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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE DNA MODIFICATION METHYLTRANSFERASE ENCODED WITHIN PROPHAGE CP-933R (E.COLI)
 
Authors :  Y. Patskovsky, U. A. Ramagopal, R. Toro, M. Gilmore, M. Iizuka, J. M. Sau S. K. Burley, S. C. Almo, New York Sgx Research Center For Struct Genomics (Nysgxrc)
Date :  10 Feb 09  (Deposition) - 24 Feb 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Methyltransferase, Dna-Binding, Nad-Binding, Structural Genomics, Protein Structure Initiative, Psi, New York Structural Genomix Research Consortium, Nysgxrc, New York Sgx Research Center For Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, U. A. Ramagopal, R. Toro, M. Gilmore, M. Iizuka, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Dna Modification Methyltransferase Encoded Within Prophage Cp-933R (E. Coli)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CYTOSINE-SPECIFIC METHYLTRANSFERASE
    Atcc: 700927
    Chains: A
    EC Number: 2.1.1.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSGX3(BC)
    Expression System Strain: BL21(DE3)-CODON+RIL (STRATAGENE)
    Expression System Taxid: 562
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Gene: ECS1953, Z2389
    Organism Scientific: ESCHERICHIA COLI O157:H7 EDL933
    Organism Taxid: 155864

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:160 , ARG A:162 , SER A:350 , HOH A:502BINDING SITE FOR RESIDUE CL A 401
2AC2SOFTWARETYR A:98 , ARG A:130 , PHE A:134 , HOH A:455BINDING SITE FOR RESIDUE GOL A 402
3AC3SOFTWAREARG A:130 , ASN A:131 , PHE A:134 , SER A:259 , LYS A:260 , ILE A:261BINDING SITE FOR RESIDUE GOL A 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3G7U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3G7U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3G7U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3G7U)

(-) Exons   (0, 0)

(no "Exon" information available for 3G7U)

(-) 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    
   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:348
 aligned with Q8X8S5_ECO57 | Q8X8S5 from UniProtKB/TrEMBL  Length:383

    Alignment length:368
                             1                                                                                                                                                                                                                                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359        
         Q8X8S5_ECO57     - -MNVIDLFSGVGGLSLGAARAGFDVKMAVEIDQHAINTHAINFPRSLHVQEDVSLLNAEIIKGFFKNDMPIDGIIGGPPCQGFSSIGKGNPDDSRNQLYMHFYRLVSELQPLFFLAENVPGIMQEKYSGIRNKAFNLVSGDYDILDPIKVKASDYGAPTIRTRYFFIGVKKSLKLDISDEVFMPKMIDPVTVKDALYGLPDIIDANWQSDSESWRTIKKDRKGGFYEKLWGQIPRNVGDTESIAKLKNNIISGCTGTLHSKIVQERYASLSFGETDKISRSTRLDPNGFCPTLRAGTARDKGSFQAVRPIHPYHPRVITPREAARLQGFPDWFRFHVTKWHSFRQIGNSVSPIVAEYILKGLYNLLNK 367
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhh.eeeeee..hhhhhhhhhhhh...eee..hhhhhhhhhhhhhhh......eeee........-------hhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhh.eee...eeee.hhhh.....eeeeeeeee.hhh...hhhhh........hhhhhh.......eee........ee......hhhhhhhhh.......hhhhhhhhhh.ee...eee..hhhhhhhhhh........................-------------............hhhhhhhhhh.........hhhhhhhhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g7u A   0 SLNVIDLFSGVGGLSLGAARAGFDVKMAVEIDQHAINTHAINFPRSLHVQEDVSLLNAEIIKGFFKNDMPIDGIIGGPPCQGFS-------DDSRNQLYMHFYRLVSELQPLFFLAENVPGIMQEKYSGIRNKAFNLVSGDYDILDPIKVKASDYGAPTIRTRYFFIGVKKSLKLDISDEVFMPKMIDPVTVKDALYGLPDIIDANWQSDSESWRTIKKDRKGGFYEKLWGQIPRNVGDTESIAKLKNNIISGCTGTLHSKIVQERYASLSFGETDKISRSTRLDPNGFCPTL-------------VRPIHPYHPRVITPREAARLQGFPDWFRFHVTKWHSFRQIGNSVSPIVAEYILKGLYNLLNE 367
                                     9        19        29        39        49        59        69        79   |     - |      99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289  |      -      |309       319       329       339       349       359        
                                                                                                              83      91                                                                                                                                                                                                      292           306
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3G7U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3G7U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G7U)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8X8S5_ECO57 | Q8X8S5)
molecular function
    GO:0003886    DNA (cytosine-5-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + DNA containing cytosine = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0090116    C-5 methylation of cytosine    The covalent transfer of a methyl group to C-5 of cytosine in a DNA molecule.
    GO:0009307    DNA restriction-modification system    A defense process found in many bacteria and archaea that protects the organism from invading foreign DNA by cleaving it with a restriction endonuclease. The organism's own DNA is protected by methylation of a specific nucleotide, which occurs immediately following replication, in the same target site as the restriction enzyme.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.

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