2JG3 - JenaLib

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Title :   MTAQI WITH BAZ

Authors :   G. Pljevaljcic, A. J. Scheidig, E. Weinhold

Date :   07 Feb 07 (Deposition) - 07 Aug 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Transferase-Dna Complex, Dna, Transferase, Base Flipping, Restriction System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Pljevaljcic, F. Schmidt, A. J. Scheidig, R. Lurz, E. Weinhold
Quantitative Labeling Of Long Plasmid Dna With Nanometer Precision.
Chembiochem V. 8 1516 2007
PubMed-ID: 17654629 | Reference-DOI: 10.1002/CBIC.200700294
(for further references see the PDB file header)

Molecule 1 - MODIFICATION METHYLASE TAQI
	Chains	:	A, D
	EC Number	:	2.1.1.72
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PA1/MTAQ-A49A
	Expression System Strain	:	ER2267
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS AQUATICUS
	Organism Taxid	:	271
	Other Details	:	ADENINE-SPECIFIC METHYLTRANSFERASE TAQI, M. TAQI
	Strain	:	YT1
	Synonym	:	ADENINE-SPECIFIC METHYLTRANSFERASE TAQI, M TAQI

*Molecule 2 - 5'-D(GPAPCPAPTPCPGP6MAPAPCP)-3'*
	Chains	:	C, F
	Synthetic	:	YES

*Molecule 3 - 5'-D(GPTPTPCPGPAPTPGPTPCP)-3'*
	Chains	:	B, E
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B	C
Biological Unit 2 (1x)	:				D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 8)

No.	Name	Count	Type	Full Name
1	6MA	2	Mod. Nucleotide	N6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE
2	BA2	2	Ligand/Ion	5'-DEOXY-5'-(ETHYLAMINO)-8-{[4-({5-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANOYL}AMINO)BUTYL]AMINO}ADENOSINE
3	GOL	2	Ligand/Ion	GLYCEROL
4	K	2	Ligand/Ion	POTASSIUM ION

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	6MA	1	Mod. Nucleotide	N6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE
2	BA2	1	Ligand/Ion	5'-DEOXY-5'-(ETHYLAMINO)-8-{[4-({5-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANOYL}AMINO)BUTYL]AMINO}ADENOSINE
3	GOL	2	Ligand/Ion	GLYCEROL
4	K	-1	Ligand/Ion	POTASSIUM ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	6MA	1	Mod. Nucleotide	N6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE
2	BA2	1	Ligand/Ion	5'-DEOXY-5'-(ETHYLAMINO)-8-{[4-({5-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANOYL}AMINO)BUTYL]AMINO}ADENOSINE
3	GOL	-1	Ligand/Ion	GLYCEROL
4	K	-1	Ligand/Ion	POTASSIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	BA2 A:1415 , DA B:6	BINDING SITE FOR RESIDUE K B1011
2	AC2	SOFTWARE	PRO D:107 , BA2 D:1416 , DA E:6	BINDING SITE FOR RESIDUE K D1415
3	AC3	SOFTWARE	ALA A:47 , GLU A:71 , ILE A:72 , ASP A:73 , ALA A:76 , ALA A:88 , ASP A:89 , PHE A:90 , ASN A:105 , PRO A:107 , PHE A:146 , GOL A:1416 , HOH A:2037 , HOH A:2286 , DA B:6 , K B:1011	BINDING SITE FOR RESIDUE BA2 A1415
4	AC4	SOFTWARE	ILE A:72 , ASP A:89 , VAL A:121 , TYR A:129 , BA2 A:1415 , HOH A:2287	BINDING SITE FOR RESIDUE GOL A1416
5	AC5	SOFTWARE	LYS A:139 , ASP A:173 , HOH A:2114 , DT B:2 , DT B:3 , HOH B:2047 , HOH B:2048 , DA C:19 , DC C:20	BINDING SITE FOR RESIDUE GOL B1012
6	AC6	SOFTWARE	ALA D:47 , GLU D:71 , ILE D:72 , ALA D:76 , ALA D:88 , ASP D:89 , PHE D:90 , PHE D:146 , K D:1415 , HOH D:2259 , DA E:6	BINDING SITE FOR RESIDUE BA2 D1416

(no "SS Bond" information available for 2JG3)

(no "Cis Peptide Bond" information available for 2JG3)

(no "SAP(SNP)/Variant" information available for 2JG3)

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.	MTTA_THEAQ	102-108	2	A:102-108 D:102-108

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.	MTTA_THEAQ	102-108	1	A:102-108 -

