Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
(-)Biological Unit 5
(-)Biological Unit 6
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)
Image Biological Unit 5
Biological Unit 5  (Jmol Viewer)
Image Biological Unit 6
Biological Unit 6  (Jmol Viewer)

(-) Description

Title :  T4DAM IN COMPLEX WITH ADOHCY AND 15-MER OLIGONUCLEOTIDE SHOWING SEMI-SPECIFIC AND SPECIFIC CONTACT
 
Authors :  J. R. Horton, K. Liebert, S. Hattman, A. Jeltsch, X. Cheng
Date :  02 Jan 05  (Deposition) - 17 May 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.69
Chains :  Asym. Unit :  A,B,C,D,E,F,0,1,2,3,4,5,6,7,8,9
Biol. Unit 1:  A,1,2  (1x)
Biol. Unit 2:  B,7,8  (1x)
Biol. Unit 3:  C,3,4  (1x)
Biol. Unit 4:  D,5,6  (1x)
Biol. Unit 5:  E,0,9  (1x)
Biol. Unit 6:  F  (1x)
Keywords :  T4Dam, Methyltransferase, Dna, Protein-Dna Complex, 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(*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*G)-3'
    Chains1, 2, 3, 4, 5, 6, 7, 8, 9, 0
    EngineeredYES
    Other DetailsSYNTHESIZED BY NEW ENGLAND BIOLABS
    SyntheticYES
 
Molecule 2 - DNA ADENINE METHYLASE
    ChainsA, B, C, D, E, F
    EC Number2.1.1.72
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPJW2
    Expression System StrainGM 2971
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneDAM
    Organism ScientificENTEROBACTERIA PHAGE T4
    Organism Taxid10665
    SynonymDEOXYADENOSYL-METHYLTRANSFERASE, M.ECOT4DAM

 Structural Features

(-) Chains, Units

  12345678910111213141516
Asymmetric Unit ABCDEF0123456789
Biological Unit 1 (1x)A      12       
Biological Unit 2 (1x) B           78 
Biological Unit 3 (1x)  C      34     
Biological Unit 4 (1x)   D       56   
Biological Unit 5 (1x)    E 0        9
Biological Unit 6 (1x)     F          

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2CL4Ligand/IonCHLORIDE ION
3SAH6Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 6 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREDT 4:401BINDING SITE FOR RESIDUE CL 8 600
02AC2SOFTWAREDT 1:101BINDING SITE FOR RESIDUE CL 1 602
03AC3SOFTWAREDT 2:201BINDING SITE FOR RESIDUE CL 2 603
04AC4SOFTWAREHOH 1:604 , HOH 1:605 , HOH 1:607 , HOH 2:606 , HOH 2:609 , HOH B:502 , HOH B:503 , HOH B:504BINDING SITE FOR RESIDUE CA 2 502
05AC5SOFTWAREHOH 3:612 , HOH 3:613 , HOH 3:615 , HOH 4:614 , HOH 4:619 , HOH A:497 , HOH A:498 , HOH A:499BINDING SITE FOR RESIDUE CA 4 508
06AC6SOFTWARETYR A:7 , ASN A:10 , LYS A:11 , LEU A:31 , 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 , PRO A:173 , TYR A:181 , PHE A:184 , HOH A:427 , HOH A:489 , HOH C:461BINDING SITE FOR RESIDUE SAH A 401
07AC7SOFTWAREHOH A:490 , TYR 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 , HIS B:156 , PHE B:157 , ASP B:171 , PRO B:173 , TYR B:181 , PHE B:184 , HOH B:422 , HOH B:437BINDING SITE FOR RESIDUE SAH B 402
08AC8SOFTWAREHOH B:462 , TYR C:7 , GLY C:9 , ASN C:10 , LYS C:11 , PHE C:32 , CYS C:33 , GLY C:34 , GLY C:35 , SER C:37 , ASP C:50 , ILE C:51 , GLN C:52 , HIS C:156 , PHE C:157 , ASP C:171 , PRO C:173 , TYR C:181 , PHE C:184 , HOH C:408 , HOH C:418BINDING SITE FOR RESIDUE SAH C 403
09AC9SOFTWARETYR D:7 , ASN D:10 , LYS D:11 , PHE D:32 , CYS D:33 , GLY D:34 , GLY D:35 , SER D:37 , ASP D:50 , ILE D:51 , GLN D:52 , LEU D:155 , HIS D:156 , PHE D:157 , ASP D:171 , PRO D:173 , TYR D:181 , PHE D:184 , HOH D:412BINDING SITE FOR RESIDUE SAH D 404
10BC1SOFTWARETYR E:7 , ASN E:10 , LYS E:11 , LEU E:31 , PHE E:32 , CYS E:33 , GLY E:34 , GLY E:35 , SER E:37 , VAL E:38 , ASP E:50 , ILE E:51 , GLN E:52 , HIS E:156 , PHE E:157 , ASP E:171 , TYR E:181 , PHE E:184 , HOH E:408 , HOH E:416BINDING SITE FOR RESIDUE SAH E 405
11BC2SOFTWARETYR F:7 , GLY F:9 , ASN F:10 , LYS F:11 , LEU F:31 , PHE F:32 , CYS F:33 , GLY F:34 , GLY F:35 , LEU F:36 , SER F:37 , ASN F:49 , ASP F:50 , ILE F:51 , HIS F:156 , PHE F:157 , ASP F:171 , TYR F:181BINDING SITE FOR RESIDUE SAH F 406

