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(-) Description

Authors :  S. E. Tsutakawa, S. Classen, B. R. Chapados, A. Arvai, D. L. Finger, G. Gu C. G. Tomlinson, P. Thompson, A. H. Sarker, B. Shen, P. K. Cooper, J. A. G J. A. Tainer
Date :  06 Jan 11  (Deposition) - 27 Apr 11  (Release) - 27 Apr 11  (Revision)
Resolution :  2.32
Chains :  Asym./Biol. Unit :  A,D,E,F
Keywords :  Helix-3 Turn-Helix, Hydrophobic Wedge, 3' Flap Binding Site, Hydrolase-Dna Complex, Dna Repair, Replication, Flap Endonuclease, Fen, Fen1, Dna, Nuclease, 5' Flap, Ss-Dsdna Junction, Helix-2 Turn- Helix, H2Th, H3Th, Divalent Cation, Metal Helical Gateway, Cap, Acid Block, Two Metal Mechanism, Unpaired, 5' Nuclease, Human, Long Patch Base Excision Repair (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  S. E. Tsutakawa, S. Classen, B. R. Chapados, A. S. Arvai, L. D. Finger, G. Guenther, C. G. Tomlinson, P. Thompson, A. H. Sarker, B. Shen, P. K. Cooper, J. A. Grasby, J. A. Tainer
Human Flap Endonuclease Structures, Dna Double-Base Flipping, And A Unified Understanding Of The Fen1 Superfamily.
Cell(Cambridge, Mass. ) V. 145 198 2011
PubMed-ID: 21496641  |  Reference-DOI: 10.1016/J.CELL.2011.03.004

(-) Compounds

    EC Number3.1.-.-
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET29B
    Expression System StrainROSETTA2(DE3)PLYSS
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneFEN1, RAD2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
Molecule 2 - DNA (5'- D(*AP*CP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*T)-3')
    Other Details - SourceSYNTHESIZED
Molecule 3 - DNA (5'-D(*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*GP*T)-3')
    Other Details - SourceSYNTHESIZED
Molecule 4 - DNA (5'-D(*AP*CP*CP*GP*TP*CP*C)-3')
    Other Details - SourceSYNTHESIZED

 Structural Features

(-) Chains, Units

Asymmetric/Biological Unit ADEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
1AC1SOFTWAREASP A:86 , GLU A:158 , HOH A:361 , HOH A:376 , HOH A:422 , HOH A:683 , SO4 A:1201BINDING SITE FOR RESIDUE SM A 1001
2AC2SOFTWAREGLU A:160 , ASP A:179 , ASP A:181 , HOH A:356 , HOH A:379 , HOH A:422 , SO4 A:1201 , HOH E:277BINDING SITE FOR RESIDUE SM A 1002
3AC3SOFTWAREGLU A:57 , GLU A:285 , GLU A:313 , GLN A:342 , HOH A:574 , HOH A:575 , HOH A:605BINDING SITE FOR RESIDUE SM A 1003
4AC4SOFTWAREGLU A:57 , GLU A:59 , GLU A:313 , GLN A:342 , HOH A:576 , HOH A:577 , HOH A:658BINDING SITE FOR RESIDUE SM A 1004
6AC6SOFTWARELYS A:93 , ARG A:100 , ASP A:233 , HOH A:376 , HOH A:379 , HOH A:422 , SM A:1001 , SM A:1002 , DT E:1 , HOH E:277BINDING SITE FOR RESIDUE SO4 A 1201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q8L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3Q8L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q8L)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
1XPG_1PS00841 XPG protein signature 1.FEN1_HUMAN79-93  1A:79-93
2XPG_2PS00842 XPG protein signature 2.FEN1_HUMAN149-163  1A:149-163

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000003058852ENSE00001327269chr11:61562813-615647081896FEN1_HUMAN1-3873871A:2-342 (gaps)344

(-) 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 FEN1_HUMAN | P39748 from UniProtKB/Swiss-Prot  Length:380

    Alignment length:344
                                    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       281       291       301       311       321       331       341    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains XPG_N-3q8lA02 A:2-107                                                                                     --------------------------------------XPG_I-3q8lA01 A:146-233                                                                 ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------XPG_1          -------------------------------------------------------XPG_2          -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.2  PDB: A:2-342 (gaps) UniProt: 1-387 [INCOMPLETE]                                                                                                                                                                                                                                                                                                Transcript 1
                                    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       281       291       301       311       321       331    |  338    
                                                                                                                                                                                                                                                                                                                                                                        336 337     

Chain D from PDB  Type:DNA  Length:18
                 3q8l D   1 ACTCTGCCTCAAGACGGT  18

Chain E from PDB  Type:DNA  Length:12
                 3q8l E   1 TTGAGGCAGAGT  12

Chain F from PDB  Type:DNA  Length:7
                 3q8l F   1 ACCGTCC   7

   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  (0, 0)

(no "SCOP Domain" information available for 3Q8L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q8L)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
Clan: PIN (27)

(-) Gene Ontology  (36, 36)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FEN1_HUMAN | P39748)
molecular function
    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:0017108    5'-flap endonuclease activity    Catalysis of the cleavage of a 5' flap structure in DNA, but not other DNA structures; processes the 5' ends of Okazaki fragments in lagging strand DNA synthesis.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004523    RNA-DNA hybrid ribonuclease activity    Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
    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:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0008309    double-stranded DNA exodeoxyribonuclease activity    Catalysis of the sequential cleavage of mononucleotides from a free 5' or 3' terminus of a double-stranded DNA molecule.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    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:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    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).
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: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:0043137    DNA replication, removal of RNA primer    Removal of the Okazaki RNA primer from the lagging strand of replicating DNA, by a combination of the actions of DNA polymerase, DNA helicase and an endonuclease.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0009650    UV protection    Any process in which an organism or cell protects itself from ultraviolet radiation (UV), which may also result in resistance to repeated exposure to UV.
    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:0006302    double-strand break repair    The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.
    GO:0000724    double-strand break repair via homologous recombination    The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule.
    GO:0007613    memory    The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task).
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0000722    telomere maintenance via recombination    Any recombinational process that contributes to the maintenance of proper telomeric length.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.


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 Related Entries

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

        FEN1_HUMAN | P397481u7b 1ul1 3q8k 3q8m 3uvu 5e0v 5fv7 5k97 5kse 5um9

(-) Related Entries Specified in the PDB File

3q8k 3q8m