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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ALKA HOST/GUEST COMPLEX 8OXOGUANINE:ADENINE BASE PAIR
 
Authors :  B. R. Bowman, S. Lee, S. Wang, G. L. Verdine
Date :  19 Apr 08  (Deposition) - 02 Sep 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Alka, 8Oxoguanine, Dna Repair, Host/Guest Complex, Dna Structure, Dna Damage, Hydrolase, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. R. Bowman, S. Lee, S. Wang, G. L. Verdine
Structure Of The E. Coli Dna Glycosylase Alka Bound To The Ends Of Duplex Dna: A System For The Structure Determination Of Lesion-Containing Dna.
Structure V. 16 1166 2008
PubMed-ID: 18682218  |  Reference-DOI: 10.1016/J.STR.2008.04.012
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA-3-METHYLADENINE GLYCOSYLASE 2
    Chains: A, B, C, D
    EC Number: 3.2.2.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30
    Expression System Strain: BL21(DE3)
    Expression System Vector Type: PLASMID
    Gene: ALKA, AIDA
    Organism Scientific: ESCHERICHIA COLI
    Synonym: DNA-3-METHYLADENINE GLYCOSYLASE II, 3- METHYLADENINE-DNA GLYCOSYLASE II, INDUCIBLE, TAG II, DNA-3- METHYLADENINE GLYCOSIDASE II
 
Molecule 2 - DNA (5'-D(*DGP*DAP*DCP*DAP*DTP*DGP*DAP*(8OG) P*DTP*DGP*DCP*DC)-3')
    Chains: E, G
    Engineered: YES
    Other Details: 8OXOGUANINE CONTAINING DNA
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*DGP*DGP*DCP*DAP*DAP*DTP*DCP*DAP*DTP*DGP*DTP*DC)-3')
    Chains: F, H
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
18OG2Mod. Nucleotide8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 3CVS)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Pro A:8 -Pro A:9
2Lys A:261 -Pro A:262
3Pro B:8 -Pro B:9
4Lys B:261 -Pro B:262
5Pro C:8 -Pro C:9
6Lys C:261 -Pro C:262
7Pro D:8 -Pro D:9
8Lys D:261 -Pro D:262

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALKYLBASE_DNA_GLYCOSPS00516 Alkylbase DNA glycosidases alkA family signature.3MG2_ECOLI214-238
 
 
 		  4A:214-238
B:214-238
C:214-238
D:214-238

(-) Exons   (0, 0)

(no "Exon" information available for 3CVS)

(-) 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:282
 aligned with 3MG2_ECOLI | P04395 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:282
                                    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  
           3MG2_ECOLI     1 MYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDEA 282
               SCOP domains d3cvsa2 A:1-99 3-Methyladenine DNA glycosylase II (gene alkA or aidA)                              d3cvsa1 A:100-282 3-Methyladenine DNA glycosylase II (gene alkA or aidA)                                                                                                                SCOP domains
               CATH domains 3cvsA01 A:1-112 DNA-3-methyladenine glycosylase ii                                                              3cvsA02 A:113-230 Hypothetical protein; domain 2                                                                      3cvsA03 A:231-282                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhhhh....eee....eeeeeee..eeeeeeeeee....eeeeee.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...........hhhhhhhhhhh....hhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh........hhhhhhhhhh.....hhhhhhhhhhhhh.........hhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALKYLBASE_DNA_GLYCOS     -------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cvs A   1 MYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDEA 282
                                    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  


Chain B from PDB  Type:PROTEIN  Length:282
 aligned with 3MG2_ECOLI | P04395 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:282
                                    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  
           3MG2_ECOLI     1 MYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDEA 282
               SCOP domains d3cvsb2 B:1-99 3-Methyladenine DNA glycosylase II (gene alkA or aidA)                              d3cvsb1 B:100-282 3-Methyladenine DNA glycosylase II (gene alkA or aidA)                                                                                                                SCOP domains
               CATH domains 3cvsB01 B:1-112 DNA-3-methyladenine glycosylase ii                                                              3cvsB02 B:113-230 Hypothetical protein; domain 2                                                                      3cvsB03 B:231-282                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhhh.....eee....eeeeeee..eeeeeeeeee....eeeeee.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhheee..eeeeee..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh.....hhhhhhhhhhhhh.........hhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALKYLBASE_DNA_GLYCOS     -------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cvs B   1 MYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDEA 282
                                    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  


Chain C from PDB  Type:PROTEIN  Length:282
 aligned with 3MG2_ECOLI | P04395 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:282
                                    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  
           3MG2_ECOLI     1 MYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDEA 282
               SCOP domains d3cvsc2 C:1-99 3-Methyladenine DNA glycosylase II (gene alkA or aidA)                              d3cvsc1 C:100-282 3-Methyladenine DNA glycosylase II (gene alkA or aidA)                                                                                                                SCOP domains
               CATH domains 3cvsC01 C:1-112 DNA-3-methyladenine glycosylase ii                                                              3cvsC02 C:113-230 Hypothetical protein; domain 2                                                                      3cvsC03 C:231-282                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhhhh....eee....eeeeeee..eeeeeeeeee....eeeeee.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhheee..eeeeee..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh........hhhhhhhhhh.....hhhhhhhhhhhhh.........hhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALKYLBASE_DNA_GLYCOS     -------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cvs C   1 MYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDEA 282
                                    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  


Chain D from PDB  Type:PROTEIN  Length:282
 aligned with 3MG2_ECOLI | P04395 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:282
                                    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  
           3MG2_ECOLI     1 MYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDEA 282
               SCOP domains d3cvsd2 D:1-99 3-Methyladenine DNA glycosylase II (gene alkA or aidA)                              d3cvsd1 D:100-282 3-Methyladenine DNA glycosylase II (gene alkA or aidA)                                                                                                                SCOP domains
               CATH domains 3cvsD01 D:1-112 DNA-3-methyladenine glycosylase ii                                                              3cvsD02 D:113-230 Hypothetical protein; domain 2                                                                      3cvsD03 D:231-282                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhhhh....eee....eeeeeee..eeeeeeeeee....eeeeee.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..........hhhhhhhhhhh....hhhhhhhhhhhhhhhhh.............hhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhhhhhh.....hhhhhhhhhhhhh.........hhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALKYLBASE_DNA_GLYCOS     -------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cvs D   1 MYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDEA 282
                                    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  


Chain E from PDB  Type:DNA  Length:12
                                            
                 3cvs E   1 GACATGAgTGCC  12
                                   |10  
                                   8-8OG


Chain F from PDB  Type:DNA  Length:12
                                            
                 3cvs F  14 GGCAATCATGTC  25
                                    23  


Chain G from PDB  Type:DNA  Length:12
                                            
                 3cvs G   1 GACATGAgTGCC  12
                                   |10  
                                   8-8OG


Chain H from PDB  Type:DNA  Length:12
                                            
                 3cvs H  14 GGCAATCATGTC  25
                                    23
   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, 8)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (3, 12)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CVS)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (3MG2_ECOLI | P04395)
molecular function
    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: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.
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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        3MG2_ECOLI | P04395: 1diz 1mpg 1pvs 3cvt 3cw7 3cwa 3cws 3cwt 3cwu 3d4v 3ogd 3oh6 3oh9

(-) Related Entries Specified in the PDB File

3cvt 3cw7 3cwa 3cws 3cwt 3cwu