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(-) Description

Title :  CRYSTAL STRUCTURE OF DNA-3-METHYLADENINE GLYCOSIDASE (10174367) FROM BACILLUS HALODURANS AT 2.55 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  25 May 06  (Deposition) - 25 Jul 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  10174367, Dna-3-Methyladenine Glycosidase, Ec 3. 2. 2. -, Structural Genomics, Psi-2, Protein Structure Initiative, Joint Center For Structural Genomics, Jcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Dna-3-Methyladenine Glycosidase (10174367) From Bacillus Halodurans At 2. 55 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DNA-3-METHYLADENINE GLYCOSIDASE
    Chains: A, B, C
    EC Number: 3.2.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 10174367
    Organism Scientific: BACILLUS HALODURANS
    Organism Taxid: 86665

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric Unit (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2H56)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2H56)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ala A:187 -Pro A:188
2Ala B:187 -Pro B:188
3Ala C:187 -Pro C:188

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2H56)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2H56)

(-) Exons   (0, 0)

(no "Exon" information available for 2H56)

(-) 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:218
 aligned with Q9KC25_BACHD | Q9KC25 from UniProtKB/TrEMBL  Length:221

    Alignment length:218
                             1                                                                                                                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209        
         Q9KC25_BACHD     - -MRYFSTDSPEVKTIVAQDSRLFQFIEIAGEVQLPTKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLVGGALEKPEQLYRVSDEALRQAGVSKRKIEYIRHVCEHVESGRLDFTELEGAEATTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLSVGDVGLQRGAKWLYGNGEGDGKKLLIYHGKAWAPYETVACLYLWKAAGTFAEEYRSLEELLHH 217
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhh.hhhhhhhhhhhh.eeee...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhh....hhhhhhhhhhhh..........hhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h56 A   0 HmRYFSTDSPEVKTIVAQDSRLFQFIEIAGEVQLPTKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLVGGALEKPEQLYRVSDEALRQAGVSKRKIEYIRHVCEHVESGRLDFTELEGAEATTVIEKLTAIKGIGQWTAEmFmmFSLGRLDVLSVGDVGLQRGAKWLYGNGEGDGKKLLIYHGKAWAPYETVACLYLWKAAGTFAEEYRSLEELLHH 217
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139 | ||  149       159       169       179       189       199       209        
                             |                                                                                                                                         141-MSE                                                                        
                             1-MSE                                                                                                                                       143-MSE                                                                      
                                                                                                                                                                          144-MSE                                                                     


Chain B from PDB  Type:PROTEIN  Length:217
 aligned with Q9KC25_BACHD | Q9KC25 from UniProtKB/TrEMBL  Length:221

    Alignment length:217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
         Q9KC25_BACHD     1 MRYFSTDSPEVKTIVAQDSRLFQFIEIAGEVQLPTKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLVGGALEKPEQLYRVSDEALRQAGVSKRKIEYIRHVCEHVESGRLDFTELEGAEATTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLSVGDVGLQRGAKWLYGNGEGDGKKLLIYHGKAWAPYETVACLYLWKAAGTFAEEYRSLEELLHH 217
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...hhhhhhhh..hhhhhhhhhhhh.eee....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhh....hhhhhhhhhhhh..........hhhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h56 B   1 mRYFSTDSPEVKTIVAQDSRLFQFIEIAGEVQLPTKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLVGGALEKPEQLYRVSDEALRQAGVSKRKIEYIRHVCEHVESGRLDFTELEGAEATTVIEKLTAIKGIGQWTAEmFmmFSLGRLDVLSVGDVGLQRGAKWLYGNGEGDGKKLLIYHGKAWAPYETVACLYLWKAAGTFAEEYRSLEELLHH 217
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140| ||   150       160       170       180       190       200       210       
                            1-MSE                                                                                                                                     141-MSE                                                                        
                                                                                                                                                                        143-MSE                                                                      
                                                                                                                                                                         144-MSE                                                                     


Chain C from PDB  Type:PROTEIN  Length:204
 aligned with Q9KC25_BACHD | Q9KC25 from UniProtKB/TrEMBL  Length:221

    Alignment length:220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
         Q9KC25_BACHD     1 MRYFSTDSPEVKTIVAQDSRLFQFIEIAGEVQLPTKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQLVGGALEKPEQLYRVSDEALRQAGVSKRKIEYIRHVCEHVESGRLDFTELEGAEATTVIEKLTAIKGIGQWTAEMFMMFSLGRLDVLSVGDVGLQRGAKWLYGNGEGDGKKLLIYHGKAWAPYETVACLYLWKAAGTFAEEYRSLEELLHHGNQ 220
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...hhhhhhhhh.hhhhhhhhhhhh.eee....hhhhhhhhhhhhh..hhhhhhhhhhhhhhh---..........-hhhhhhh.-.hhhhhhhhhhhhhhhhh......-------.hhhhhhh----.hhhhhhhhhhhh..........hhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h56 C   1 mRYFSTDSPEVKTIVAQDSRLFQFIEIAGEVQLPTKPNPFQSLVSSIVEQQLSIKAASAIYGRVEQL---ALEKPEQLYR-SDEALRQA-VSKRKIEYIRHVCEHVESGRLDFT-------TTVIEKLT----IGQWTAEmFmmFSLGRLDVLSVGDVGLQRGAKWLYGNGEGDGKKLLIYHGKAWAPYETVACLYLWKAAGTFAEEYRSLEELLHHGNQ 220
                            |       10        20        30        40        50        60      |  -|       80 |      |-|      100       110   |     - |      |-   |   140| ||   150       160       170       180       190       200       210       220
                            1-MSE                                                            67  71       80 |     89 |                    114     122    129  134      | ||                                                                            
                                                                                                            82       91                                               141-MSE                                                                           
                                                                                                                                                                        143-MSE                                                                         
                                                                                                                                                                         144-MSE
   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 2H56)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2H56)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2H56)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q9KC25_BACHD | Q9KC25)
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.
    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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