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(-) Description

Title :  COMPLEX OF ESCHERICHIA COLI DNA ADENINE METHYLTRANSFERASE (DAM) WITH ADOMET AND A 5-BP NON-CANONICAL SITE (GTTTA )
 
Authors :  J. R. Horton, X. Cheng
Date :  15 Nov 14  (Deposition) - 15 Apr 15  (Release) - 20 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.39
Chains :  Asym./Biol. Unit :  A,F,G
Keywords :  Dam Methylation, Gatc Recognition, Base Flipping, Bacterial Virulence, Methylation-Independent Transcriptional Repressor, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Horton, X. Zhang, R. M. Blumenthal, X. Cheng
Structures Of Escherichia Coli Dna Adenine Methyltransferas (Dam) In Complex With A Non-Gatc Sequence: Potential Implications For Methylation-Independent Transcriptional Repression.
Nucleic Acids Res. V. 43 4296 2015
PubMed-ID: 25845600  |  Reference-DOI: 10.1093/NAR/GKV251

(-) Compounds

Molecule 1 - DNA ADENINE METHYLASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: HMS174(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DAM, ECMDS42_2833
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 1110693
    Strain: K-12 SUBSTR. MDS42
 
Molecule 2 - DNA (5'-D(*AP*CP*TP*TP*AP*AP*AP*CP*TP*TP*AP*A)-3')
    Chains: F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*TP*TP*TP*AP*AP*GP*TP*TP*TP*AP*AP*G)-3')
    Chains: G
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AFG

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:10 , ALA A:11 , GLY A:12 , PRO A:34 , PHE A:35 , ASP A:54 , ILE A:55 , SER A:164 , TYR A:165 , ASP A:181 , PRO A:182 , PRO A:183 , TYR A:184 , HOH A:427BINDING SITE FOR RESIDUE SAM A 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 4RTR)

(-) 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    
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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:244
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhh....eeee.....hhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhh..eeeee.hhhhhhh.....eeeee.........hhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhh...eeeee...eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rtr A   3 KNRAFLKWAGGKYPLLDDIKRHLPKGECLVEPFVGAGSVFLNTDFSRYILADINSDLISLYNIVKMRTDEYVQAARELFVPETNCAEVYYQFREEFNKSQDPFRRAVLFLYLNRYGYNGLCRYNLRGEFNVPFGRYKKPYFPEAELYHFAEKAQNAFFYCESYADSMARADDSSVVYCDPPYAPLSFTLEQQAHLAEIAEGLVERHIPVLISNHDTMLTREWYQRAKLHVVKVDELLALYKPGV 272
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182    || 204       214       224       234       244 ||    268    
                                                                                                                                                                                                                  187|                                           246|           
                                                                                                                                                                                                                   200                                            261           


Chain F from PDB  Type:DNA  Length:11
                                           
                 4rtr F   2 CTTAAACTTAA  12
                                    11 


Chain G from PDB  Type:DNA  Length:12
                                            
                 4rtr G   1 TTTAAGTTTAAG  12
                                    10
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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 4RTR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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  DMA_ECOLI | P0AEE8
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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 4gom 4gon 4goo 4rtj 4rtk 4rtl 4rtm 4rtn 4rto 4rtp 4rtq 4rts

(-) Related Entries Specified in the PDB File

2g1p STRUCTURE OF E. COLI DNA ADENINE METHYLTRANSFERASE (DAM) WITH COGNATE SEQUENCE
2ore BINARY STRUCTURE OF E.COLI DAM
4rtj
4rtk
4rtl
4rtm
4rtn
4rto
4rtp
4rtq
4rts