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Title :   CRYSTAL STRUCTURE OF THE ADENINE-SPECIFIC DNA METHYLTRANSFERASE M.TAQI COMPLEXED WITH THE COFACTOR ANALOG AETA AND A 10 BP DNA CONTAINING 2-AMINOPURINE AT THE TARGET POSITION AND AN ABASIC SITE ANALOG AT THE TARGET BASE PARTNER POSITION

Authors :   T. Lenz, A. J. Scheidig, E. Weinhold

Date :   12 Sep 06 (Deposition) - 29 May 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Dna, Dna Methyltransferase, 2-Aminopurine, Abasic Site Analog, Base Flipping, Nucleotide Flipping, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Lenz, E. Y. M. Bonnist, G. Pljevaljcic, R. K. Neely, D. T. F. Dryden, A. J. Scheidig, A. C. Jones, E. Weinhold
2-Aminopurine Flipped Into The Active Site Of The Adenine-Specific Dna Methyltransferase M. Taqi: Crystal Structures And Time-Resolved Fluorescence
J. Am. Chem. Soc. V. 129 6240 2007
PubMed-ID: 17455934 | Reference-DOI: 10.1021/JA069366N
(for further references see the PDB file header)

*Molecule 1 - 5'-D(GPTPTPCPGP(2PR)PTPGPTPC)-3'*
	Chains	:	B, E
	Engineered	:	YES
	Other Details	:	SOLID-PHASE DNA SYNTHESIS USING COMMERCIALLY AVAILABLE PHOSPHORAMIDITES
	Synthetic	:	YES

*Molecule 2 - 5'-D(GPAPCPAP(3DR)PCPGP(6MA)PAPC)-3'*
	Chains	:	C, F
	Engineered	:	YES
	Other Details	:	SOLID-PHASE DNA SYNTHESIS USING COMMERCIALLY AVAILABLE PHOSPHORAMIDITES
	Synthetic	:	YES

Molecule 3 - 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
	Gene	:	TAQIM
	Organism Scientific	:	THERMUS AQUATICUS
	Organism Taxid	:	271
	Strain	:	YT1
	Synonym	:	ADENINE-SPECIFIC METHYLTRANSFERASE TAQI, M.TAQI

		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 (5, 15)

No.	Name	Count	Type	Full Name
1	2PR	2	Mod. Nucleotide	2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5'-MONOPHOSPHATE
2	3DR	2	Mod. Nucleotide	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
3	6MA	2	Mod. Nucleotide	N6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE
4	GOL	7	Ligand/Ion	GLYCEROL
5	NEA	2	Ligand/Ion	5'-DEOXY-5'-[2-(AMINO)ETHYLTHIO]ADENOSINE

Biological Unit 1 (5, 7)

No.	Name	Count	Type	Full Name
1	2PR	1	Mod. Nucleotide	2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5'-MONOPHOSPHATE
2	3DR	1	Mod. Nucleotide	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
3	6MA	1	Mod. Nucleotide	N6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE
4	GOL	3	Ligand/Ion	GLYCEROL
5	NEA	1	Ligand/Ion	5'-DEOXY-5'-[2-(AMINO)ETHYLTHIO]ADENOSINE

Biological Unit 2 (5, 8)

No.	Name	Count	Type	Full Name
1	2PR	1	Mod. Nucleotide	2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5'-MONOPHOSPHATE
2	3DR	1	Mod. Nucleotide	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
3	6MA	1	Mod. Nucleotide	N6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE
4	GOL	4	Ligand/Ion	GLYCEROL
5	NEA	1	Ligand/Ion	5'-DEOXY-5'-[2-(AMINO)ETHYLTHIO]ADENOSINE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:21 , 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:3002 , HOH A:3163 , HOH A:3189 , HOH A:3200 , HOH A:3277 , HOH A:3305	BINDING SITE FOR RESIDUE NEA A 2001
2	AC2	SOFTWARE	VAL D:21 , ALA D:47 , GLU D:71 , ILE D:72 , ASP D:73 , ALA D:76 , ALA D:88 , ASP D:89 , PHE D:90 , ASN D:105 , PRO D:107 , PHE D:146 , GOL D:3003 , HOH D:3109 , HOH D:3170 , HOH D:3243 , HOH D:3297	BINDING SITE FOR RESIDUE NEA D 2002
3	AC3	SOFTWARE	GLU A:317 , HOH A:3195 , HOH A:3313 , HOH A:3332 , HOH A:3384 , ALA D:233 , GLU D:234 , TYR D:235	BINDING SITE FOR RESIDUE GOL A 3001
4	AC4	SOFTWARE	TYR A:129 , LEU A:142 , NEA A:2001 , HOH A:3273 , HOH A:3411	BINDING SITE FOR RESIDUE GOL A 3002
5	AC5	SOFTWARE	ILE D:72 , TYR D:129 , LEU D:142 , NEA D:2002 , HOH D:3165 , HOH D:3359	BINDING SITE FOR RESIDUE GOL D 3003
6	AC6	SOFTWARE	ARG D:42 , ARG D:66 , GLU D:84 , ILE D:86 , PRO D:95 , HOH D:3072 , HOH D:3222	BINDING SITE FOR RESIDUE GOL D 3004
7	AC7	SOFTWARE	HIS A:278 , PRO A:279 , GLU A:321 , PRO D:81 , GOL D:3006	BINDING SITE FOR RESIDUE GOL D 3005
8	AC8	SOFTWARE	LYS A:277 , ARG D:58 , THR D:63 , TYR D:65 , PHE D:67 , TRP D:82 , GOL D:3005 , HOH D:3228	BINDING SITE FOR RESIDUE GOL D 3006
9	AC9	SOFTWARE	TYR A:191 , LEU A:192 , ASP A:219 , THR A:220 , GLN A:221 , GLU A:222 , ARG A:389 , HOH A:3034 , HOH A:3439 , HOH A:3440	BINDING SITE FOR RESIDUE GOL A 3007

