1YFJ | PD0623 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Biological Unit 6 (Jmol Viewer)

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)

*Molecule 1 - 5'- D(TPCPAPCPAPGPGPAPTPCPCPTPGPTPG)-3'**
	Chains	:	1, 2, 3, 4, 5, 6, 7, 8, 9, 0
	Engineered	:	YES
	Other Details	:	SYNTHESIZED BY NEW ENGLAND BIOLABS
	Synthetic	:	YES

Molecule 2 - DNA ADENINE METHYLASE
	Chains	:	A, B, C, D, E, F
	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

		1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16
Asymmetric Unit	:	A	B	C	D	E	F	0	1	2	3	4	5	6	7	8	9
Biological Unit 1 (1x)	:	A							1	2
Biological Unit 2 (1x)	:		B												7	8
Biological Unit 3 (1x)	:			C							3	4
Biological Unit 4 (1x)	:				D								5	6
Biological Unit 5 (1x)	:					E		0									9
Biological Unit 6 (1x)	:						F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	CL	4	Ligand/Ion	CHLORIDE ION
3	SAH	6	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 5 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 6 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	DT 4:401	BINDING SITE FOR RESIDUE CL 8 600
02	AC2	SOFTWARE	DT 1:101	BINDING SITE FOR RESIDUE CL 1 602
03	AC3	SOFTWARE	DT 2:201	BINDING SITE FOR RESIDUE CL 2 603
04	AC4	SOFTWARE	HOH 1:604 , HOH 1:605 , HOH 1:607 , HOH 2:606 , HOH 2:609 , HOH B:502 , HOH B:503 , HOH B:504	BINDING SITE FOR RESIDUE CA 2 502
05	AC5	SOFTWARE	HOH 3:612 , HOH 3:613 , HOH 3:615 , HOH 4:614 , HOH 4:619 , HOH A:497 , HOH A:498 , HOH A:499	BINDING SITE FOR RESIDUE CA 4 508
06	AC6	SOFTWARE	TYR 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:461	BINDING SITE FOR RESIDUE SAH A 401
07	AC7	SOFTWARE	HOH 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:437	BINDING SITE FOR RESIDUE SAH B 402
08	AC8	SOFTWARE	HOH 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:418	BINDING SITE FOR RESIDUE SAH C 403
09	AC9	SOFTWARE	TYR 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:412	BINDING SITE FOR RESIDUE SAH D 404
10	BC1	SOFTWARE	TYR 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:416	BINDING SITE FOR RESIDUE SAH E 405
11	BC2	SOFTWARE	TYR 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:181	BINDING SITE FOR RESIDUE SAH F 406

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

Asymmetric Unit

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

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

Asymmetric Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	N6_MTASE	PS00092	N-6 Adenine-specific DNA methylases signature.	DMA_BPT4	168-174	6	A:168-174 B:168-174 C:168-174 D:168-174 E:168-174 F:168-174

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	N6_MTASE	PS00092	N-6 Adenine-specific DNA methylases signature.	DMA_BPT4	168-174	1	A:168-174 - - - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	N6_MTASE	PS00092	N-6 Adenine-specific DNA methylases signature.	DMA_BPT4	168-174	1	- B:168-174 - - - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	N6_MTASE	PS00092	N-6 Adenine-specific DNA methylases signature.	DMA_BPT4	168-174	1	- - C:168-174 - - -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	N6_MTASE	PS00092	N-6 Adenine-specific DNA methylases signature.	DMA_BPT4	168-174	1	- - - D:168-174 - -

Biological Unit 5 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	N6_MTASE	PS00092	N-6 Adenine-specific DNA methylases signature.	DMA_BPT4	168-174	1	- - - - E:168-174 -

Biological Unit 6 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	N6_MTASE	PS00092	N-6 Adenine-specific DNA methylases signature.	DMA_BPT4	168-174	1	- - - - - F:168-174

(no "Exon" information available for 1YFJ)

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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: S-adenosyl-L-methionine-dependent methyltransferases (533)

Superfamily: S-adenosyl-L-methionine-dependent methyltransferases (533)

Family: N6 adenine-specific DNA methylase, DAM (13)

Protein domain: DNA methylase T4DAM (7)

Bacteriophage T4 [TaxId: 10665] (5)

1a	d1yfja1	A:1-259
1b	d1yfjb_	B:
1c	d1yfjc_	C:
1d	d1yfjd_	D:
1e	d1yfje_	E:
1f	d1yfjf_	F:

Asymmetric Unit

Classes(

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Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Vaccinia Virus protein VP39 (378)

[unclassified] (23)

1a	1yfjA01	A:1-51,A:147-259
1b	1yfjB01	B:1-51,B:147-259
1c	1yfjC01	C:1-51,C:147-259
1d	1yfjD01	D:1-51,D:147-259
1e	1yfjE01	E:1-51,E:147-259
1f	1yfjF01	F:1-51,F:147-259

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Adenine-specific Methyltransferase; domain 2 (6)

Homologous Superfamily: Adenine-specific Methyltransferase, Domain 2 (6)

[unclassified] (4)

2a	1yfjA02	A:52-146
2b	1yfjB02	B:52-146
2c	1yfjC02	C:52-146
2d	1yfjD02	D:52-146
2e	1yfjE02	E:52-146
2f	1yfjF02	F:52-146

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: MethyltransfD12 (6)

Enterobacteria phage T4 (Bacteriophage T4) (5)

1a	MethyltransfD12-1yfjF01	F:7-235
1b	MethyltransfD12-1yfjF02	F:7-235
1c	MethyltransfD12-1yfjF03	F:7-235
1d	MethyltransfD12-1yfjF04	F:7-235
1e	MethyltransfD12-1yfjF05	F:7-235
1f	MethyltransfD12-1yfjF06	F:7-235

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.

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	1yfj
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	DMA_BPT4 \| P04392
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	2.1.1.72
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	DMA_BPT4 \| P04392	:	1q0s 1q0t 1yf3 1yfl

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

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SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 6)

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SCOP Domains (1, 6)

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