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(-) Description

Title :  STRUCTURAL AND BIOCHEMICAL EXPLORATION OF A CRITICAL AMINO ACID IN HUMAN 8-OXOGUANINE GLYCOSYLASE
 
Authors :  D. P. Norman, S. J. Chung, G. L. Verdine
Date :  25 Oct 02  (Deposition) - 04 Mar 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Hhh-Gpd, Glycosylase, Dna-Repair, Oxoguanine, Hydrolase, Lyase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. P. Norman, S. J. Chung, G. L. Verdine
Structural And Biochemical Exploration Of A Critical Amino Acid In Human 8-Oxoguanine Glycosylase
Biochemistry V. 42 1564 2003
PubMed-ID: 12578369  |  Reference-DOI: 10.1021/BI026823D
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA COMPLEMENT STRAND
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA INHIBITOR STRAND
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - N-GLYCOSYLASE/DNA LYASE
    Chains: A
    EC Number: 3.2.2.-, 4.2.99.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET30A
    Expression System Strain: BL21 DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: OGG1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HOGG1 ENZYME, 8-OXOGUANOSINE DNA GLYCOSYLASE/DNA- (APURINIC OR APYRIMIDINIC SITE) LYASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
13DR1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2CA1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDA C:22 , HOH C:32BINDING SITE FOR RESIDUE CA C 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N3A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1N3A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (10, 10)

Asymmetric/Biological Unit (10, 10)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_024831G12EOGG1_HUMANPolymorphism772520254AG12E
02UniProtVAR_009519R46QOGG1_HUMANPolymorphism104893751AR46Q
03UniProtVAR_024832A85SOGG1_HUMANPolymorphism17050550AA85S
04UniProtVAR_024833R131QOGG1_HUMANPolymorphism747638147AR131Q
05UniProtVAR_009520R154HOGG1_HUMANPolymorphism56053615AR154H
06UniProtVAR_014487R229QOGG1_HUMANPolymorphism1805373AR229Q
07UniProtVAR_024834S232TOGG1_HUMANUnclassified  ---AS232T
08UniProtVAR_018890A288VOGG1_HUMANPolymorphism3219012AA288V
09UniProtVAR_014488S320TOGG1_HUMANPolymorphism1801128AS320T
10UniProtVAR_018891D322NOGG1_HUMANPolymorphism3219014AD322N
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1N3A)

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003446291aENSE00002157661chr3:9791628-9792107480OGG1_HUMAN1-46461A:9-4638
1.2bENST000003446292bENSE00001669842chr3:9792629-9792876248OGG1_HUMAN46-129841A:46-129 (gaps)84
1.3aENST000003446293aENSE00001644854chr3:9793454-9793633180OGG1_HUMAN129-189611A:129-18961
1.4ENST000003446294ENSE00001165146chr3:9796388-9796569182OGG1_HUMAN189-249611A:189-24961
1.5ENST000003446295ENSE00001661907chr3:9798155-9798305151OGG1_HUMAN250-300511A:250-30051
1.6aENST000003446296aENSE00001764469chr3:9798451-979850050OGG1_HUMAN300-316171A:300-31617
1.6jENST000003446296jENSE00001651617chr3:9798745-9799197453OGG1_HUMAN317-345291A:317-3259

(-) 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:314
 aligned with OGG1_HUMAN | O15527 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:317
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       
           OGG1_HUMAN     9 RRMGHRTLASTPALWASIPCPRSELRLDLVLPSGQSFRWREQSPAHWSGVLADQVWTLTQTEEQLHCTVYRGDKSQASRPTPDELEAVRKYFQLDVTLAQLYHHWGSVDSHFQEVAQKFQGVRLLRQDPIECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALAGPEVEAHLRKLGLGYRARYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTKVADCICLMALDKPQAVPVDVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFFRSLWGPYAGWAQAVLFSADLRQ 325
               SCOP domains d1n3aa2 A:9-135 8-oxoguanine glycosylase                                                                                       d1n3aa1 A:136-325 8-oxoguanine glycosylase                                                                                                                                                     SCOP domains
               CATH domains 1n3aA01 A:9-100  [code=3.30.310.40, no name defined]                                        ---1n3aA02              -----------1n3aA03 A:136-261 Hypothetical protein; domain 2                                                                              ---1n3aA02 A:104-124,A:265-323                                -- CATH domains
               Pfam domains ----------------OGG_N-1n3aA02 A:25-141                                                                                               HhH-GPD-1n3aA01 A:142-301                                                                                                                                       ------------------------ Pfam domains
         Sec.struct. author ..........hhhhheeee......hhhhhh........eeee..eeeee....eeeeee...eeeeeee.---......hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh....hhhhhhhhhhhhhhhhh.eeeee..eeee...hhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh........hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---E---------------------------------Q--------------------------------------S---------------------------------------------Q----------------------H--------------------------------------------------------------------------Q--T-------------------------------------------------------V-------------------------------T-N--- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:9-46 UniProt: 1-46  ----------------------------------------------------------------------------------Exon 1.3a  PDB: A:129-189 UniProt: 129-189                   ------------------------------------------------------------Exon 1.5  PDB: A:250-300 UniProt: 250-300          ----------------Exon 1.6j Transcript 1 (1)
           Transcript 1 (2) -------------------------------------Exon 1.2b  PDB: A:46-129 (gaps) UniProt: 46-129                                     -----------------------------------------------------------Exon 1.4  PDB: A:189-249 UniProt: 189-249                    --------------------------------------------------Exon 1.6a        --------- Transcript 1 (2)
                 1n3a A   9 GSEGHRTLASTPALWASIPCPRSELRLDLVLPSGQSFRWREQSPAHWSGVLADQVWTLTQTEEQLHCTVYR---SQASRPTPDELEAVRKYFQLDVTLAQLYHHWGSVDSHFQEVAQKFQGVRLLRQDPIECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALAGPEVEAHLRKLGLGYRARYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTKVADCICLMALDKPQAVPVQVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFFRSLWGPYAGWAQAVLFSADLRQ 325
                                    18        28        38        48        58        68        78|   |   88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       
                                                                                                 79  83                                                                                                                                                                                                                                                  


