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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN AAG DNA REPAIR GLYCOSYLASE COMPLEXED WITH 1,N6-ETHENOADENINE-DNA
 
Authors :  A. Y. Lau, M. D. Wyatt, B. J. Glassner, L. D. Samson, T. Ellenberger
Date :  08 Jun 00  (Deposition) - 11 Dec 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,D,E
Keywords :  Protein-Dna Complex, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Y. Lau, M. D. Wyatt, B. J. Glassner, L. D. Samson, T. Ellenberger
Molecular Basis For Discriminating Between Normal And Damaged Bases By The Human Alkyladenine Glycosylase, Aag.
Proc. Natl. Acad. Sci. Usa V. 97 13573 2000
PubMed-ID: 11106395  |  Reference-DOI: 10.1073/PNAS.97.25.13573
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDA) P*TP*TP*GP*CP*CP*T)-3')
    ChainsD
    EngineeredYES
    Other Details1,N6-ETHENOADENINE-DNA
    SyntheticYES
 
Molecule 2 - DNA (5'- D(*GP*GP*CP*AP*AP*TP*CP*AP*TP*GP*TP*CP*A)-3')
    ChainsE
    EngineeredYES
    SyntheticYES
 
Molecule 3 - 3-METHYL-ADENINE DNA GLYCOSYLASE
    ChainsA
    EC Number3.2.2.20
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPLM1
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAAG, ALKYLADENINE DNA GLYCOSYLASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ADE

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1EDA1Mod. Nucleotide3-[2-DEOXY-RIBOFURANOSYL]-3H-1,3,4,5A,8-PENTAAZA-AS-INDACENE-5'-MONOPHOSPHATE
2NA1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:42 , MET A:149 , SER A:171 , SER A:172 , GLY A:174 , ALA A:177BINDING SITE FOR RESIDUE NA A 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F4R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1F4R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_050096Q93R3MG_HUMANPolymorphism25671AQ93R
2UniProtVAR_014833R120C3MG_HUMANPolymorphism2308313AR120C
3UniProtVAR_014834R141Q3MG_HUMANPolymorphism2308312AR141Q
4UniProtVAR_014835A258V3MG_HUMANPolymorphism769193AA258V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1F4R)

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2dENST000002194312dENSE00001815669chr16:128256-128332773MG_HUMAN-00--
1.3aENST000002194313aENSE00000842196chr16:129138-1293301933MG_HUMAN1-13130--
1.4aENST000002194314aENSE00001702894chr16:129424-1296992763MG_HUMAN14-105921A:82-10524
1.5ENST000002194315ENSE00000663759chr16:133051-1332552053MG_HUMAN106-174691A:106-17469
1.6cENST000002194316cENSE00001892380chr16:135400-1358414423MG_HUMAN174-2981251A:174-294 (gaps)121