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

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

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

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 2IBT)

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
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Chain A from PDB  Type:PROTEIN  Length:393
 aligned with MTTA_THEAQ | P14385 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:393
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410   
           MTTA_THEAQ    21 VETPPEVVDFMVSLAEAPRGGRVLEPACAHGPFLRAFREAHGTAYRFVGVEIDPKALDLPPWAEGILADFLLWEPGEAFDLILGNPPYGIVGEASKYPIHVFKAVKDLYKKAFSTWKGKYNLYGAFLEKAVRLLKPGGVLVFVVPATWLVLEDFALLREFLAREGKTSVYYLGEVFPQKKVSAVVIRFQKSGKGLSLWDTQESESGFTPILWAEYPHWEGEIIRFETEETRKLEISGMPLGDLFHIRFAARSPEFKKHPAVRKEPGPGLVPVLTGRNLKPGWVDYEKNHSGLWMPKERAKELRDFYATPHLVVAHTKGTRVVAAWDERAYPWREEFHLLPKEGVRLDPSSLVQWLNSEAMQKHVRTLYRDFVPHLTLRMLERLPVRREYGFHT 413
               SCOP domains d2ibta1 A:21-243 DNA methylase TaqI, N-terminal domain                                                                                                                                                                         d2ibta2 A:244-413 DNA methylase TaqI, C-terminal domain                                                                                                                    SCOP domains
               CATH domains 2ibtA01 A:21-243 Vaccinia Virus protein VP39                                                                                                                                                                                   2ibtA02 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...........eeeee.hhhhh.....eeeeee.................hhhhhhhhhhhh.......hhhhhhhhhhhhheeeeeeeeeeee.hhhhhhhhhhhhhhhhhhheeeeeeee.........eeeeeee.....eeeeeeeee..eeeeeeeeee...........hhhhhhhhh..ee....eeeee..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
                 2ibt A  21 VETPPEVVDFMVSLAEAPRGGRVLEPACAHGPFLRAFREAHGTAYRFVGVEIDPKALDLPPWAEGILADFLLWEPGEAFDLILGNPPYGIVGEASKYPIHVFKAVKDLYKKAFSTWKGKYNLYGAFLEKAVRLLKPGGVLVFVVPATWLVLEDFALLREFLAREGKTSVYYLGEVFPQKKVSAVVIRFQKSGKGLSLWDTQESESGFTPILWAEYPHWEGEIIRFETEETRKLEISGMPLGDLFHIRFAARSPEFKKHPAVRKEPGPGLVPVLTGRNLKPGWVDYEKNHSGLWMPKERAKELRDFYATPHLVVAHTKGTRVVAAWDERAYPWREEFHLLPKEGVRLDPSSLVQWLNSEAMQKHVRTLYRDFVPHLTLRMLERLPVRREYGFHT 413
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410

Chain B from PDB  Type:DNA  Length:10
                                          
                 2ibt B   1 GTTCGgTGTC  10
                                 |  10
                                 6-2PR

Chain C from PDB  Type:DNA  Length:10
                                          
                 2ibt C  11 GACAxCGaAC  20
                                |  |20
                               15-3DR 
                                  18-6MA

