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(-) Description

Title :  3-METHYLADENINE DNA-GLYCOSYLASE FROM ARCHAEOGLOBUS FULGIDUS
 
Authors :  I. Leiros, M. P. Nabong, K. Grosvik, J. Ringvoll, G. T. Haugland, L. Uldal, K. Reite, I. K. Olsbu, I. Knaevelsrud, E. Moe, O. A. Andersen, N. K. Birkeland, P. Ruoff, A. Klungland, S. Bjelland
Date :  22 Feb 07  (Deposition) - 10 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alka, Dna Repair, N1-Methyladenine, N3-Methylcytosine, Hyperthermophiles, Archaeoglobus Fulgidus, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Leiros, M. P. Nabong, K. Grosvik, J. Ringvoll, G. T. Haugland, L. Uldal, K. Reite, I. K. Olsbu, I. Knaevelsrud, E. Moe, O. A. Andersen, N. K. Birkeland, P. Ruoff, A. Klungland, S. Bjelland
Structural Basis For Enzymatic Excision Of N1- Methyladenine And N3-Methylcytosine From Dna
Embo J. V. 26 2206 2007
PubMed-ID: 17396151  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601662

(-) Compounds

Molecule 1 - 3-METHYLADENINE DNA-GLYCOSYLASE
    Chains: A, B
    EC Number: 3.2.2.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-11A
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234
    Strain: VC 16
    Synonym: ALKA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2NA4Ligand/IonSODIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NA-1Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:213 , PHE A:215 , ILE A:218 , HOH A:2239BINDING SITE FOR RESIDUE NA A1296
2AC2SOFTWARELEU A:21 , PRO A:22 , LEU A:24 , THR A:26 , ASP A:28 , HOH A:2027BINDING SITE FOR RESIDUE NA A1297
3AC3SOFTWARETHR B:213 , PHE B:215 , ILE B:218 , HOH B:2231BINDING SITE FOR RESIDUE NA B1296
4AC4SOFTWARELEU B:21 , PRO B:22 , LEU B:24 , THR B:26 , ASP B:28 , HOH B:2029BINDING SITE FOR RESIDUE NA B1297
5AC5SOFTWARELYS A:15 , PHE A:18 , TYR A:79 , GLY A:112 , LEU A:113 , HOH A:2283 , HOH A:2284BINDING SITE FOR RESIDUE GOL A1298
6AC6SOFTWAREASN A:234 , PHE A:236 , ALA A:266 , GLY A:271 , HOH A:2285BINDING SITE FOR RESIDUE GOL A1299
7AC7SOFTWARELYS B:15 , PHE B:18 , TYR B:79 , GLY B:112 , LEU B:113 , HOH B:2284 , HOH B:2285BINDING SITE FOR RESIDUE GOL B1298
8AC8SOFTWAREASN B:234 , VAL B:235 , PHE B:236 , ALA B:266 , GLY B:271 , HOH B:2286BINDING SITE FOR RESIDUE GOL B1299

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JHJ)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:26 -Pro A:27
2Thr B:26 -Pro B:27

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JHJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2JHJ)

(-) Exons   (0, 0)

(no "Exon" information available for 2JHJ)

(-) Sequences/Alignments

Asymmetric 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:290
 aligned with O28163_ARCFU | O28163 from UniProtKB/TrEMBL  Length:295

    Alignment length:295
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290     
         O28163_ARCFU     1 MWRIELKHAVNWELKMKFFVLPELPTPDVVESGVWRRAIVLDGRAVAVMAYPESERTIVVEGNFENREWEAVRRKLVEYLGLQNPEELYRFMDGDEKLRMLKNRFYGFGRAGLMSMSVFEGIAKAIIQQQISFVVAEKLAAKIVGRFGDEVEWNGLKFYGFPTQEAILKAGVEGLRECGLSRRKAELIVEIAKEENLEELKEWGEEEAYEYLTSFKGIGRWTAELVLSMALGKNVFPADDLGVRRAVSRLYFNGEIQSAEKVREIARERFGRFARDILFYLFLYDRFFSKKTELV 295
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....hhhhhhhh..........eee..eeeeeeee..eeeeeeeeeee..eeeeee..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.eeee..eeee...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.........hhhhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.-----. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jhj A   1 MWRIELKHAVNWELKMKFFVLPELPTPDVVESGVWRRAIVLDGRAVAVMAYPESERTIVVEGNFENREWEAVRRKLVEYLGLQNPEELYRFMDGDEKLRMLKNRFYGFGRAGLMSMSVFEGIAKAIIQQQISFVVAEKLAAKIVGRFGDEVEWNGLKFYGFPTQEAILKAGVEGLRECGLSRRKAELIVEIAKEENLEELKEWGEEEAYEYLTSFKGIGRWTAELVLSMALGKNVFPADDLGVRRAVSRLYFNGEIQSAEKVREIARERFGRFARDILFYLFLYDRFFS-----V 295
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280        |-    |
                                                                                                                                                                                                                                                                                                                          289   295


Chain B from PDB  Type:PROTEIN  Length:291
 aligned with O28163_ARCFU | O28163 from UniProtKB/TrEMBL  Length:295

    Alignment length:295
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290     
         O28163_ARCFU     1 MWRIELKHAVNWELKMKFFVLPELPTPDVVESGVWRRAIVLDGRAVAVMAYPESERTIVVEGNFENREWEAVRRKLVEYLGLQNPEELYRFMDGDEKLRMLKNRFYGFGRAGLMSMSVFEGIAKAIIQQQISFVVAEKLAAKIVGRFGDEVEWNGLKFYGFPTQEAILKAGVEGLRECGLSRRKAELIVEIAKEENLEELKEWGEEEAYEYLTSFKGIGRWTAELVLSMALGKNVFPADDLGVRRAVSRLYFNGEIQSAEKVREIARERFGRFARDILFYLFLYDRFFSKKTELV 295
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------HhH-GPD-2jhjB01 B:123-272                                                                                                                             ----------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------HhH-GPD-2jhjB02 B:123-272                                                                                                                             ----------------------- Pfam domains (2)
         Sec.struct. author .eeee.....hhhhhhhh..........eee..eeeeeeee..eeeeeeeeeee..eeeeee..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.eeee..eeee...hhhhhhhhhhhhhhh...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.........hhhhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.----.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jhj B   1 MWRIELKHAVNWELKMKFFVLPELPTPDVVESGVWRRAIVLDGRAVAVMAYPESERTIVVEGNFENREWEAVRRKLVEYLGLQNPEELYRFMDGDEKLRMLKNRFYGFGRAGLMSMSVFEGIAKAIIQQQISFVVAEKLAAKIVGRFGDEVEWNGLKFYGFPTQEAILKAGVEGLRECGLSRRKAELIVEIAKEENLEELKEWGEEEAYEYLTSFKGIGRWTAELVLSMALGKNVFPADDLGVRRAVSRLYFNGEIQSAEKVREIARERFGRFARDILFYLFLYDRFFS----LV 295
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280        |-   | 
                                                                                                                                                                                                                                                                                                                          289  294
   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 2JHJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2JHJ)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: HHH (112)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (O28163_ARCFU | O28163)
molecular function
    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.
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.

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 Related Entries

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UniProtKB/TrEMBL
        O28163_ARCFU | O28163: 2jhn

(-) Related Entries Specified in the PDB File

2jhn 3-METHYLADENINE DNA-GLYCOSYLASE FROM ARCHAEOGLOBUS FULGIDUS