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(-) Description

Title :  CRYSTAL STRUCTURE OF A TRAPPED REACTION INTERMEDIATE OF THE DNA REPAIR ENZYME ENDONUCLEASE VIII WITH DNA
 
Authors :  G. Golan, D. O. Zharkov, R. Gilboa, A. S. Fernandes, J. H. Kycia, S. E. Gerchman, R. A. Rieger, A. P. Grollman, G. Shoham
Date :  04 Oct 01  (Deposition) - 04 Oct 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.42
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Hydrolase/Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. O. Zharkov, G. Golan, R. Gilboa, A. S. Fernandes, S. E. Gerchman, J. H. Kycia, R. A. Rieger, A. P. Grollman, G. Shoham
Structural Analysis Of An Escherichia Coli Endonuclease Viii Covalent Reaction Intermediate.
Embo J. V. 21 789 2002
PubMed-ID: 11847126  |  Reference-DOI: 10.1093/EMBOJ/21.4.789
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*GP*G)-3'
    ChainsB
    EngineeredYES
    SyntheticYES
 
Molecule 2 - 5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)- 3'
    ChainsC
    EngineeredYES
    SyntheticYES
 
Molecule 3 - ENDONUCLEASE VIII
    ChainsA
    EC Number3.2.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET13A
    Expression System StrainB834(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneNEI
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1PED1Mod. NucleotidePENTANE-3,4-DIOL-5-PHOSPHATE
2SO43Ligand/IonSULFATE ION
3ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:237 , CYS A:240 , CYS A:257 , CYS A:260BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWAREARG A:8 , ASN A:12 , GLY A:213 , HOH A:627 , HOH A:906 , HOH A:918BINDING SITE FOR RESIDUE SO4 A 551
3AC3SOFTWAREARG A:112 , LYS A:140 , ALA A:191 , ASP A:195 , HOH A:636 , HOH A:863 , HOH A:909 , HOH A:938BINDING SITE FOR RESIDUE SO4 A 552
4AC4SOFTWAREASN A:190 , ALA A:191 , HOH A:610 , HOH A:866 , HOH A:915 , HOH A:946BINDING SITE FOR RESIDUE SO4 A 553

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K3W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1K3W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K3W)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FPG_CATPS51068 Formamidopyrimidine-DNA glycosylase catalytic domain profile.END8_ECOLI2-111  1A:1-110
2ZF_FPG_2PS51066 Zinc finger FPG-type profile.END8_ECOLI229-263  1A:228-262
3ZF_FPG_1PS01242 Zinc finger FPG-type signature.END8_ECOLI238-262  1A:237-261

(-) Exons   (0, 0)

(no "Exon" information available for 1K3W)

(-) 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:254
 aligned with END8_ECOLI | P50465 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:262
                                    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  
           END8_ECOLI     2 PEGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKPYQSQLIGQHVTHVETRGKALLTHFSNDLTLYSHNQLYGVWRVVDTGEEPQTTRVLRVKLQTADKTILLYSASDIEMLTPEQLTTHPFLQRVGPDVLDPNLTPEVVKERLLSPRFRNRQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLEIPRFSYATRGQVDENKHHGALFRFKVFHRDGEPCERCGSIIEKTTLSSRPFYWCPGCQH 263
               SCOP domains d1k3wa2 A:1-124 Endonuclease VIII                                                                                           d1k3wa1 A:125-214 Endonuclease VIII                                                       --------d1k3wa3 A:223-262 Endonuclease VIII      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Fapy_DNA_glyco-1k3wA03 A:1-110                                                                                --------------H2TH-1k3wA01 A:125-214                                                                    -------------------zf-FPG_IleRS-1k3wA02          Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhh...eeeeeee..eeeeee....eeeee.....eeeeee..........eeeeee...eeeeee...eeeee..hhhhhhhhhhhh.........hhhhhhhhhhh......hhhhhh.........hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..--------......................eeeee..eeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) FPG_CAT  PDB: A:1-110 UniProt: 2-111                                                                          ---------------------------------------------------------------------------------------------------------------------ZF_FPG_2  PDB: A:228-262            PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZF_FPG_1  PDB: A:237-261 - PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k3w A   1 PEGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKTYQSQLIGQHVTHVETRGKALLTHFSNDLTLYSHNQLYGVWRVVDTGEEPQTTRVLRVKLQTADKTILLYSASDIEMLRPEQLTTHPFLQRVGPDVLDPNLTPEVVKERLLSPRFRNRQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLEIPRFSYATRGQ--------ALFRFKVFHRDGEPCERCGSIIEKTTLSSRPFYWCPGCQH 262
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   |     -  |    230       240       250       260  
                                                                                                                                                                                                                                               214      223                                       

Chain B from PDB  Type:DNA  Length:8
                                        
                 1k3w B 405 TCATCCTG 412

Chain C from PDB  Type:DNA  Length:11
                                           
                 1k3w C 422 CAGGAxGAAGC 432
                                 | 431 
                               427-PED 

   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  (0, 0)

(no "CATH Domain" information available for 1K3W)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: H2TH (43)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (END8_ECOLI | P50465)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003906    DNA-(apurinic or apyrimidinic site) endonuclease activity    Catalysis of the cleavage of the C-O-P bond in the AP site created when DNA glycosylase removes a damaged base, involved in the DNA base excision repair pathway (BER).
    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:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    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:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0016799    hydrolase activity, hydrolyzing N-glycosyl compounds    Catalysis of the hydrolysis of any N-glycosyl bond.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    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:0000703    oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity    Catalysis of the removal oxidized pyrimidine bases by cleaving the N-C1' glycosidic bond between the oxidized pyrimidine and the deoxyribose sugar. The reaction involves formation of a covalent enzyme-pyrimidine base intermediate. Release of the enzyme and free base by a beta-elimination or a beta, gamma-elimination mechanism results in the cleavage of the DNA backbone 3' of the apyrimidinic (AP) site.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    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: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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0006289    nucleotide-excision repair    A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).

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 Related Entries

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

UniProtKB/Swiss-Prot
        END8_ECOLI | P504651k3x 1q39 1q3b 1q3c 2ea0 2opf 2oq4

(-) Related Entries Specified in the PDB File

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