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Gly A:44 -Pro A:45
2Gly B:44 -Pro B:45
3Gly C:44 -Pro C:45
4Gly D:44 -Pro D:45
5Gly E:44 -Pro E:45
6Gly F:44 -Pro F:45

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 6)

Asymmetric Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1N6_MTASEPS00092 N-6 Adenine-specific DNA methylases signature.DMA_BPT4168-174
 
 
 
 
 
  6A:168-174
B:168-174
C:168-174
D:168-174
E:168-174
F:168-174
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1N6_MTASEPS00092 N-6 Adenine-specific DNA methylases signature.DMA_BPT4168-174
 
 
 
 
 
  1A:168-174
-
-
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1N6_MTASEPS00092 N-6 Adenine-specific DNA methylases signature.DMA_BPT4168-174
 
 
 
 
 
  1-
B:168-174
-
-
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1N6_MTASEPS00092 N-6 Adenine-specific DNA methylases signature.DMA_BPT4168-174
 
 
 
 
 
  1-
-
C:168-174
-
-
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1N6_MTASEPS00092 N-6 Adenine-specific DNA methylases signature.DMA_BPT4168-174
 
 
 
 
 
  1-
-
-
D:168-174
-
-
Biological Unit 5 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1N6_MTASEPS00092 N-6 Adenine-specific DNA methylases signature.DMA_BPT4168-174
 
 
 
 
 
  1-
-
-
-
E:168-174
-
Biological Unit 6 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1N6_MTASEPS00092 N-6 Adenine-specific DNA methylases signature.DMA_BPT4168-174
 
 
 
 
 
  1-
-
-
-
-
F:168-174

(-) Exons   (0, 0)

(no "Exon" information available for 1YFJ)

(-) Sequences/Alignments

Asymmetric 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 0 from PDB  Type:DNA  Length:15
                                                
