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(-) Description

Title :  BINARY 3' COMPLEX OF T7 DNA POLYMERASE WITH A DNA PRIMER/TEMPLATE CONTAINING A DISORDERED CIS-SYN THYMINE DIMER ON THE TEMPLATE
 
Authors :  Y. Li, S. Dutta, S. Doublie, H. M. Bdour, J. S. Taylor, T. Ellenberger
Date :  05 Mar 04  (Deposition) - 06 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,P,T
Keywords :  Dna Polymerase, Fidelity, Lesion Bypass, Thymine Dimer, Open, Close, Transferase/Electron Transport/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Li, S. Dutta, S. Doublie, H. M. Bdour, J. S. Taylor, T. Ellenberger
Nucleotide Insertion Opposite A Cis-Syn Thymine Dimer By A Replicative Dna Polymerase From Bacteriophage T7.
Nat. Struct. Mol. Biol. V. 11 784 2004
PubMed-ID: 15235589  |  Reference-DOI: 10.1038/NSMB792
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*C*GP*GP*CP*CP*AP*GP*TP*GP*CP* CP*(2DT))-3'
    ChainsP
    EngineeredYES
    Other DetailsDNA PRIMER
    SyntheticYES
 
Molecule 2 - 5'-D(*CP*CP*CP*(TTD) P*AP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP* CP*G)-3'
    ChainsT
    EngineeredYES
    Other DetailsDNA TEMPLATE
    SyntheticYES
 
Molecule 3 - DNA POLYMERASE
    ChainsA
    EC Number2.7.7.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Gene5
    MutationYES
    Organism ScientificENTEROBACTERIA PHAGE T7
    Organism Taxid10760
    SynonymT7 DNA POLYMERASE
 
Molecule 4 - THIOREDOXIN 1
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABPT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
12DT1Mod. Nucleotide3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:5 , HOH A:5030 , HOH A:5202 , HOH A:5203 , HOH A:5204 , HOH A:5206BINDING SITE FOR RESIDUE MG A 4003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SKW)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:434 -Pro A:435
2Ile B:75 -Pro B:76

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SKW)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_1PS00194 Thioredoxin family active site.THIO_ECOLI25-43  1B:24-42
2DNA_POLYMERASE_APS00447 DNA polymerase family A signature.DPOL_BPT7518-537  1A:518-537

(-) Exons   (0, 0)

(no "Exon" information available for 1SKW)

(-) 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:678
 aligned with DPOL_BPT7 | P00581 from UniProtKB/Swiss-Prot  Length:704