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.	MTTA_THEAQ	102-108	1	- D:102-108

(no "Exon" information available for 2JG3)

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:392
 aligned with MTTA_THEAQ | P14385 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:392
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412  
           MTTA_THEAQ    23 TPPEVVDFMVSLAEAPRGGRVLEPACAHGPFLRAFREAHGTAYRFVGVEIDPKALDLPPWAEGILADFLLWEPGEAFDLILGNPPYGIVGEASKYPIHVFKAVKDLYKKAFSTWKGKYNLYGAFLEKAVRLLKPGGVLVFVVPATWLVLEDFALLREFLAREGKTSVYYLGEVFPQKKVSAVVIRFQKSGKGLSLWDTQESESGFTPILWAEYPHWEGEIIRFETEETRKLEISGMPLGDLFHIRFAARSPEFKKHPAVRKEPGPGLVPVLTGRNLKPGWVDYEKNHSGLWMPKERAKELRDFYATPHLVVAHTKGTRVVAAWDERAYPWREEFHLLPKEGVRLDPSSLVQWLNSEAMQKHVRTLYRDFVPHLTLRMLERLPVRREYGFHTS 414
               SCOP domains d2jg3a1 A:23-243 automated matches                                                                                                                                                                                           d2jg3a2 A:244-414 automated matches                                                                                                                                         SCOP domains
               CATH domains 2jg3A01 A:23-243 Vaccinia Virus protein VP39                                                                                                                                                                                 2jg3A02 A:244-412 Adenine-n6-DNA-methyltransferase Taqi, Chain A, domain 2                                                                                               -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh......eeeee....hhhhhhhhhhhh...eeeeee............eeee.hhhhh.....eeeeee.................hhhhhhhhhhhh.......hhhhhhhhhhhhheeeeeeeeeeee.hhhhhhhhhhhhhhhhhhheeeeeeee.........eeeeeee.....eeeeeeeee..eeeeeeeeee...........hhhhhhhhh..eehhhheeeee..hhhhhhhh..........eee..hhh.ee..ee.........eee.hhhhhhhhhhhh.eeee.........eeee.........eeeee...eeehhhhhhhhhhhhhhhhhhhhhhh......hhhhhh..ee....eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------N6_MTAS------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jg3 A  23 TPPEVVDFMVSLAEAPRGGRVLEPACAHGPFLRAFREAHGTAYRFVGVEIDPKALDLPPWAEGILADFLLWEPGEAFDLILGNPPYGIVGEASKYPIHVFKAVKDLYKKAFSTWKGKYNLYGAFLEKAVRLLKPGGVLVFVVPATWLVLEDFALLREFLAREGKTSVYYLGEVFPQKKVSAVVIRFQKSGKGLSLWDTQESESGFTPILWAEYPHWEGEIIRFETEETRKLEISGMPLGDLFHIRFAARSPEFKKHPAVRKEPGPGLVPVLTGRNLKPGWVDYEKNHSGLWMPKERAKELRDFYATPHLVVAHTKGTRVVAAWDERAYPWREEFHLLPKEGVRLDPSSLVQWLNSEAMQKHVRTLYRDFVPHLTLRMLERLPVRREYGFHTS 414
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412

Chain B from PDB  Type:DNA  Length:10
                                          
                 2jg3 B   1 GTTCGATGTC  10
                                    10

Chain C from PDB  Type:DNA  Length:10
                                          
                 2jg3 C  11 GACATCGaAC  20
                                   |20
                                  18-6MA

