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(-) Description

Title :  DPNM DNA ADENINE METHYLTRANSFERASE FROM STREPTOCCOCUS PNEUMONIAE COMPLEXED WITH S-ADENOSYLMETHIONINE
 
Authors :  P. H. Tran, Z. R. Korszun, S. Cerritelli, S. S. Springhorn, S. A. Lacks
Date :  03 Sep 98  (Deposition) - 23 Dec 98  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Dna Adenine Methyltransferase, Methyltransferase, Methylase, Dna Methyltransferase Group Alpha, S-Adenosylmethionine, Dna N6-Adenine Methylation, Dpnii Restriction-Modification System, Gatc Methylation, Rossmann Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. H. Tran, Z. R. Korszun, S. Cerritelli, S. S. Springhorn, S. A. Lacks
Crystal Structure Of The Dpnm Dna Adenine Methyltransferase From The Dpnii Restriction System Of Streptococcus Pneumoniae Bound To S-Adenosylmethionine.
Structure V. 6 1563 1998
PubMed-ID: 9862809  |  Reference-DOI: 10.1016/S0969-2126(98)00154-3
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (ADENINE-SPECIFIC METHYLTRANSFERASE DPNII 1)
    Chains: A
    EC Number: 2.1.1.72
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: DPNM
    Expression System Plasmid: PLS211
    Expression System Taxid: 562
    Gene: DPNM
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313
    Other Details: S-ADENOSYLMETHIONINE
    Strain: HB264
    Synonym: M.DPNII 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1HG1Ligand/IonMERCURY (II) ION
2SAM1Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:70BINDING SITE FOR RESIDUE HG A 301
2AC2SOFTWARETRP A:17 , THR A:18 , GLY A:19 , GLY A:20 , LYS A:21 , PHE A:43 , VAL A:44 , GLY A:45 , GLY A:46 , GLY A:47 , ALA A:48 , ASP A:62 , PHE A:63 , GLY A:176 , ASP A:177 , PHE A:178 , ASP A:194 , PRO A:195 , HOH A:402 , HOH A:409 , HOH A:444 , HOH A:902BINDING SITE FOR RESIDUE SAM A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DPM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DPM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DPM)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1N6_MTASEPS00092 N-6 Adenine-specific DNA methylases signature.MTD21_STREE191-197  1A:191-197

(-) Exons   (0, 0)

(no "Exon" information available for 2DPM)

(-) 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:258
 aligned with MTD21_STREE | P04043 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:275
                                    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     
          MTD21_STREE    10 TLQPFTKWTGGKRQLLPVIRELIPKTYNRYFEPFVGGGALFFDLAPKDAVINDFNAELINCYQQIKDNPQELIEILKVHQEYNSKEYYLDLRSADRDERIDMMSEVQRAARILYMLRVNFNGLYRVNSKNQFNVPYGRYKNPKIVDEELISAISVYINNNQLEIKVGDFEKAIVDVRTGDFVYFDPPYIPLSETSAFTSYTHEGFSFADQVRLRDAFKRLSDTGAYVMLSNSSSALVEELYKDFNIHYVEATRTNGAKSSSRGKISEIIVTNYEK 284
               SCOP domains d2dpma_ A: DNA methylase DpnM                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2dpmA01 A:10-64,A:168-284 Vaccinia Virus protein VP39  2dpmA02 A:65-167 Adenine-specific Methyltransferase, Domain 2                                          2dpmA01 A:10-64,A:168-284 Vaccini     a Virus protein VP39                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhh.......eee......hhhhhh...eeeeee..hhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhh............hhhhhhhhhhhhhh............................hhhhhhhhhhhhh.eeeeee..hhhhh.......eeeee......-----..........hhhhhhhhhhhhhhh....eeeeeee..hhhhhh....eeeee.------------....eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------N6_MTAS--------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dpm A  10 TLQPFTKWTGGKRQLLPVIRELIPKTYNRYFEPFVGGGALFFDLAPKDAVINDFNAELINCYQQIKDNPQELIEILKVHQEYNSKEYYLDLRSADRDERIDMMSEVQRAARILYMLRVNFNGLYRVNSKNQFNVPYGRYKNPKIVDEELISAISVYINNNQLEIKVGDFEKAIVDVRTGDFVYFDPPYIPL-----FTSYTHEGFSFADQVRLRDAFKRLSDTGAYVMLSNSSSALVEELYKDFNIHYVE------------GKISEIIVTNYEK 284
                                    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         -  |    279     
                                                                                                                                                                                                                        200   206                                                  259          272
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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, 1)

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

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DPM)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MTD21_STREE | P04043)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0009007    site-specific DNA-methyltransferase (adenine-specific) activity    Catalysis of the reaction: S-adenosyl-L-methionine + DNA adenine = S-adenosyl-L-homocysteine + DNA 6-methylaminopurine.
    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:0032775    DNA methylation on adenine    The covalent transfer of a methyl group to N-6 of adenine 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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