Chain D from PDB  Type:PROTEIN  Length:393
 aligned with MTTA_THEAQ | P14385 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:393
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410   
           MTTA_THEAQ    21 VETPPEVVDFMVSLAEAPRGGRVLEPACAHGPFLRAFREAHGTAYRFVGVEIDPKALDLPPWAEGILADFLLWEPGEAFDLILGNPPYGIVGEASKYPIHVFKAVKDLYKKAFSTWKGKYNLYGAFLEKAVRLLKPGGVLVFVVPATWLVLEDFALLREFLAREGKTSVYYLGEVFPQKKVSAVVIRFQKSGKGLSLWDTQESESGFTPILWAEYPHWEGEIIRFETEETRKLEISGMPLGDLFHIRFAARSPEFKKHPAVRKEPGPGLVPVLTGRNLKPGWVDYEKNHSGLWMPKERAKELRDFYATPHLVVAHTKGTRVVAAWDERAYPWREEFHLLPKEGVRLDPSSLVQWLNSEAMQKHVRTLYRDFVPHLTLRMLERLPVRREYGFHT 413
               SCOP domains d2ibtd1 D:21-243 DNA methylase TaqI, N-terminal domain                                                                                                                                                                         d2ibtd2 D:244-413 DNA methylase TaqI, C-terminal domain                                                                                                                    SCOP domains
               CATH domains 2ibtD01 D:21-243 Vaccinia Virus protein VP39                                                                                                                                                                                   2ibtD02 D:244-412 Adenine-n6-DNA-methyltransferase Taqi, Chain A, domain 2                                                                                               - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh......eeeee....hhhhhhhhhhhh...eeeeee...........eeeee.hhhhh.....eeeeee.................hhhhhhhhhhhh.......hhhhhhhhhhhhheeeeeeeeeeee.hhhhhhhhhhhhhhhhhhheeeeeeee.........eeeeeee.....eeeeeeee....eeeeeeeee...........hhhhhhhhhh.eehhhheeeee..hhhhhhh............ee..hhh.ee..ee.........eehhhhhhhhhhhhhh.eeee.........eeee.........eeeee...eeehhhhhhhhhhhhhhhhhhhhhhh......hhhhhhh.ee....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------N6_MTAS----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ibt D  21 VETPPEVVDFMVSLAEAPRGGRVLEPACAHGPFLRAFREAHGTAYRFVGVEIDPKALDLPPWAEGILADFLLWEPGEAFDLILGNPPYGIVGEASKYPIHVFKAVKDLYKKAFSTWKGKYNLYGAFLEKAVRLLKPGGVLVFVVPATWLVLEDFALLREFLAREGKTSVYYLGEVFPQKKVSAVVIRFQKSGKGLSLWDTQESESGFTPILWAEYPHWEGEIIRFETEETRKLEISGMPLGDLFHIRFAARSPEFKKHPAVRKEPGPGLVPVLTGRNLKPGWVDYEKNHSGLWMPKERAKELRDFYATPHLVVAHTKGTRVVAAWDERAYPWREEFHLLPKEGVRLDPSSLVQWLNSEAMQKHVRTLYRDFVPHLTLRMLERLPVRREYGFHT 413
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410

Chain E from PDB  Type:DNA  Length:10
                                          
                 2ibt E   1 GTTCGgTGTC  10
                                 |  10
                                 6-2PR

Chain F from PDB  Type:DNA  Length:10
                                          
                 2ibt F  11 GACAxCGaAC  20
                                |  |20
                               15-3DR 
                                  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

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	2ibtA01	A:21-243
1b	2ibtD01	D:21-243

Architecture: Alpha-Beta Complex (3881)

Topology: Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2 (12)

Homologous Superfamily: Adenine-n6-DNA-methyltransferase Taqi, Chain A, domain 2 (12)

[unclassified] (3)

2a	2ibtA02	A:244-412
2b	2ibtD02	D:244-412

(no "Pfam Domain" information available for 2IBT)

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.

Asymmetric Unit
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	Cis Peptide Bonds
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Biological Units
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	2ibt
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	MTTA_THEAQ \| P14385
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	2.1.1.72
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	MTTA_THEAQ \| P14385
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UniProtKB/Swiss-Prot
	MTTA_THEAQ \| P14385	:	1aqi 1aqj 1g38 2adm 2ibs 2ih2 2ih4 2ih5 2jg3 2np6 2np7

1aqi	ADENINE-SPECIFIC DNA METHYLTRANSFERASE M.TAQI/SAH COMPLEX
1aqj	ADENINE-SPECIFIC DNA METHYLTRANSFERASE M.TAQI/SINEFUNGIN COMPLEX
1g38	ADENINE-SPECIFIC DNA METHYLTRANSFERASE M.TAQI/DNA/AETA COMPLEX
2adm	ADENINE-SPECIFIC DNA METHYLTRANSFERASE M.TAQI/SAM COMPLEX
2ibs	ADENINE-SPECIFIC DNA METHYLTRANSFERASE M.TAQI/2PR-DNA/AETA COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 15)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 4)

CATH Domains (2, 4)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

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