(-) 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:199
 aligned with 3MG_HUMAN | P29372 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:213
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   
            3MG_HUMAN    82 HLTRLGLEFFDQPAVPLARAFLGQVLVRRLPNGTELRGRIVETEAYLGPEDEAAHSRGGRQTPRNRGMFMKPGTLYVYIIYGMYFCMNISSQGDGACVLLRALEPLEGLETMRQLRSTLRKGTASRVLKDRELCSGPSKLCQALAINKSFDQRDLAQDEAVWLERGPLEPSEPAVVAAARVGVGHAGEWARKPLRFYVRGSPWVSVVDRVAEQ 294
               SCOP domains d1f4ra_ A: 3-methyladenine DNA glycosylase (AAG, ANPG, MPG)                                                                                                                                                           SCOP domains
               CATH domains 1f4rA00 A:82-294 3-methyladenine DNA Glycosylase; Chain A                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh.hhhhhhhhhh..eeeee.....eeeeeeeeeeee.........hhhhh....hhhhhh....eeeeee...eeeeeee......eeeeeeeeeeehhhhhhhhh..--------..hhhhh..hhhhhhhhh..hhhhh.........eeee...------.eeee........hhhhhh..eeee.........hhhhhh Sec.struct. author
                 SAPs(SNPs) -----------R--------------------------C--------------------Q--------------------------------------------------------------------------------------------------------------------V------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4a  PDB: A:82-105Exon 1.5  PDB: A:106-174 UniProt: 106-174                            ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------Exon 1.6c  PDB: A:174-294 (gaps) UniProt: 174-298 [INCOMPLETE]                                                            Transcript 1 (2)
                 1f4r A  82 HLTRLGLEFFDQPAVPLARAFLGQVLVRRLPNGTELRGRIVETEAYLGPEDEAAHSRGGRQTPRNRGMFMKPGTLYVYIIYGMYFCMNISSQGDGACVLLRALEPLEGLETMRQLRST--------VLKDRELCSGPSKLCQALAINKSFDQRDLAQDEAVWLERGP------AVVAAARVGVGHAGEWARKPLRFYVRGSPWVSVVDRVAEQ 294
                                    91       101       111       121       131       141       151       161       171       181       191       | -      |211       221       231       241      |  -   |   261       271       281       291   
                                                                                                                                               199      208                                     248    255                                       

Chain D from PDB  Type:DNA  Length:12
                                            
                 1f4r D   1 GACATGaTTGCC  12
                                  | 10  
                                  7-EDA 

Chain E from PDB  Type:DNA  Length:12
                                            
                 1f4r E  15 GCAATCATGTCA  26
                                    24  

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F4R)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (3MG_HUMAN | P29372)
molecular function
    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:0008725    DNA-3-methyladenine glycosylase activity    Catalysis of the reaction: DNA containing 3-methyladenine + H2O = DNA with abasic site + 3-methyladenine. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the damaged DNA 3-methyladenine and the deoxyribose sugar to remove the 3-methyladenine, leaving an abasic site.
    GO:0052822    DNA-3-methylguanine glycosylase activity    Catalysis of the reaction: DNA containing 3-methylguanine + H2O = DNA with abasic site + 3-methylguanine. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the damaged DNA 3-methylguanine and the deoxyribose sugar to remove the 3-methylguanine, leaving an abasic site.
    GO:0052821    DNA-7-methyladenine glycosylase activity    Catalysis of the reaction: DNA containing 7-methyladenine + H2O = DNA with abasic site + 7-methyladenine. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the damaged DNA 7-methyladenine and the deoxyribose sugar to remove the 7-methyladenine, leaving an abasic site.
    GO:0043916    DNA-7-methylguanine glycosylase activity    Catalysis of the reaction: DNA containing 7-methylguanine + H2O = DNA with abasic site + 7-methylguanine. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the damaged DNA 7-methylguanine and the deoxyribose sugar to remove the 7-methylguanine, leaving an abasic site.
    GO:0003905    alkylbase DNA N-glycosylase activity    Catalysis of the reaction: DNA with alkylated base + H2O = DNA with abasic site + alkylated base. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar to remove an alkylated base, leaving an apyrimidinic or apurinic site.
    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: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:0006307    DNA dealkylation involved in DNA repair    The repair of alkylation damage, e.g. the removal of the alkyl group at the O6-position of guanine by O6-alkylguanine-DNA alkyltransferase (AGT).
    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: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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0042645    mitochondrial nucleoid    The region of a mitochondrion to which the DNA is confined.
    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: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
        3MG_HUMAN | P293721bnk 1ewn 1f6o 3qi5 3uby

(-) Related Entries Specified in the PDB File

1bnk CRYSTAL STRUCTURE OF A HUMAN ALKYLBASE-DNA REPAIR ENZYME COMPLEXED TO DNA: MECHANISMS FOR NUCLEOTIDE FLIPPING AND BASE EXCISION
1ewn CRYSTAL STRUCTURE OF THE HUMAN AAG DNA REPAIR GLYCOSYLASE COMPLEXED WITH 1,N6-ETHENOADENINE-DNA