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(-) Description

Title :  A NON-COGNATE COMPLEX OF ESCHERICHIA COLI DNA ADENINE METHYLTRANSFERASE (DAM) WITH DNA AND SINEFUNGIN
 
Authors :  J. R. Horton, X. Cheng
Date :  15 Nov 14  (Deposition) - 15 Apr 15  (Release) - 20 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
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(*TP*CP*TP*AP*GP*AP*TP*CP*TP*AP*GP*A)-3')
    Chains: F, 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  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2SFG1Ligand/IonSINEFUNGIN

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:10 , ALA A:11 , GLY A:12 , LYS A:14 , PRO A:34 , PHE A:35 , VAL A:36 , ALA A:38 , GLY A:39 , SER A:40 , ASP A:54 , ILE A:55 , SER A:164 , TYR A:165 , ASP A:181 , HOH A:409 , HOH A:414 , HOH A:437BINDING SITE FOR RESIDUE SFG A 301
2AC2SOFTWAREARG A:95 , GLU A:130 , DA G:10BINDING SITE FOR RESIDUE EDO A 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RTJ)

(-) 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:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhh....eeee.....hhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhh.eeeee.hhhhhhh.....eeeee............hhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhh...eeeee.........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rtj A   3 KNRAFLKWAGGKYPLLDDIKRHLPKGECLVEPFVGAGSVFLNTDFSRYILADINSDLISLYNIVKMRTDEYVQAARELFVPETNCAEVYYQFREEFNKSQDPFRRAVLFLYLNRYGYNGLCRYNLRGEFNVPFGRYKKPYFPEAELYHFAEKAQNAFFYCESYADSMARADDSSVVYCDPPYAPLSTNSFTLEQQAHLAEIAEGLVERHIPVLISNHDTMLTREWYQRAKLHVVKVRRRKKVDELLALYKP 270
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182     ||201       211       221       231       241       259       269 
                                                                                                                                                                                                                   188|                                                249|            
                                                                                                                                                                                                                    198                                                 258            


Chain F from PDB  Type:DNA  Length:12
                                            
                 4rtj F   1 TCTAGATCTAGA  12
                                    10  


Chain G from PDB  Type:DNA  Length:12
                                            
                 4rtj G   1 TCTAGATCTAGA  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 4RTJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4rtk 4rtl 4rtm 4rtn 4rto 4rtp 4rtq 4rtr 4rts

(-) Related Entries Specified in the PDB File

2gip STRUCTURE OF E. COLI DNA ADENINE METHYLTRANSFERASE (DAM)
2ore BINARY STRUCTURE OF E.COLI DAM
4rtk
4rtl
4rtm
4rtn
4rto
4rtp
4rtq
4rtr
4rts