    Alignment length:704
                                    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    
            DPOL_BPT7     1 MIVSDIEANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAYLDALEAEVARGGLIVFHNGHKYDVPALTKLAKLQLNREFHLPRENCIDTLVLSRLIHSNLKDTDMGLLRSGKLPGKRFGSHALEAWGYRLGEMKGEYKDDFKRMLEEQGEEYVDGMEWWNFNEEMMDYNVQDVVVTKALLEKLLSDKHYFPPEIDFTDVGYTTFWSESLEAVDIEHRAAWLLAKQERNGFPFDTKAIEELYVELAARRSELLRKLTETFGSWYQPKGGTEMFCHPRTGKPLPKYPRIKTPKVGGIFKKPKNKAQREGREPCELDTREYVAGAPYTPVEHVVFNPSSRDHIQKKLQEAGWVPTKYTDKGAPVVDDEVLEGVRVDDPEKQAAIDLIKEYLMIQKRIGQSAEGDKAWLRYVAEDGKIHGSVNPNGAVTGRATHAFPNLAQIPGVRSPYGEQCRAAFGAEHHLDGITGKPWVQAGIDASGLELRCLAHFMARFDNGEYAHEILNGDIHTKNQIAAELPTRDNAKTFIYGFLYGAGDEKIGQIVGAGKERGKELKKKFLENTPAIAALRESIQQTLVESSQWVAGEQQVKWKRRWIKGLDGRKVHVRSPHAALNTLLQSAGALICKLWIIKTEEMLVEKGLKHGWDGDFAYMAWVHDEIQVGCRTEEIAQVVIETAQEAMRWVGDHWNFRCLLDTEGKMGPNWAICH 704
               SCOP domains d1skwa1 A:1-210 Exonuclease domain of T7 DNA polymerase                                                                                                                                                           d1skwa2 A:211-704 T7 phage DNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1skwA01 A:1-232  [code=3.30.420.10, no name defined]                                                                                                                                                                                    1skwA02 A:233-414 Taq DNA Polymerase; Chain T, domain 4                                                                                                                               1skwA03 A:415-477,A:590-704                                    1skwA04 A:478-589 5' to 3' exonuclease, C-terminal subdomain                                                    1skwA03 A:415-477,A:590-704  [code=3.30.70.370, no name defined]                                                    CATH domains
               Pfam domains -RNase_H_2-1skwA01 A:2-186                                                                                                                                                                ---------------------------------------------------------------------------------------------------------------------         DNA_pol_A-1skwA02 A:313-703                                                                                                                                                                                                                                                                                                                                                                            - Pfam domains
         Sec.struct. author .eeeeeee..hhhhh..eeeeeeee.....eeeehhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhh.....hhh.eeehhhhhhhhh...........hhhhh..------..hhhhhhhhhhhhhhhhhhhhhhh........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee....................................---------..............eeeeee.....hhhhhhhhhhh................hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh....ee..eee.........eee.............hhhhhhhhhhhhhh.........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhhh......hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.-----------.....eee.....eee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee...eeeeee.hhhhhhhhhhhhhhhhhhhhhhh.......eeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYMERASE_A    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1skw A   1 MIVSDIEANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAYLDALEAEVARGGLIVFHNGHKYDVPALTKLAKLQLNREFHLPRENCIDTLVLSRLIHSNLKDTDMGLLRSGKLPG------ALEAWGYRLGEMKGEYKDDFKRMLEEQGEEYVDGMEWWNFNEEMMDYNVQDVVVTKALLEKLLSDKHYFPPEIDFTDVGYTTFWSESLEAVDIEHRAAWLLAKQERNGFPFDTKAIEELYVELAARRSELLRKLTETFGSWYQPKGGTEMFCHPRTGKPLPKYPRIKTPKVGGIFKKPKN---------CELDTREYVAGAPYTPVEHVVFNPSSRDHIQKKLQEAGWVPTKYTDKGAPVVDDEVLEGVRVDDPEKQAAIDLIKEYLMIQKRIGQSAEGDKAWLRYVAEDGKIHGSVNPNGAVTGRATHAFPNLAQIPGVRSPYGEQCRAAFGAEHHLDGITGKPWVQAGIDASGLELRCLAHFMARFDNGEYAHEILNGDIHTKNQIAAELPTRDNAKTFIYGFLYGAGDEKIGQIVGAGKERGKELKKKFLENTPAIAALRESIQQTLVE-----------KWKRRWIKGLDGRKVHVRSPHAALNTLLQSAGALICKLWIIKTEEMLVEKGLKHGWDGDFAYMAWVHDEIQVGCRTEEIAQVVIETAQEAMRWVGDHWNFRCLLDTEGKMGPNWAICH 704
                                    10        20        30        40        50        60        70        80        90       100       110      |  -   |   130       140       150       160       170       180       190       200       210       220       230       240       250       260       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    |    -      |590       600       610       620       630       640       650       660       670       680       690       700    
                                                                                                                                              117    124                                                                                                                                                                                303       313                                                                                                                                                                                                                                                                   575         587                                                                                                                     

Chain B from PDB  Type:PROTEIN  Length:105
 aligned with THIO_ECOLI | P0AA25 from UniProtKB/Swiss-Prot  Length:109

