1Q0T | PD0460 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   TERNARY STRUCTURE OF T4DAM WITH ADOHCY AND DNA

Authors :   Z. Yang, J. R. Horton, L. Zhou, X. J. Zhang, A. Dong, X. Zhang, S. L. Schlagman, V. Kossykh, S. Hattman, X. Cheng

Date :   17 Jul 03 (Deposition) - 23 Sep 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,C  (1x)
Biol. Unit 2: B,D  (1x)

Keywords :   T4Dam, Methyltransferase, Dna, Transferase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Yang, J. R. Horton, L. Zhou, X. J. Zhang, A. Dong, X. Zhang, S. L. Schlagman, V. Kossykh, S. Hattman, X. Cheng
Structure Of The Bacteriophage T4 Dna Adenine Methyltransferase
Nat. Struct. Biol. V. 10 849 2003
PubMed-ID: 12937411 | Reference-DOI: 10.1038/NSB973
(for further references see the PDB file header)

*Molecule 1 - 5'-D(APCPAPGPGPAPTPCPCPTPGPT)-3'*
	Chains	:	C, D
	Engineered	:	YES
	Other Details	:	PALINDROMIC 12 BASE PAIR DNA DUPLEX
	Synthetic	:	YES

Molecule 2 - DNA ADENINE METHYLASE
	Chains	:	A, B
	EC Number	:	2.1.1.72
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PJW2
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DAM
	Organism Scientific	:	ENTEROBACTERIA PHAGE T4
	Organism Taxid	:	10665
	Synonym	:	DEOXYADENOSYL-METHYLTRANSFERASE, M.ECOT4DAM

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	IOD	2	Ligand/Ion	IODIDE ION
2	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	IOD	1	Ligand/Ion	IODIDE ION
2	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	IOD	1	Ligand/Ion	IODIDE ION
2	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	DC D:423	BINDING SITE FOR RESIDUE IOD D 1
2	AC2	SOFTWARE	DC C:403	BINDING SITE FOR RESIDUE IOD C 2
3	AC3	SOFTWARE	TYR A:7 , ASN A:10 , LYS A:11 , PHE A:32 , CYS A:33 , GLY A:34 , GLY A:35 , SER A:37 , VAL A:38 , 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 , TRP A:185	BINDING SITE FOR RESIDUE SAH A 300
4	AC4	SOFTWARE	TYR B:7 , ASN B:10 , LYS B:11 , PHE B:32 , CYS B:33 , GLY B:35 , LEU B:36 , 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	BINDING SITE FOR RESIDUE SAH B 301

(no "SS Bond" information available for 1Q0T)

Asymmetric Unit

No.	Residues
1	Gly A:44	-	Pro A:45
2	Gly B:44	-	Pro B:45

(no "SAP(SNP)/Variant" information available for 1Q0T)

Asymmetric Unit (1, 2)

	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	2	A:168-174 B: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

(no "Exon" information available for 1Q0T)

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 A from PDB  Type:PROTEIN  Length:241
 aligned with DMA_BPT4 | P04392 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:259
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250         
             DMA_BPT4     1 MLGAIAYTGNKQSLLPELKSHFPKYNRFVDLFCGGLSVSLNVNGPVLANDIQEPIIEMYKRLINVSWDDVLKVIKQYKLSKTSKEEFLKLREDYNKTRDPLLLYVLHFHGFSNMIRINDKGNFTTPFGKRTINKNSEKQYNHFKQNCDKIIFSSLHFKDVKILDGDFVYVDPPYLITVADYNKFWSEDEEKDLLNLLDSLNDRGIKFGQSNVLEHHGKENTLLKEWSKKYNVKHLNKKYVFNIYHSKEKNGTDEVYIFN 259
               SCOP domains d1q0ta_ A: DNA methylase T4DAM                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1q0tA01 A:1-51,A:147-259                           1q0tA02 A:52-146 Adenine-specific Methyltransferase, Domain 2                                  1q0tA01 A:1-51,A:147-259 Vaccinia Virus protein VP39                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhh......eeee...............eeee..hhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhh..eeee..hhhhh.....eeeee........hhhhhh.hhhhhhhhhhhhhhhhh....eeeee..ee..eehhhhhhhhhh......------------------.ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------N6_MTAS------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q0t A   1 MLGAIAYTGNKQSLLPELKSHFPKYNRFVDLFCGGLSVSLNVNGPVLANDIQEPIIEMYKRLINVSWDDVLKVIKQYKLSKTSKEEFLKLREDYNKTRDPLLLYVLHFHGFSNMIRINDKGNFTTPFGKRTINKNSEKQYNHFKQNCDKIIFSSLHFKDVKILDGDFVYVDPPYLITVADYNKFWSEDEEKDLLNLLDSLNDRGIKFGQSNVLEHHGKENTLLKEWSKKYNVKHL------------------EVYIFN 259
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    |    -         -   |     
                                                                                                                                                                                                                                                                    235                254