                1yfj 0 1001 TCACAGGATCCTGTG 1015
                                  1010     

Chain 1 from PDB  Type:DNA  Length:15
                                                
                1yfj 1  101 TCACAGGATCCTGTG  115
                                   110     

Chain 2 from PDB  Type:DNA  Length:15
                                                
                1yfj 2  201 TCACAGGATCCTGTG  215
                                   210     

Chain 3 from PDB  Type:DNA  Length:15
                                                
                1yfj 3  301 TCACAGGATCCTGTG  315
                                   310     

Chain 4 from PDB  Type:DNA  Length:15
                                                
                1yfj 4  401 TCACAGGATCCTGTG  415
                                   410     

Chain 5 from PDB  Type:DNA  Length:14
                                               
                1yfj 5  502 CACAGGATCCTGTG  515
                                   511    

Chain 6 from PDB  Type:DNA  Length:15
                                                
                1yfj 6  601 TCACAGGATCCTGTG  615
                                   610     

Chain 7 from PDB  Type:DNA  Length:15
                                                
                1yfj 7  701 TCACAGGATCCTGTG  715
                                   710     

Chain 8 from PDB  Type:DNA  Length:15
                                                
                1yfj 8  801 TCACAGGATCCTGTG  815
                                   810     

Chain 9 from PDB  Type:DNA  Length:15
                                                
                1yfj 9  901 TCACAGGATCCTGTG  915
                                   910     

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 d1yfja1 A:1-259 DNA methylase T4DAM                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1yfjA01 A:1-51,A:147-259                           1yfjA02 A:52-146 Adenine-specific Methyltransferase, Domain 2                                  1yfjA01 A:1-51,A:147-259 Vaccinia Virus protein VP39                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhh....eeee.......hhhhh...eeee..hhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhh..eeee..hhhhh.....eeeee........hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.ee..eehhhhhhhhh..eeee.hhhhhhhhhh........eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------N6_MTAS------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1yfj A    1 MLGAIAYTGNKQSLLPELKSHFPKYNRFVDLFCGGLSVSLNVNGPVLANDIQEPIIEMYKRLINVSWDDVLKVIKQYKLSKTSKEEFLKLREDYNKTRDPLLLYVLHFHGFSNMIRINDKGNFTTPFGKRTINKNSEKRFNHFKQNCDKIIFSSLHFKDVKILDGDFVYVDPPYLITVADYNKFWSEDEEKDLLNLLDSLNDRGIKFGLSNVLEHHGKENTLLKEWSKKYNVKHLNKKYVFNIYHSKEKNGTDEVYIFN  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: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 d1yfjb_ B: DNA methylase T4DAM                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1yfjB01 B:1-51,B:147-259                           1yfjB02 B:52-146 Adenine-specific Methyltransferase, Domain 2                                  1yfjB01 B:1-51,B:147-259 Vaccinia Virus protein VP39                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhh......eeee.......hhhhh...eeee..hhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh..................hhhhhhhhhhhhhhh..eeee..hhhhh.....eeeee........hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.ee..eehhhhhhhhh..eeee.hhhhhhhhh.........eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------N6_MTAS------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1yfj B    1 MLGAIAYTGNKQSLLPELKSHFPKYNRFVDLFCGGLSVSLNVNGPVLANDIQEPIIEMYKRLINVSWDDVLKVIKQYKLSKTSKEEFLKLREDYNKTRDPLLLYVLHFHGFSNMIRINDKGNFTTPFGKRTINKNSEKRFNHFKQNCDKIIFSSLHFKDVKILDGDFVYVDPPYLITVADYNKFWSEDEEKDLLNLLDSLNDRGIKFGLSNVLEHHGKENTLLKEWSKKYNVKHLNKKYVFNIYHSKEKNGTDEVYIFN  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 C 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 d1yfjc_ C: DNA methylase T4DAM                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1yfjC01 C:1-51,C:147-259                           1yfjC02 C:52-146 Adenine-specific Methyltransferase, Domain 2                                  1yfjC01 C:1-51,C:147-259 Vaccinia Virus protein VP39                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhh....eeee.......hhhhh...eeee..hhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhh....eeee..hhhhh.....eeeee........hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eehhhhhhhhh..eeee.hhhhhhhhh.......eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------N6_MTAS------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1yfj C    1 MLGAIAYTGNKQSLLPELKSHFPKYNRFVDLFCGGLSVSLNVNGPVLANDIQEPIIEMYKRLINVSWDDVLKVIKQYKLSKTSKEEFLKLREDYNKTRDPLLLYVLHFHGFSNMIRINDKGNFTTPFGKRTINKNSEKRFNHFKQNCDKIIFSSLHFKDVKILDGDFVYVDPPYLITVADYNKFWSEDEEKDLLNLLDSLNDRGIKFGLSNVLEHHGKENTLLKEWSKKYNVKHLNKKYVFNIYHSKEKNGTDEVYIFN  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 D from PDB  Type:PROTEIN  Length:254
 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 d1yfjd_ D: DNA methylase T4DAM                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1yfjD01 D:1-51,D:147-259                           1yfjD02 D:52-146 Adenine-specific Methyltransferase, Domain 2                                  1yfjD01 D:1-51,D:147-259 Vaccinia Virus protein VP39                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhh......eeee.......hhhhh...eeee..hhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhh....eeee..hhhhh.....eeeee........hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.ee..eehhhhhhhhh..eeee.hhhhhhh..-----....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------N6_MTAS------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1yfj D    1 MLGAIAYTGNKQSLLPELKSHFPKYNRFVDLFCGGLSVSLNVNGPVLANDIQEPIIEMYKRLINVSWDDVLKVIKQYKLSKTSKEEFLKLREDYNKTRDPLLLYVLHFHGFSNMIRINDKGNFTTPFGKRTINKNSEKRFNHFKQNCDKIIFSSLHFKDVKILDGDFVYVDPPYLITVADYNKFWSEDEEKDLLNLLDSLNDRGIKFGLSNVLEHHGKENTLLKEWSKKYNVKHLNKKYVFNIY-----NGTDEVYIFN  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         
                                                                                                                                                                                                                                                                             244   250         

