       ----------2ibkA04 A:244-341  [code=3.30.1490.100, no name defined]                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhh...eeeeee.......eeeeeehhhhhh.......hhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh....eeeee..eeeee......hhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee....eeeeeee.....hhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --UMUC  PDB: A:3-187 UniProt: 3-187                                                                                                                                                        ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ibk A   1 MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI 341
                                    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 

Chain D from PDB  Type:DNA  Length:14
                                              
                 2ibk D   1 GGGGGAAGGATTAT  14
                                    10    

Chain E from PDB  Type:DNA  Length:17
                                                 
                 2ibk E 102 TCATGAATCCTTCCCCC 118
                                   111       

   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

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IBK)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DPO4_SULSO | Q97W02)
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_SULSO | Q97W021jx4 1jxl 1n48 1n56 1ryr 1rys 1s0m 1s0n 1s0o 1s10 1s97 1s9f 2ago 2agp 2agq 2asd 2asj 2asl 2atl 2au0 2bq3 2bqr 2bqu 2br0 2c22 2c28 2c2d 2c2e 2c2r 2ia6 2imw 2j6s 2j6t 2j6u 2jef 2jeg 2jei 2jej 2r8g 2r8h 2r8i 2rdi 2rdj 2uvr 2uvu 2uvv 2uvw 2v4q 2v4r 2v9w 2va2 2va3 2w8k 2w8l 2w9a 2w9b 2w9c 2xc9 2xca 2xcp 3fds 3gii 3gij 3gik 3gil 3gim 3khg 3khh 3khl 3khr 3m9m 3m9n 3m9o 3pr4 3pr5 3pvx 3pw0 3pw2 3pw4 3pw5 3pw7 3qz7 3qz8 3raq 3rax 3rb0 3rb3 3rb4 3rb6 3rbd 3rbe 3t5h 3t5j 3t5k 3t5l 3v6h 3v6j 3v6k 4f4w 4f4x 4f4y 4f4z 4f50 4fbt 4fbu 4g3i 4gc6 4gc7 4juz 4jv0 4jv1 4jv2 4qw8 4qw9 4qwa 4qwb 4qwc 4qwd 4qwe 4rua 4ruc 4rzr 4tqr 4tqs 5edw

(-) Related Entries Specified in the PDB File

2ia6 BYPASS OF MAJOR BENZOPYRENE-DG ADDUCT BY Y-FAMILY DNA POLYMERASE WITH UNIQUE STRUCTURAL GAP