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(-) Description

Title :  THE STRUCTURAL BASIS OF 3-METHYLADENINE RECOGNITION BY 3-METHYLADENINE DNA GLYCOSYLASE I (TAG) FROM STAPHYLOCOCCUS AUREUS
 
Authors :  X. Yan, J. H. Naismith
Date :  08 Feb 12  (Deposition) - 22 Feb 12  (Release) - 20 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Keywords :  Hydrolase, 3-Methyladenine Recognition, Dna Repair (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Zhu, X. Yan, L. G. Carter, H. Liu, S. Graham, P. J. Coote, J. H. Naismit
A Model For 3-Methyladenine Recognition By 3-Methyladenine Dna Glycosylase I (Tag) From Staphylococcus Aureus.
Acta Crystallogr. , Sect. F V. 68 610 2012
PubMed-ID: 22684054  |  Reference-DOI: 10.1107/S1744309112016363

(-) Compounds

Molecule 1 - DNA-3-METHYLADENINE GLYCOSYLASE I
    Chains: A, B, C, D, E
    EC Number: 3.2.2.20
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST14
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: C43
    Expression System Vector Type: PLASMID
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Strain: MSSA476
    Synonym: 3-METHYLADENINE DNA GLYCOSYLASE I

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): A    
Biological Unit 2 (1x):  B   
Biological Unit 3 (1x):   C  
Biological Unit 4 (1x):    D 
Biological Unit 5 (1x):     E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1ADK5Ligand/Ion3-METHYL-3H-PURIN-6-YLAMINE
2SO44Ligand/IonSULFATE ION
3ZN5Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ADK1Ligand/Ion3-METHYL-3H-PURIN-6-YLAMINE
2SO41Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ADK1Ligand/Ion3-METHYL-3H-PURIN-6-YLAMINE
2SO4-1Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1ADK1Ligand/Ion3-METHYL-3H-PURIN-6-YLAMINE
2SO41Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1ADK1Ligand/Ion3-METHYL-3H-PURIN-6-YLAMINE
2SO4-1Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 5 (2, 3)
No.NameCountTypeFull Name
1ADK1Ligand/Ion3-METHYL-3H-PURIN-6-YLAMINE
2SO42Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:4 , HIS A:17 , HIS A:175 , CYS A:179BINDING SITE FOR RESIDUE ZN A 200
02AC2SOFTWARETYR A:13 , TYR A:16 , TRP A:21 , GLU A:38 , TRP A:46 , HOH A:2097BINDING SITE FOR RESIDUE ADK A 400
03AC3SOFTWARECYS B:4 , HIS B:17 , HIS B:175 , CYS B:179BINDING SITE FOR RESIDUE ZN B 200
04AC4SOFTWAREPHE B:6 , TYR B:13 , TYR B:16 , TRP B:21 , GLU B:38 , TRP B:46 , ALA B:168 , HOH B:2218BINDING SITE FOR RESIDUE ADK B 400
05AC5SOFTWARECYS C:4 , HIS C:17 , HIS C:175 , CYS C:179BINDING SITE FOR RESIDUE ZN C 200
06AC6SOFTWAREPHE C:6 , TYR C:13 , TYR C:16 , TRP C:21 , GLU C:38 , TRP C:46 , HOH C:2162 , HOH C:2167BINDING SITE FOR RESIDUE ADK C 400
07AC7SOFTWARECYS D:4 , HIS D:17 , HIS D:175 , CYS D:179BINDING SITE FOR RESIDUE ZN D 200
08AC8SOFTWAREPHE D:6 , TYR D:13 , TYR D:16 , TRP D:21 , GLU D:38 , TRP D:46 , HOH D:2029 , HOH D:2155BINDING SITE FOR RESIDUE ADK D 400
09AC9SOFTWARECYS E:4 , HIS E:17 , HIS E:175 , CYS E:179BINDING SITE FOR RESIDUE ZN E 200
10BC1SOFTWAREPHE E:6 , TYR E:13 , TYR E:16 , TRP E:21 , GLU E:38 , TRP E:46 , HOH E:2103BINDING SITE FOR RESIDUE ADK E 400
11BC2SOFTWAREGLY A:158 , PRO A:159 , VAL A:160 , THR A:161 , HOH A:2256 , HOH A:2275 , HOH A:2276 , HOH A:2277 , HOH A:2278BINDING SITE FOR RESIDUE SO4 A1187
12BC3SOFTWAREGLY C:158 , PRO C:159 , VAL C:160 , THR C:161 , HOH C:2161 , HOH C:2168 , HOH C:2169BINDING SITE FOR RESIDUE SO4 C1187
13BC4SOFTWAREGLY E:158 , PRO E:159 , VAL E:160 , THR E:161 , HOH E:2092 , HOH E:2104 , HOH E:2105BINDING SITE FOR RESIDUE SO4 E1187
14BC5SOFTWARELYS E:33 , LYS E:53 , HOH E:2033BINDING SITE FOR RESIDUE SO4 E1188

