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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI DNA ADENINE METHYLTRANSFERASE IN COMPLEX WITH AZA-SAM
 
Authors :  J. E. Harmer, P. L. Roach
Date :  20 Aug 12  (Deposition) - 26 Feb 14  (Release) - 26 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  D,E,F
Biol. Unit 1:  D,E,F  (1x)
Biol. Unit 2:  D  (1x)
Biol. Unit 3:  E  (1x)
Biol. Unit 4:  F  (1x)
Keywords :  Transferase, Methylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. E. Harmer, J. C. Mckelvie, G. Hobley, P. L. Roach
Structural Basis Of Selective N-6 Adenine Methyltransferase Inhibition By Transition State Mimic
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DNA ADENINE METHYLASE
    Chains: D, E, F
    EC Number: 2.1.1.72
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: B3387, DAM, JW3350
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
    Synonym: DNA ADENINE METHYLTRANSFERASE, DEOXYADENOSYL- METHYLTRANSFERASE, M.ECODAM

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : DEF
Biological Unit 1 (1x): DEF
Biological Unit 2 (1x): D  
Biological Unit 3 (1x):  E 
Biological Unit 4 (1x):   F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
10Y03Ligand/Ion5'-{[(3S)-3-AMINO-3-CARBOXYPROPYL]AMINO}-5'-DEOXYADENOSINE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
10Y03Ligand/Ion5'-{[(3S)-3-AMINO-3-CARBOXYPROPYL]AMINO}-5'-DEOXYADENOSINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
10Y01Ligand/Ion5'-{[(3S)-3-AMINO-3-CARBOXYPROPYL]AMINO}-5'-DEOXYADENOSINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
10Y01Ligand/Ion5'-{[(3S)-3-AMINO-3-CARBOXYPROPYL]AMINO}-5'-DEOXYADENOSINE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
10Y01Ligand/Ion5'-{[(3S)-3-AMINO-3-CARBOXYPROPYL]AMINO}-5'-DEOXYADENOSINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP D:10 , PHE D:35 , ASP D:54 , ILE D:55 , SER D:164 , TYR D:165 , ASP D:181 , PRO D:182 , PRO D:183 , TYR D:184BINDING SITE FOR RESIDUE 0Y0 D 301
2AC2SOFTWARETRP E:10 , ALA E:11 , PRO E:34 , PHE E:35 , ASP E:54 , ILE E:55 , SER E:164 , TYR E:165 , ASP E:181 , PRO E:182 , PRO E:183 , TYR E:184BINDING SITE FOR RESIDUE 0Y0 E 301
3AC3SOFTWARETRP F:10 , ALA F:11 , PRO F:34 , PHE F:35 , GLY F:37 , ASP F:54 , ILE F:55 , TYR F:165 , ASP F:181 , PRO F:182 , PRO F:183 , TYR F:184BINDING SITE FOR RESIDUE 0Y0 F 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GOM)

(-) 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 D from PDB  Type:PROTEIN  Length:243
                                                                                                                                                                                                                                                                                   
               SCOP domains d4gomd_ D: automated matches                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhh....eeee.....hhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhh..eeeee.hhhhhhh.....eeeee..........hhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhh...eeeee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gom D   3 KNRAFLKWAGGKYPLLDDIKRHLPKGECLVEPFVGAGSVFLNTDFSRYILADINSDLISLYNIVKMRTDEYVQAARELFVPETNCAEVYYQFREEFNKSQDPFRRAVLFLYLNRYGYNGLCRYNLRGEFNVPFGRYKKPYFPEAELYHFAEKAQNAFFYCESYADSMARADDASVVYCDPPYAPLNSFTLEQQAHLAEIAEGLVERHIPVLISNHDTMLTREWYQRAKLHVVKVDELLALYKP 270
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182    || 203       213       223       233       243  ||   267   
                                                                                                                                                                                                                  187|                                            246|         
                                                                                                                                                                                                                   199                                             261         


Chain E from PDB  Type:PROTEIN  Length:244
                                                                                                                                                                                                                                                                                    
               SCOP domains d4gome_ E: automated matches                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhh....eeee.....hhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhh.eeeee.hhhhhhh.....eeeee.........hhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhh...eeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gom E   3 KNRAFLKWAGGKYPLLDDIKRHLPKGECLVEPFVGAGSVFLNTDFSRYILADINSDLISLYNIVKMRTDEYVQAARELFVPETNCAEVYYQFREEFNKSQDPFRRAVLFLYLNRYGYNGLCRYNLRGEFNVPFGRYKKPYFPEAELYHFAEKAQNAFFYCESYADSMARADDASVVYCDPPYAPLSFTLEQQAHLAEIAEGLVERHIPVLISNHDTMLTREWYQRAKLHVVKVKVDELLALYKP 270
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182    || 204       214       224       234       244  ||   266    
                                                                                                                                                                                                                  187|                                            247|          
                                                                                                                                                                                                                   200                                             260          


Chain F from PDB  Type:PROTEIN  Length:244
                                                                                                                                                                                                                                                                                    
               SCOP domains d4gomf_ F: automated matches                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhh....eeee.....hhhhhh....eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhh.eeee..hhhhhhhh....eeeee..........hhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhh...eeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gom F   3 KNRAFLKWAGGKYPLLDDIKRHLPKGECLVEPFVGAGSVFLNTDFSRYILADINSDLISLYNIVKMRTDEYVQAARELFVPETNCAEVYYQFREEFNKSQDPFRRAVLFLYLNRYGYNGLCRYNLRGEFNVPFGRYKKPYFPEAELYHFAEKAQNAFFYCESYADSMARADDASVVYCDPPYAPLNSFTLEQQAHLAEIAEGLVERHIPVLISNHDTMLTREWYQRAKLHVVKVVDELLALYKP 270
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182    || 203       213       223       233       243   ||  266    
                                                                                                                                                                                                                  187|                                             247|         
                                                                                                                                                                                                                   199                                              261
   Legend:   → Mismatch (orange background)
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  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  (1, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GOM)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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  4gom
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  DMA_ECOLI | P0AEE8
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  2.1.1.72
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 Related Entries

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

UniProtKB/Swiss-Prot
        DMA_ECOLI | P0AEE8: 2g1p 2ore 4gbe 4gol 4gon 4goo 4rtj 4rtk 4rtl 4rtm 4rtn 4rto 4rtp 4rtq 4rtr 4rts

(-) Related Entries Specified in the PDB File

4gbe 4gol 4gon 4goo