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(-) Description

Authors :  K. Pereira, L. Serre, C. Zelwer, B. Castaing
Date :  03 Jun 03  (Deposition) - 03 Aug 04  (Release) - 13 Jul 11  (Revision)
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,D,E
Keywords :  Dna Repair, Fpg, Mutm, Abasic Site, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  K. Pereira De Jesus, L. Serre, C. Zelwer, B. Castaing
Structural Insights Into Abasic Site For Fpg Specific Binding And Catalysis: Comparative High-Resolution Crystallographic Studies Of Fpg Bound To Various Models Of Abasic Site Analogues-Containing Dna.
Nucleic Acids Res. V. 33 5936 2005
PubMed-ID: 16243784  |  Reference-DOI: 10.1093/NAR/GKI879
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*CP*G)- 3')
    Other DetailsSYNTHETIC
Molecule 2 - DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3')
    Other DetailsSYNTHETIC
    EC Number3.2.2.23
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMAL-C
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism Taxid1359

 Structural Features

(-) Chains, Units

Asymmetric/Biological Unit ADE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
3ZN1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
2AC2SOFTWARETYR A:58 , HIS A:72 , ARG A:74 , THR A:113 , GLU A:115 , TYR A:125 , LYS A:129 , GOL A:1002 , HOH A:1063 , DT D:9 , DT D:10BINDING SITE FOR RESIDUE GOL A 1001
3AC3SOFTWAREARG A:74 , CYS A:248 , GOL A:1001 , HOH A:1093 , HOH A:1165 , DT D:10 , HOH E:61BINDING SITE FOR RESIDUE GOL A 1002
4AC4SOFTWAREARG A:16 , GLN A:20 , LEU A:81 , THR A:83 , ASP A:85 , PHE A:98 , ASP A:100 , GLY A:101BINDING SITE FOR RESIDUE GOL A 1003
5AC5SOFTWAREGLY A:259 , ARG A:260 , HOH A:1082 , HOH A:1182 , DT D:6 , DT D:8 , DT D:9 , HOH D:18 , DA E:20 , DA E:21BINDING SITE FOR RESIDUE GOL A 1004

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
1FPG_CATPS51068 Formamidopyrimidine-DNA glycosylase catalytic domain profile.FPG_LACLC2-113  1A:1-112
2ZF_FPG_2PS51066 Zinc finger FPG-type profile.FPG_LACLC238-272  1A:236-270
3ZF_FPG_1PS01242 Zinc finger FPG-type signature.FPG_LACLC247-271  1A:245-269

(-) Exons   (0, 0)

(no "Exon" information available for 1PJI)

(-) 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:267
 aligned with FPG_LACLC | P42371 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:272
                                    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  
               SCOP domains d1pjia2 A:1-131 DNA repair protein MutM (Fpg)                                                                                      d1pjia 1 A:132-218 DNA repair protein MutM (Fpg)                                        ----d1pjia3 A:223-271 DNA repair protein MutM (Fpg)   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Fapy_DNA_glyco-1pjiA03 A:1-115                                                                                     ---------------H2TH-1p jiA01 A:131-223                                                                       ------------------zf-FPG_IleRS-1pjiA02 A:242-271 Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.....eeee.hhhhh..hhhhhhhhhh...eeeeeee..eeeeee...eeeeee.....eeeee.........eeeeeee..eeeeee......eeeeee..hhhhhhhhhh.......-...hhhhhhhhhhhh..hhhhhhhh.......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh....----.......hhhhhh.................eeeee..eeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) FPG_CAT  PDB: A:1-112 UniProt: 2-113                                                                            ----------------------------------------------------------------------------------------------------------------------------ZF_FPG_2  PDB: A:236-270           - PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZF_FPG_1  PDB: A:245-269 -- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                                    10        20        30        40        50        60        70        80        90       100       110       120       130      |139       149       159       169       179       189       199       209        |-   |   229       239       249       259       269  
                                                                                                                                                                  137 |                                                                             218  223                                                

Chain D from PDB  Type:DNA  Length:14
                 1pji D   1 CTCTTTxTTTCTCG  14
                                  | 10    

Chain E from PDB  Type:DNA  Length:14
                 1pji E  15 GCGAGAAACAAAGA  28

   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 1PJI)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
Clan: H2TH (43)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FPG_LACLC | P42371)
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) lyase activity    Catalysis of the cleavage of the C-O-P bond 3' to the apurinic or apyrimidinic site in DNA by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.
    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: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:0008534    oxidized purine nucleobase lesion DNA N-glycosylase activity    Catalysis of the removal of oxidized purine bases by cleaving the N-C1' glycosidic bond between the oxidized purine and the deoxyribose sugar. The reaction involves the formation of a covalent enzyme-substrate 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 apurinic (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: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)

        FPG_LACLC | P423711kfv 1nnj 1pjj 1pm5 1tdz 1xc8 2xzf 2xzu 3c58 4pcz 4pd2 4pdg 4pdi

(-) Related Entries Specified in the PDB File

1kfv 1nnj