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(-) Description

Title :  BINARY STRUCTURE OF T4DAM WITH ADOHCY
 
Authors :  Z. Yang, J. R. Horton, L. Zhou, X. J. Zhang, A. Dong, X. Zhang, S. L. Schlagman, V. Kossykh, S. Hattman, X. Cheng
Date :  17 Jul 03  (Deposition) - 23 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  T4Dam, Methyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Yang, J. R. Horton, L. Zhou, X. J. Zhang, A. Dong, X. Zhang, S. L. Schlagman, V. Kossykh, S. Hattman, X. Cheng
Structure Of The Bacteriophage T4 Dna Adenine Methyltransferase
Nat. Struct. Biol. V. 10 849 2003
PubMed-ID: 12937411  |  Reference-DOI: 10.1038/NSB973
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA ADENINE METHYLASE
    Chains: A
    EC Number: 2.1.1.72
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PJW2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DAM
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Synonym: DEOXYADENOSYL-METHYLTRANSFERASE, M.ECOT4DAM

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:7 , ASN A:10 , LYS A:11 , PHE A:32 , CYS A:33 , GLY A:34 , GLY A:35 , SER A:37 , ASP A:50 , ILE A:51 , GLN A:52 , HIS A:156 , PHE A:157 , ASP A:171 , TYR A:181 , PHE A:184 , HOH A:314 , HOH A:318 , HOH A:322BINDING SITE FOR RESIDUE SAH A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q0S)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:44 -Pro A:45

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q0S)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1N6_MTASEPS00092 N-6 Adenine-specific DNA methylases signature.DMA_BPT4168-174  1A:168-174

(-) Exons   (0, 0)

(no "Exon" information available for 1Q0S)

(-) 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:241
 aligned with DMA_BPT4 | P04392 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:259
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250         
             DMA_BPT4     1 MLGAIAYTGNKQSLLPELKSHFPKYNRFVDLFCGGLSVSLNVNGPVLANDIQEPIIEMYKRLINVSWDDVLKVIKQYKLSKTSKEEFLKLREDYNKTRDPLLLYVLHFHGFSNMIRINDKGNFTTPFGKRTINKNSEKQYNHFKQNCDKIIFSSLHFKDVKILDGDFVYVDPPYLITVADYNKFWSEDEEKDLLNLLDSLNDRGIKFGQSNVLEHHGKENTLLKEWSKKYNVKHLNKKYVFNIYHSKEKNGTDEVYIFN 259
               SCOP domains d1q0sa_ A: DNA methylase T4DAM                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1q0sA01 A:1-51,A:147-259                           1q0sA02 A:52-146 Adenine-specific Methyltransferase, Domain 2                                  1q0sA01 A:1-51,A:147-259 Vaccinia Virus protein VP39                                                              CATH domains
               Pfam domains ------MethyltransfD12-1q0sA01 A:7-235                                                                                                                                                                                                      ------------------------ Pfam domains
         Sec.struct. author .............hhhhhhh......eeee.......hhhhh...eeee..hhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhh..eeee..hhhhh.....eeeee........hhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhh..eee..------------------.eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------N6_MTAS------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q0s A   1 MLGAIAYTGNKQSLLPELKSHFPKYNRFVDLFCGGLSVSLNVNGPVLANDIQEPIIEMYKRLINVSWDDVLKVIKQYKLSKTSKEEFLKLREDYNKTRDPLLLYVLHFHGFSNMIRINDKGNFTTPFGKRTINKNSEKQYNHFKQNCDKIIFSSLHFKDVKILDGDFVYVDPPYLITVADYNKFWSEDEEKDLLNLLDSLNDRGIKFGQSNVLEHHGKENTLLKEWSKKYNVKHL------------------EVYIFN 259
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    |    -         -   |     
                                                                                                                                                                                                                                                                    235                254
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DMA_BPT4 | P04392)
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:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DMA_BPT4 | P04392: 1q0t 1yf3 1yfj 1yfl

(-) Related Entries Specified in the PDB File

1q0t TERNARY STRUCTURE OF T4DAM WITH ADOHCY AND DNA