Chain D from PDB  Type:PROTEIN  Length:392
 aligned with MTTA_THEAQ | P14385 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:392
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412  
           MTTA_THEAQ    23 TPPEVVDFMVSLAEAPRGGRVLEPACAHGPFLRAFREAHGTAYRFVGVEIDPKALDLPPWAEGILADFLLWEPGEAFDLILGNPPYGIVGEASKYPIHVFKAVKDLYKKAFSTWKGKYNLYGAFLEKAVRLLKPGGVLVFVVPATWLVLEDFALLREFLAREGKTSVYYLGEVFPQKKVSAVVIRFQKSGKGLSLWDTQESESGFTPILWAEYPHWEGEIIRFETEETRKLEISGMPLGDLFHIRFAARSPEFKKHPAVRKEPGPGLVPVLTGRNLKPGWVDYEKNHSGLWMPKERAKELRDFYATPHLVVAHTKGTRVVAAWDERAYPWREEFHLLPKEGVRLDPSSLVQWLNSEAMQKHVRTLYRDFVPHLTLRMLERLPVRREYGFHTS 414
               SCOP domains d2jg3d1 D:23-243 automated matches                                                                                                                                                                                           d2jg3d2 D:244-414 automated matches                                                                                                                                         SCOP domains
               CATH domains 2jg3D01 D:23-243 Vaccinia Virus protein VP39                                                                                                                                                                                 2jg3D02 D:244-412 Adenine-n6-DNA-methyltransferase Taqi, Chain A, domain 2                                                                                               -- CATH domains
           Pfam domains (1) -----------------Methyltransf_26-2jg3D01 D:40-166                                                                                               ---------------------------------------------------------------------------------------------------------------------------TaqI_C-2jg3D03 D:290-405                                                                                            --------- Pfam domains (1)
           Pfam domains (2) -----------------Methyltransf_26-2jg3D02 D:40-166                                                                                               ---------------------------------------------------------------------------------------------------------------------------TaqI_C-2jg3D04 D:290-405                                                                                            --------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhh......eeeee....hhhhhhhhhhhh...eeeeee...........eeeee.hhhhh.....eeeeee.................hhhhhhhhhhhh.......hhhhhhhhhhhhheeeeeeeeeeee.hhhhhhhhhhhhhhhhhhheeeeeeee.........eeeeeee.....eeeeeeee....eeeeeeeee...........hhhhhhhhhh.eehhhheeeee..hhhhhhh...........eee..hhh.ee..ee.........eee.hhhhhhhhhhhh.eeee.........eeee.........eeeee...eeehhhhhhhhhhhhhhhhhhhhhhh......hhhhhh..ee....eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------N6_MTAS------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jg3 D  23 TPPEVVDFMVSLAEAPRGGRVLEPACAHGPFLRAFREAHGTAYRFVGVEIDPKALDLPPWAEGILADFLLWEPGEAFDLILGNPPYGIVGEASKYPIHVFKAVKDLYKKAFSTWKGKYNLYGAFLEKAVRLLKPGGVLVFVVPATWLVLEDFALLREFLAREGKTSVYYLGEVFPQKKVSAVVIRFQKSGKGLSLWDTQESESGFTPILWAEYPHWEGEIIRFETEETRKLEISGMPLGDLFHIRFAARSPEFKKHPAVRKEPGPGLVPVLTGRNLKPGWVDYEKNHSGLWMPKERAKELRDFYATPHLVVAHTKGTRVVAAWDERAYPWREEFHLLPKEGVRLDPSSLVQWLNSEAMQKHVRTLYRDFVPHLTLRMLERLPVRREYGFHTS 414
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412

Chain E from PDB  Type:DNA  Length:10
                                          
                 2jg3 E   1 GTTCGATGTC  10
                                    10

Chain F from PDB  Type:DNA  Length:10
                                          
                 2jg3 F  11 GACATCGaAC  20
                                   |20
                                  18-6MA

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

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: Methyltransf_26 (3)

Thermus aquaticus (3)

1a	Methyltransf_26-2jg3D01	D:40-166
1b	Methyltransf_26-2jg3D02	D:40-166

Clan: TRD (7)

Family: TaqI_C (3)

Thermus aquaticus (3)

2a	TaqI_C-2jg3D03	D:290-405
2b	TaqI_C-2jg3D04	D:290-405

Asymmetric Unit(hide GO term definitions)

Chain A,D (MTTA_THEAQ | P14385)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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:0006304	DNA modification	The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties.
	GO:0009307	DNA restriction-modification system	A defense process found in many bacteria and archaea that protects the organism from invading foreign DNA by cleaving it with a restriction endonuclease. The organism's own DNA is protected by methylation of a specific nucleotide, which occurs immediately following replication, in the same target site as the restriction enzyme.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.

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	2jg3
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UniProtKB/Swiss-Prot
	MTTA_THEAQ \| P14385	:	1aqi 1aqj 1g38 2adm 2ibs 2ibt 2ih2 2ih4 2ih5 2np6 2np7

1aqi	STRUCTURE OF ADENINE-N6-DEOXYRIBONUCLEIC ACID -METHYLTRANSFERASE TAQI
1aqj	STRUCTURE OF ADENINE-N6-DEOXYRIBONUCLEIC ACID -METHYLTRANSFERASE TAQI
1g38	ADENINE-SPECIFIC METHYLTRANSFERASE M. TAQ I/ DNA COMPLEX
2adm	ADENINE-N6-DEOXYRIBONUCLEIC ACID- METHYLTRANSFERASE TAQI

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

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SCOP Domains (2, 4)

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