    Alignment length:105
                                    13        23        33        43        53        63        73        83        93       103     
           THIO_ECOLI     4 KIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANL 108
               SCOP domains d1skwb_ B: Thioredoxin                                                                                    SCOP domains
               CATH domains 1skwB00 B:3-107 Glutaredoxin                                                                              CATH domains
               Pfam domains Thioredoxin-1skwB01 B:3-106                                                                             - Pfam domains
         Sec.struct. author ..ee....hhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeee......hhhhhh..ee.eeeeee..eeeeeee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------THIOREDOXIN_1      ----------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1skw B   3 KIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANL 107
                                    12        22        32        42        52        62        72        82        92       102     

Chain P from PDB  Type:DNA  Length:8
                                        
                 1skw P  14 CAGTGCCt  21
                                   |
                                  21-2DT

Chain T from PDB  Type:DNA  Length:10
                                          
                 1skw T   6 AGGCACTGGC  15
                                    15

   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  (3, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (5, 5)

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

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: RNase_H (288)

(-) Gene Ontology  (25, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DPOL_BPT7 | P00581)
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:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    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:0039693    viral DNA genome replication    The replication of a viral DNA genome.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.

Chain B   (THIO_ECOLI | P0AA25)
molecular function
    GO:0016671    oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces disulfide.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0034599    cellular response to oxidative stress    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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0006662    glycerol ether metabolic process    The chemical reactions and pathways involving glycerol ethers, any anhydride formed between two organic hydroxy compounds, one of which is glycerol.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0000103    sulfate assimilation    The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DPOL_BPT7 | P005811skr 1sks 1sl0 1sl1 1sl2 1t7p 1t8e 1tk0 1tk5 1tk8 1tkd 1x9m 1x9s 1x9w 1zyq 2ajq 5ikn
        THIO_ECOLI | P0AA251f6m 1keb 1m7t 1oaz 1skr 1sks 1sl0 1sl1 1sl2 1srx 1t7p 1t8e 1tho 1tk0 1tk5 1tk8 1tkd 1txx 1x9m 1x9s 1x9w 1xoa 1xob 1zcp 1zyq 1zzy 2ajq 2bto 2eio 2eiq 2eir 2fch 2fd3 2h6x 2h6y 2h6z 2h70 2h71 2h72 2h73 2h74 2h75 2h76 2o8v 2tir 2trx 3dyr 4hu7 4hu9 4hua 4x43 5hr0 5hr1 5hr2 5hr3

(-) Related Entries Specified in the PDB File

1skr T7 DNA POLYMERASE COMPLEXED PRIMER/TEMPLATE DNA CONTAINING A CIS-SYN THYMINE DIMER ON THE TEMPLATE
1sks BINARY 3' COMPLEX OF T7 DNA POLYMERASE WITH A DNA PRIMER/ TEMPLATE CONTAINING A CIS-SYN THYMINE DIMER ON THE TEMPLATE
1sl0 TERNARY 3' COMPLEX OF T7 DNA POLYMERASE WITH A DNA PRIMER/ TEMPLATE CONTAINING A DISORDERED CIS-SYN THYMINE DIMER ON THE TEMPLATE AND AN INCOMING NUCLEOTIDE
1sl1 BINARY 5' COMPLEX OF T7 DNA POLYMERASE WITH A DNA PRIMER/ TEMPLATE CONTAINING A CIS-SYN THYMINE DIMER ON THE TEMPLATE
1sl2 TERNARY 5' COMPLEX OF T7 DNA POLYMERASE WITH A DNA PRIMER/ TEMPLATE CONTAINING A CIS-SYN THYMINE DIMER ON THE TEMPLATE AND AN INCOMING NUCLEOTIDE
1t7p T7 DNA POLYMERASE COMPLEXED TO DNA PRIMER/TEMPLATE, A NUCLEOSIDE TRIPHOSPHATE, AND ITS PROCESSIVITY FACTOR THIOREDOXIN