Chain B from PDB  Type:PROTEIN  Length:241
 aligned with DMA_BPT4 | P04392 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:259
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250         
             DMA_BPT4     1 MLGAIAYTGNKQSLLPELKSHFPKYNRFVDLFCGGLSVSLNVNGPVLANDIQEPIIEMYKRLINVSWDDVLKVIKQYKLSKTSKEEFLKLREDYNKTRDPLLLYVLHFHGFSNMIRINDKGNFTTPFGKRTINKNSEKQYNHFKQNCDKIIFSSLHFKDVKILDGDFVYVDPPYLITVADYNKFWSEDEEKDLLNLLDSLNDRGIKFGQSNVLEHHGKENTLLKEWSKKYNVKHLNKKYVFNIYHSKEKNGTDEVYIFN 259
               SCOP domains d1q0tb_ B: DNA methylase T4DAM                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1q0tB01 B:1-51,B:147-259                           1q0tB02 B:52-146 Adenine-specific Methyltransferase, Domain 2                                  1q0tB01 B:1-51,B:147-259 Vaccinia Virus protein VP39                                                              CATH domains
           Pfam domains (1) ------MethyltransfD12-1q0tB01 B:7-235                                                                                                                                                                                                      ------------------------ Pfam domains (1)
           Pfam domains (2) ------MethyltransfD12-1q0tB02 B:7-235                                                                                                                                                                                                      ------------------------ Pfam domains (2)
         Sec.struct. author .............hhhhhhh......eeee...............eeee..hhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhh..eeee..hhhhh.....eeeee........hhhhhh.hhhhhhhhhhhhhhhhh....eeeee..ee..eehhhhhhhhhh......------------------.ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------N6_MTAS------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q0t B   1 MLGAIAYTGNKQSLLPELKSHFPKYNRFVDLFCGGLSVSLNVNGPVLANDIQEPIIEMYKRLINVSWDDVLKVIKQYKLSKTSKEEFLKLREDYNKTRDPLLLYVLHFHGFSNMIRINDKGNFTTPFGKRTINKNSEKQYNHFKQNCDKIIFSSLHFKDVKILDGDFVYVDPPYLITVADYNKFWSEDEEKDLLNLLDSLNDRGIKFGQSNVLEHHGKENTLLKEWSKKYNVKHL------------------EVYIFN 259
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    |    -         -   |     
                                                                                                                                                                                                                                                                    235                254

Chain C from PDB  Type:DNA  Length:12
                                            
                 1q0t C 402 ACAGGATCCTGT 413
                                   411

Chain D from PDB  Type:DNA  Length:12
                                            
                 1q0t D 422 ACAGGATCCTGT 433
                                   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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

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	1q0tA01	A:1-51,A:147-259
1b	1q0tB01	B:1-51,B: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	1q0tA02	A:52-146
2b	1q0tB02	B:52-146

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: MethyltransfD12 (6)

Enterobacteria phage T4 (Bacteriophage T4) (5)

1a	MethyltransfD12-1q0tB01	B:7-235
1b	MethyltransfD12-1q0tB02	B:7-235

Asymmetric 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.

Asymmetric Unit
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	1q0t
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	DMA_BPT4 \| P04392	:	1q0s 1yf3 1yfj 1yfl

1q0s	BINARY STRUCTURE OF T4DAM WITH ADOHCY

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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