Chain E from PDB  Type:PROTEIN  Length:243
 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 d1yfje_ E: DNA methylase T4DAM                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1yfjE01 E:1-51,E:147-259                           1yfjE02 E:52-146 Adenine-specific Methyltransferase, Domain 2                                  1yfjE01 E:1-51,E:147-259 Vaccinia Virus protein VP39                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhh....eeee.......hhhhh...eeee..hhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhh.eeee..hhhhh.....eeeee........hhhhhhhhhhhhhhhhhhhhhhhhh...eee.ee.......hhhhhhhhh.......----------------..ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------N6_MTAS------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1yfj E    1 MLGAIAYTGNKQSLLPELKSHFPKYNRFVDLFCGGLSVSLNVNGPVLANDIQEPIIEMYKRLINVSWDDVLKVIKQYKLSKTSKEEFLKLREDYNKTRDPLLLYVLHFHGFSNMIRINDKGNFTTPFGKRTINKNSEKRFNHFKQNCDKIIFSSLHFKDVKILDGDFVYVDPPYLITVADYNKFWSEDEEKDLLNLLDSLNDRGIKFGLSNVLEHHGKENTLLKEWSKKYNVKHL----------------TDEVYIFN  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              252       

Chain F from PDB  Type:PROTEIN  Length:243
 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 d1yfjf_ F: DNA methylase T4DAM                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1yfjF01 F:1-51,F:147-259                           1yfjF02 F:52-146 Adenine-specific Methyltransferase, Domain 2                                  1yfjF01 F:1-51,F:147-259 Vaccinia Virus protein VP39                                                              CATH domains
           Pfam domains (1) ------MethyltransfD12-1yfjF01 F:7-235                                                                                                                                                                                                      ------------------------ Pfam domains (1)
           Pfam domains (2) ------MethyltransfD12-1yfjF02 F:7-235                                                                                                                                                                                                      ------------------------ Pfam domains (2)
           Pfam domains (3) ------MethyltransfD12-1yfjF03 F:7-235                                                                                                                                                                                                      ------------------------ Pfam domains (3)
           Pfam domains (4) ------MethyltransfD12-1yfjF04 F:7-235                                                                                                                                                                                                      ------------------------ Pfam domains (4)
           Pfam domains (5) ------MethyltransfD12-1yfjF05 F:7-235                                                                                                                                                                                                      ------------------------ Pfam domains (5)
           Pfam domains (6) ------MethyltransfD12-1yfjF06 F:7-235                                                                                                                                                                                                      ------------------------ Pfam domains (6)
         Sec.struct. author ..........................eeee.......hhhhh...eee...hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhh.................eeeee........hhhhhh.hhhhhh...............eeee......................ee.----------------...eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------N6_MTAS------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1yfj F    1 MLGAIAYTGNKQSLLPELKSHFPKYNRFVDLFCGGLSVSLNVNGPVLANDIQEPIIEMYKRLINVSWDDVLKVIKQYKLSKTSKEEFLKLREDYNKTRDPLLLYVLHFHGFSNMIRINDKGNFTTPFGKRTINKNSEKRFNHFKQNCDKIIFSSLHFKDVKILDGDFVYVDPPYLITVADYNKFWSEDEEKDLLNLLDSLNDRGIKFGLSNVLEHHGKENTLLKEWSKKYNVKHL----------------TDEVYIFN  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              252       

   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, 6)

Asymmetric Unit

(-) CATH Domains  (2, 12)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
1a1yfjA01A:1-51,A:147-259
1b1yfjB01B:1-51,B:147-259
1c1yfjC01C:1-51,C:147-259
1d1yfjD01D:1-51,D:147-259
1e1yfjE01E:1-51,E:147-259
1f1yfjF01F:1-51,F:147-259

(-) Pfam Domains  (1, 6)

Asymmetric Unit

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (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 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ 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 ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:44 - Pro A:45   [ RasMol ]  
    Gly B:44 - Pro B:45   [ RasMol ]  
    Gly C:44 - Pro C:45   [ RasMol ]  
    Gly D:44 - Pro D:45   [ RasMol ]  
    Gly E:44 - Pro E:45   [ RasMol ]  
    Gly F:44 - Pro F:45   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]
    Biological Unit 5  [ Jena3D ]
    Biological Unit 6  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1yfj
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DMA_BPT4 | P04392
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.1.1.72
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  DMA_BPT4 | P04392
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        DMA_BPT4 | P043921q0s 1q0t 1yf3 1yfl

(-) Related Entries Specified in the PDB File

1q0s BINARY STRUCTURE OF T4DAM WITH ADOHCY
1q0t TERNARY STRUCTURE OF T4DAM WITH ADOHCY AND DNA
1yf3 T4DAM IN COMPLEX WITH ADOHCY AND 13-MER OLIGONUCLEOTIDE MAKING NON- AND SEMI-SPECIFIC (~1/4) CONTACT
1yfl