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AIA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AIA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AIA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AIA)

(-) Exons   (0, 0)

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(-) 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:188
                                                                                                                                                                                                                            
               SCOP domains d4aiaa_ A: automated matches                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh....hhhhhhhhhhh......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee....hhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhh..ee............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aia A  -1 GAMNECAFGTKDPVYLNYHDHVWGQPLYDSKALFKLLALESQHAGLSWLTILKKKEAYEEAFYDFEPEKVAQMTAQDIDRLMTFPNIVHHRKKLEAIVNQAQGYLKIEQAYGSFSKFLWSYVNGKPKDLQYEHASDRITVDDTATQLSKDLKQYGFKFLGPVTVFSFLEAAGLYDAHLKDCPSKPKHN 186
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178        


Chain B from PDB  Type:PROTEIN  Length:185
                                                                                                                                                                                                                         
               SCOP domains d4aiab_ B: automated matches                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhh......hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee....hhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhh..ee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aia B   1 MNECAFGTKDPVYLNYHDHVWGQPLYDSKALFKLLALESQHAGLSWLTILKKKEAYEEAFYDFEPEKVAQMTAQDIDRLMTFPNIVHHRKKLEAIVNQAQGYLKIEQAYGSFSKFLWSYVNGKPKDLQYEHASDRITVDDTATQLSKDLKQYGFKFLGPVTVFSFLEAAGLYDAHLKDCPSKPKH 185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     


Chain C from PDB  Type:PROTEIN  Length:186
                                                                                                                                                                                                                          
               SCOP domains d4aiac_ C: automated matches                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhh......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee....hhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhh..ee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4aia C   1 MNECAFGTKDPVYLNYHDHVWGQPLYDSKALFKLLALESQHAGLSWLTILKKKEAYEEAFYDFEPEKVAQMTAQDIDRLMTFPNIVHHRKKLEAIVNQAQGYLKIEQAYGSFSKFLWSYVNGKPKDLQYEHASDRITVDDTATQLSKDLKQYGFKFLGPVTVFSFLEAAGLYDAHLKDCPSKPKHN 186
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      


Chain D from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains d4aiad_ D: automated matches                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh....hhhhhhhhhhh......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee....hhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhh..ee............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aia D  -1 GAMNECAFGTKDPVYLNYHDHVWGQPLYDSKALFKLLALESQHAGLSWLTILKKKEAYEEAFYDFEPEKVAQMTAQDIDRLMTFPNIVHHRKKLEAIVNQAQGYLKIEQAYGSFSKFLWSYVNGKPKDLQYEHASDRITVDDTATQLSKDLKQYGFKFLGPVTVFSFLEAAGLYDAHLKDCPSKPKHN 186
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178        


Chain E from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains d4aiae_ E: automated matches                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh....hhhhhhhhhhh......hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee....hhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhh..ee............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aia E  -1 GAMNECAFGTKDPVYLNYHDHVWGQPLYDSKALFKLLALESQHAGLSWLTILKKKEAYEEAFYDFEPEKVAQMTAQDIDRLMTFPNIVHHRKKLEAIVNQAQGYLKIEQAYGSFSKFLWSYVNGKPKDLQYEHASDRITVDDTATQLSKDLKQYGFKFLGPVTVFSFLEAAGLYDAHLKDCPSKPKHN 186
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178
   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  (1, 5)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

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(no "CATH Domain" information available for 4AIA)

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(-) Related Entries Specified in the PDB File

2jg6 CRYSTAL STRUCTURE OF A 3-METHYLADENINE DNA GLYCOSYLASE I FROM STAPHYLOCOCCUS AUREUS
4ai4 CRYSTAL STRUCTURE OF E38Q MUTANT OF 3-METHYLADENINE DNA GLYCOSYLASE I FROM STAPHYLOCOCCUS AUREUS
4ai5 CRYSTAL STRUCTURE OF Y16F OF 3-METHYLADENINE DNA GLYCOSYLASE I (TAG) IN COMPLEX WITH 3-METHYLADENINE