Chain B from PDB  Type:DNA  Length:15
                                               
                 1n3a B   1 GGTAGACCTGGACGC  15
                                    10     


Chain C from PDB  Type:DNA  Length:15
                                               
                 1n3a C  16 GCGTCCAxGTCTACC  30
                                   |25     
                                  23-3DR
   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
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: HHH (112)
(-)
Clan: TBP-like (48)

(-) Gene Ontology  (41, 41)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (OGG1_HUMAN | O15527)
molecular function
    GO:0034039    8-oxo-7,8-dihydroguanine DNA N-glycosylase activity    Catalysis of the removal of 8-oxo-7,8-dihydroguanine bases by cleaving the N-C1' glycosidic bond between the oxidized purine and the deoxyribose sugar.
    GO:0019104    DNA N-glycosylase activity    Catalysis of the removal of damaged bases by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic/apyrimidinic (AP) site.
    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: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:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
    GO:0032357    oxidized purine DNA binding    Interacting selectively and non-covalently with oxidized purine residues in DNA.
    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: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:0002526    acute inflammatory response    Inflammation which comprises a rapid, short-lived, relatively uniform response to acute injury or antigenic challenge and is characterized by accumulations of fluid, plasma proteins, and granulocytic leukocytes. An acute inflammatory response occurs within a matter of minutes or hours, and either resolves within a few days or becomes a chronic inflammatory response.
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    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:0071276    cellular response to cadmium ion    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 cadmium (Cd) ion stimulus.
    GO:0045007    depurination    The disruption of the bond between the sugar in the backbone and the A or G base, causing the base to be removed and leaving a depurinated sugar.
    GO:0045008    depyrimidination    The disruption of the bond between the sugar in the backbone and the C or T base, causing the base to be removed and leaving a depyrimidinated sugar.
    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:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:1901291    negative regulation of double-strand break repair via single-strand annealing    Any process that stops, prevents or reduces the frequency, rate or extent of double-strand break repair via single-strand annealing.
    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).
    GO:0033683    nucleotide-excision repair, DNA incision    A process that results in the endonucleolytic cleavage of the damaged strand of DNA. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound.
    GO:0033158    regulation of protein import into nucleus, translocation    Any process that modulates the vectorial transfer of a protein from the cytoplasm into the nucleus, across the nuclear membrane.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0032355    response to estradiol    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
    GO:0045471    response to ethanol    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethanol stimulus.
    GO:0051593    response to folic acid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a folic acid stimulus.
    GO:0009416    response to light stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light.
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (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:0009314    response to radiation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation.
cellular component
    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:0016363    nuclear matrix    The dense fibrillar network lying on the inner side of the nuclear membrane.
    GO:0016607    nuclear speck    A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        OGG1_HUMAN | O15527: 1ebm 1fn7 1hu0 1ko9 1lwv 1lww 1lwy 1m3h 1m3q 1n39 1n3c 1yqk 1yql 1yqm 1yqr 2i5w 2nob 2noe 2nof 2noh 2noi 2nol 2noz 2xhi 3ih7 3ktu 5an4

(-) Related Entries Specified in the PDB File

1ebm K249Q HOGG1 BOUND TO OXOG CONTAINING DNA
1fn7 WILD-TYPE HOGG1 BOUND TO ABASIC THF INHIBITOR
1ko9 UNBOUND HOGG1
1n39 D268E HOGG1 BOUND TO ABASIC THF INHIBITOR