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(-) Description

Authors :  C. A. Brautigam, K. Aschheim, T. A. Steitz
Date :  22 Jun 99  (Deposition) - 30 Jun 99  (Release) - 13 Apr 11  (Revision)
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Exonuclease, Two Metal Ions, Single-Stranded Dna, Transferase/Dna, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  C. A. Brautigam, K. Aschheim, T. A. Steitz
Structural Elucidation Of The Binding And Inhibitory Properties Of Lanthanide (Iii) Ions At The 3'-5' Exonucleolytic Active Site Of The Klenow Fragment
Chem. Biol. V. 6 901 1999
PubMed-ID: 10631518  |  Reference-DOI: 10.1016/S1074-5521(00)80009-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*GP*CP*TP*TP*AP*CP*GP*C)-3'
    EC Number2.7.7.7
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPCJ155
    Expression System StrainCJ376
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymPOL I

 Structural Features

(-) Chains, Units

Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
1Asp A:673 -Pro A:674

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
1DNA_POLYMERASE_APS00447 DNA polymerase family A signature.DPO1_ECOLI754-773  1A:754-773

(-) Exons   (0, 0)

(no "Exon" information available for 1QSL)

(-) 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:601
 aligned with DPO1_ECOLI | P00582 from UniProtKB/Swiss-Prot  Length:928

    Alignment length:605
                                   333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       923     
               SCOP domains d1qsla1 A:324-518 Exonuclease domain of prokaryotic DNA polymerase                                                                                                                                 d1qsla2 A:519-928 DNA polymerase I (Klenow fragment)                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains --1qslA01 A:326-542  [code=3.30.420.10, no name defined]                                                                                                                                                                   1qslA02 A:543-658 Taq DNA Polymerase; Chain T, domain 4                                                             1qslA03 A:659-708,A:853-927                       1qslA04 A:709-852 5' to 3' exonuclease, C-terminal subdomain                                                                                    1qslA03 A:659-708,A:853-927  [code=, no name defined]           - CATH domains
               Pfam domains ------DNA_pol_A_exo1-1qslA01 A:330-517                                                                                                                                                            -----------------------------DNA_pol_A-1qslA02 A:547-927                                                                                                                                                                                                                                                                                                                                                                  - Pfam domains
         Sec.struct. author Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYMERASE_A    ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                                   333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593        |-   |   613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       923     
                                                                                                                                                                                                                                                                                                                602  607                                                                                                                                                                                                                                                                                                                                 

Chain B from PDB  Type:DNA  Length:4
                1qsl B 1005 ACGC 1008

   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  (4, 4)

Asymmetric/Biological Unit
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
Clan: RNase_H (288)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DPO1_ECOLI | P00582)
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:0008409    5'-3' exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' 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:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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: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:0006284    base-excision repair    In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
    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.
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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)

        DPO1_ECOLI | P005821d8y 1d9d 1d9f 1dpi 1kfd 1kfs 1kln 1krp 1ksp 2kfn 2kfz 2kzm 2kzz

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1QSL)