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(-) Description

Title :  STRUCTURE OF AN UNUSUAL 3-METHYLADENINE DNA GLYCOSYLASE II ( ALKA) FROM DEINOCOCCUS RADIODURANS
 
Authors :  E. Moe, D. R. Hall, I. Leiros, V. Talstad, J. Timmins, S. Mcsweeney
Date :  11 Apr 11  (Deposition) - 20 Apr 11  (Release) - 20 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Dna Repair (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Moe, D. R. Hall, I. Leiros, V. T. Monsen, J. Timmins, S. Mcsweeney
Structure-Function Studies Of An Unusual 3-Methyladenine Dna Glycosylase Ii (Alka) From Deinococcus Radiodurans
Acta Crystallogr. , Sect. D V. 68 703 2012
PubMed-ID: 22683793  |  Reference-DOI: 10.1107/S090744491200947X

(-) Compounds

Molecule 1 - DNA-3-METHYLADENINE GLYCOSIDASE II, PUTATIVE
    Atcc: 13939
    Chains: A, B
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299
    Strain: R1
    Synonym: ALKA - DNA-3-METHYLADENINE GLYCOSIDASE II
    Synthetic: YES

 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  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3NI2Ligand/IonNICKEL (II) ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3NI-1Ligand/IonNICKEL (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL-1Ligand/IonGLYCEROL
3NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGOL A:1228 , GLY B:110 , SER B:112 , LYS B:115BINDING SITE FOR RESIDUE CL B1226
2AC2SOFTWAREGLY B:155 , THR B:158BINDING SITE FOR RESIDUE CL B1227
3AC3SOFTWAREGLY A:110 , SER A:112 , LYS A:115 , HOH A:2078 , HOH A:2199BINDING SITE FOR RESIDUE CL A1226
4AC4SOFTWAREGLY A:155 , THR A:158BINDING SITE FOR RESIDUE CL A1227
5AC5SOFTWAREPRO A:40 , VAL A:41 , HOH A:2062 , HOH A:2074 , HOH A:2322 , HOH A:2323 , ARG B:107 , SER B:112 , TRP B:113 , CL B:1226 , HOH B:2176BINDING SITE FOR RESIDUE GOL A1228
6AC6SOFTWARENI A:1229 , HOH A:2324 , HOH A:2325 , HIS B:35 , HOH B:2048 , HOH B:2260BINDING SITE FOR RESIDUE NI B1228
7AC7SOFTWAREHIS A:35 , HOH A:2049 , HOH A:2050 , HOH A:2290 , HOH A:2324 , HOH A:2325 , NI B:1228BINDING SITE FOR RESIDUE NI A1229

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YG9)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:201 -Pro A:202
2Ala B:201 -Pro B:202

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YG9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YG9)

(-) Exons   (0, 0)

(no "Exon" information available for 2YG9)

(-) 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:207
 aligned with Q9RRB0_DEIRA | Q9RRB0 from UniProtKB/TrEMBL  Length:225

    Alignment length:207
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       
         Q9RRB0_DEIRA    19 LPAVLPPLTDHAGAVAHLSRDPVLAQVTSLCGELPVLAPTPDPFGRLVRSVAGQQLSVKAAQAIYGRLEGLPGGVVPAALLKVSGDDLRGVGLSWAKVRTVQAAAAAAVSGQIDFAHLSGQPDELVIAELVQLPGIGRWTAEMFLLFALARPDVFSSGDLALRQGVERLYPGEDWRDVTARWAPYRSLASRYLWANSARMQAGGAPL 225
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhh.hhhhhhhhhhhh.........hhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhh....hhhhhhhhhhhh..........hhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yg9 A  19 LPAVLPPLTDHAGAVAHLSRDPVLAQVTSLCGELPVLAPTPDPFGRLVRSVAGQQLSVKAAQAIYGRLEGLPGGVVPAALLKVSGDDLRGVGLSWAKVRTVQAAAAAAVSGQIDFAHLSGQPDELVIAELVQLPGIGRWTAEMFLLFALARPDVFSSGDLALRQGVERLYPGEDWRDVTARWAPYRSLASRYLWANSARMQAGGAPL 225
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       


Chain B from PDB  Type:PROTEIN  Length:206
 aligned with Q9RRB0_DEIRA | Q9RRB0 from UniProtKB/TrEMBL  Length:225

    Alignment length:206
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219      
         Q9RRB0_DEIRA    20 PAVLPPLTDHAGAVAHLSRDPVLAQVTSLCGELPVLAPTPDPFGRLVRSVAGQQLSVKAAQAIYGRLEGLPGGVVPAALLKVSGDDLRGVGLSWAKVRTVQAAAAAAVSGQIDFAHLSGQPDELVIAELVQLPGIGRWTAEMFLLFALARPDVFSSGDLALRQGVERLYPGEDWRDVTARWAPYRSLASRYLWANSARMQAGGAPL 225
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------HhH-GPD-2yg9B01 B:66-204                                                                                                                   --------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------HhH-GPD-2yg9B02 B:66-204                                                                                                                   --------------------- Pfam domains (2)
         Sec.struct. author .........hhhhhhhhh.hhhhhhhhhhhh.........hhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh..........hhhhhhhhhhhh...hhhhhhhh...hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yg9 B  20 PAVLPPLTDHAGAVAHLSRDPVLAQVTSLCGELPVLAPTPDPFGRLVRSVAGQQLSVKAAQAIYGRLEGLPGGVVPAALLKVSGDDLRGVGLSWAKVRTVQAAAAAAVSGQIDFAHLSGQPDELVIAELVQLPGIGRWTAEMFLLFALARPDVFSSGDLALRQGVERLYPGEDWRDVTARWAPYRSLASRYLWANSARMQAGGAPL 225
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219
   Legend:   → Mismatch (orange background)
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  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 2YG9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YG9)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: HHH (112)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9RRB0_DEIRA | Q9RRB0)
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: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:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
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.
    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.

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(-) Related Entries Specified in the PDB File

2yg8 STRUCTURE OF AN UNUSUAL 3-METHYLADENINE DNA GLYCOSYLASE II (ALKA) FROM DEINOCOCCUS RADIODURANS