Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  T4DAM IN COMPLEX WITH ADOHCY AND 13-MER OLIGONUCLEOTIDE MAKING NON-AND SEMI-SPECIFIC (~1/4) CONTACT
 
Authors :  J. R. Horton, K. Liebert, S. Hattman, A. Jeltsch, X. Cheng
Date :  30 Dec 04  (Deposition) - 17 May 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.29
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  T4Dam, Methyltransferase, Dna, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Horton, K. Liebert, S. Hattman, A. Jeltsch, X. Cheng
Transition From Nonspecific To Specific Dna Interactions Along The Substrate-Recognition Pathway Of Dam Methyltransferase.
Cell(Cambridge, Mass. ) V. 121 349 2005
PubMed-ID: 15882618  |  Reference-DOI: 10.1016/J.CELL.2005.02.021
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*AP*CP*CP*AP*TP*GP*AP*TP*CP*TP*GP*AP*C)-3'
    Chains: C
    Engineered: YES
    Other Details: SYNTHESIZED BY NEW ENGLAND BIOLABS
    Synthetic: YES
 
Molecule 2 - 5'-D(*TP*GP*TP*CP*AP*GP*AP*TP*CP*AP*TP*GP*G)-3'
    Chains: D
    Engineered: YES
    Other Details: SYNTHESIZED BY NEW ENGLAND BIOLABS
    Synthetic: YES
 
Molecule 3 - DNA ADENINE METHYLASE
    Chains: A, B
    EC Number: 2.1.1.72
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PJW2
    Expression System Strain: GM 2971
    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

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
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 , PHE A:184 , HOH A:499 , HOH A:510BINDING SITE FOR RESIDUE SAH A 400
2AC2SOFTWARETYR B:7 , ASN B:10 , LYS B:11 , PHE B:32 , CYS B:33 , GLY B:34 , GLY B:35 , SER B:37 , ASP B:50 , ILE B:51 , GLN B:52 , LEU B:155 , HIS B:156 , PHE B:157 , ASP B:171 , PRO B:173 , TYR B:181 , PHE B:184 , HOH B:502 , HOH B:505BINDING SITE FOR RESIDUE SAH B 401
3AC3SOFTWARETYR B:7 , THR B:8 , GLN B:52 , MET B:114 , ILE B:115 , TYR B:181 , HOH B:512BINDING SITE FOR RESIDUE GOL B 497
4AC4SOFTWARETYR A:7 , THR A:8 , GLN A:52 , MET A:114 , ILE A:115BINDING SITE FOR RESIDUE GOL A 498

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YF3)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:44 -Pro A:45
2Gly B:44 -Pro B:45

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YF3)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1N6_MTASEPS00092 N-6 Adenine-specific DNA methylases signature.DMA_BPT4168-174
 		  2A:168-174
B:168-174

(-) Exons   (0, 0)

(no "Exon" information available for 1YF3)

(-) 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:259
 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 d1yf3a1 A:1-259 DNA methylase T4DAM                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1yf3A01 A:1-51,A:147-259                           1yf3A02 A:52-146 Adenine-specific Methyltransferase, Domain 2                                  1yf3A01 A:1-51,A:147-259 Vaccinia Virus protein VP39                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhh.....eeee.......hhhhh...eeee..hhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh....................hhhhhhhhhhhhh..eeee..hhhhh.....eeeee........hhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.ee..eehhhhhhhhh..eeee.hhhhhhhhhh........eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------N6_MTAS------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yf3 A   1 MLGAIAYTGNKQSLLPELKSHFPKYNRFVDLFCGGLSVSLNVNGPVLANDIQEPIIEMYKRLINVSWDDVLKVIKQYKLSKTSKEEFLKLREDYNKTRDPLLLYVLHFHGFSNMIRINYKGNFTTPFGKRTINKNSEKRFNHFKQNCDKIIFSSLHFKDVKILDGDFVYVDPPYLITVADYNKFWSEDEEKDLLNLLDSLNDRGIKFGLSNVLEHHGKENTLLKEWSKKYNVKHLNKKYVFNIYHSKEKNGTDEVYIFN 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         


Chain B from PDB  Type:PROTEIN  Length:249
 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 d1yf3b_ B: DNA methylase T4DAM                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1yf3B01 B:1-51,B:147-259                           1yf3B02 B:52-146 Adenine-specific Methyltransferase, Domain 2                                  1yf3B01 B:1-51,B:147-259 Vaccinia Virus protein VP39                                                              CATH domains
           Pfam domains (1) ------MethyltransfD12-1yf3B01 B:7-238                                                                                                                                                                                                         --------------------- Pfam domains (1)
           Pfam domains (2) ------MethyltransfD12-1yf3B02 B:7-238                                                                                                                                                                                                         --------------------- Pfam domains (2)
         Sec.struct. author .............hhhhhhh......eeee.......hhhhh...eeee..hhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhh..eeee..hhhhh.....eeeee........hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.ee..eehhhhhhhhhh.eeee....----------.....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------N6_MTAS------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yf3 B   1 MLGAIAYTGNKQSLLPELKSHFPKYNRFVDLFCGGLSVSLNVNGPVLANDIQEPIIEMYKRLINVSWDDVLKVIKQYKLSKTSKEEFLKLREDYNKTRDPLLLYVLHFHGFSNMIRINYKGNFTTPFGKRTINKNSEKRFNHFKQNCDKIIFSSLHFKDVKILDGDFVYVDPPYLITVADYNKFWSEDEEKDLLNLLDSLNDRGIKFGLSNVLEHHGKENTLLKEWSKKYNVKHLNKK----------KNGTDEVYIFN 259
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       | -       250         
                                                                                                                                                                                                                                                                       238        249          


Chain C from PDB  Type:DNA  Length:13
                                             
                 1yf3 C 400 ACCATGATCTGAC 412
                                   409   


Chain D from PDB  Type:DNA  Length:13
                                             
                 1yf3 D 422 TGTCAGATCATGG 434
                                   431
   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, 2)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SAH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:44 - Pro A:45   [ RasMol ]  
    Gly B:44 - Pro B:45   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1yf3
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DMA_BPT4 | P04392
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.1.1.72
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  DMA_BPT4 | P04392
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        DMA_BPT4 | P04392: 1q0s 1q0t 1yfj 1yfl

(-) Related Entries Specified in the PDB File

1q0s BINARY STRUCTURE OF T4DAM WITH ADOHCY
1q0t TERNARY STRUCTURE OF T4DAM WITH ADOHCY AND DNA
1yfj
1yfl