2NP6 - JenaLib

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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 AN ABASIC SITE ANALOG AT THE TARGET POSITION

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

Date :   26 Oct 06 (Deposition) - 13 Nov 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Reference :   T. Lenz, A. J. Scheidig, E. Weinhold
Caught In The Act Ii: Visualization Of An Intermediate In The Dna Base-Flipping Pathway Induced By The Adenine-Specific Dna Methyltransferase M. Taqi
To Be Published
PubMed: search
(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
	Gene	:	TAQIM
	Organism Scientific	:	THERMUS AQUATICUS
	Organism Taxid	:	271
	Strain	:	YT1
	Synonym	:	ADENINE-SPECIFIC METHYLTRANSFERASE TAQI, M.TAQI

*Molecule 2 - 5'-D(GPTPTPCPGP(3DR)PTPGPTPC)-3'*
	Chains	:	B, E
	Engineered	:	YES
	Other Details	:	DNA TARGET STRAND CONTAINING AN ABASIC SITE ANALOG AT THE TARGET POSITION
	Other Details - Source	:	SOLID-PHASE DNA SYNTHESIS
	Synthetic	:	YES

*Molecule 3 - 5'-D(GPAPCPAPTPCPGP(6MA)PAPC)-3'*
	Chains	:	C, F
	Engineered	:	YES
	Other Details	:	DNA PARTNER STRAND CONTAINING N6-METHYLADENINE
	Other Details - Source	:	SOLID-PHASE DNA SYNTHESIS
	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 (5, 11)

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

Biological Unit 1 (4, 5)

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

Biological Unit 2 (5, 6)

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

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:20 , VAL A:21 , ALA A:47 , ALA A:49 , 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 , HOH A:724 , HOH A:788 , HOH A:850 , HOH A:907	BINDING SITE FOR RESIDUE NEA A 601
2	AC2	SOFTWARE	VAL D:21 , ALA D:47 , GLU D:71 , ILE D:72 , ALA D:88 , ASP D:89 , PHE D:90 , ASN D:105 , PRO D:107 , PHE D:146 , GOL D:701 , GOL D:702 , HOH D:786	BINDING SITE FOR RESIDUE NEA D 602
3	AC3	SOFTWARE	VAL D:121 , TYR D:129 , LEU D:142 , NEA D:602	BINDING SITE FOR RESIDUE GOL D 701
4	AC4	SOFTWARE	VAL D:21 , ASN D:105 , PRO D:106 , PRO D:107 , TYR D:108 , LYS D:199 , NEA D:602	BINDING SITE FOR RESIDUE GOL D 702
5	AC5	SOFTWARE	ILE A:242 , ARG A:244 , GLU A:246 , ARG A:402 , HOH A:869	BINDING SITE FOR RESIDUE IPA A 703
6	AC6	SOFTWARE	ARG D:296 , DG E:8 , DA F:14 , DT F:15	BINDING SITE FOR RESIDUE IPA E 704
7	AC7	SOFTWARE	ARG A:296 , DG B:8 , DT B:9 , DT C:15 , HOH C:26	BINDING SITE FOR RESIDUE IPA B 705

(no "SS Bond" information available for 2NP6)

(no "Cis Peptide Bond" information available for 2NP6)

(no "SAP(SNP)/Variant" information available for 2NP6)

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 2NP6)

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:394
 aligned with MTTA_THEAQ | P14385 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:394
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409    
           MTTA_THEAQ    20 RVETPPEVVDFMVSLAEAPRGGRVLEPACAHGPFLRAFREAHGTAYRFVGVEIDPKALDLPPWAEGILADFLLWEPGEAFDLILGNPPYGIVGEASKYPIHVFKAVKDLYKKAFSTWKGKYNLYGAFLEKAVRLLKPGGVLVFVVPATWLVLEDFALLREFLAREGKTSVYYLGEVFPQKKVSAVVIRFQKSGKGLSLWDTQESESGFTPILWAEYPHWEGEIIRFETEETRKLEISGMPLGDLFHIRFAARSPEFKKHPAVRKEPGPGLVPVLTGRNLKPGWVDYEKNHSGLWMPKERAKELRDFYATPHLVVAHTKGTRVVAAWDERAYPWREEFHLLPKEGVRLDPSSLVQWLNSEAMQKHVRTLYRDFVPHLTLRMLERLPVRREYGFHT 413
               SCOP domains -d2np6a1 A:21-243 DNA methylase TaqI, N-terminal domain                                                                                                                                                                         d2np6a2 A:244-413 DNA methylase TaqI, C-terminal domain                                                                                                                    SCOP domains
               CATH domains 2np6A01 A:20-243 Vaccinia Virus protein VP39                                                                                                                                                                                    2np6A02 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...........eeeeee.................hhhhhhhhhhhh.......hhhhhhhhhhhhheeeeeeeeeeee.hhhhhhhhhhhhhhhhhhheeeeeeee.........eeeeeee.....eeeeeeeee..eeeeeeeeee...........hhhhhhhhhh.eehhhheeeee..hhhhhhhh..........eee......ee..ee.........eee.hhhhhhhhhhhh.eeee.........eeee.........eeeee...eeehhhhhhhhhhhhhhhhhhhhhhh......hhhhhh..ee....eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------N6_MTAS----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2np6 A  20 RVETPPEVVDFMVSLAEAPRGGRVLEPACAHGPFLRAFREAHGTAYRFVGVEIDPKALDLPPWAEGILADFLLWEPGEAFDLILGNPPYGIVGEASKYPIHVFKAVKDLYKKAFSTWKGKYNLYGAFLEKAVRLLKPGGVLVFVVPATWLVLEDFALLREFLAREGKTSVYYLGEVFPQKKVSAVVIRFQKSGKGLSLWDTQESESGFTPILWAEYPHWEGEIIRFETEETRKLEISGMPLGDLFHIRFAARSPEFKKHPAVRKEPGPGLVPVLTGRNLKPGWVDYEKNHSGLWMPKERAKELRDFYATPHLVVAHTKGTRVVAAWDERAYPWREEFHLLPKEGVRLDPSSLVQWLNSEAMQKHVRTLYRDFVPHLTLRMLERLPVRREYGFHT 413
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409

Chain B from PDB  Type:DNA  Length:10
                                          
                 2np6 B   1 GTTCGxTGTC  10
                                 |  10
                                 6-3DR

Chain C from PDB  Type:DNA  Length:10
                                          
                 2np6 C  11 GACATCGaAC  20
                                   |20
                                  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 d2np6d1 D:21-243 DNA methylase TaqI, N-terminal domain                                                                                                                                                                         d2np6d2 D:244-413 DNA methylase TaqI, C-terminal domain                                                                                                                    SCOP domains
               CATH domains 2np6D01 D:21-243 Vaccinia Virus protein VP39                                                                                                                                                                                   2np6D02 D:244-412 Adenine-n6-DNA-methyltransferase Taqi, Chain A, domain 2                                                                                               - CATH domains
           Pfam domains (1) -------------------Methyltransf_26-2np6D01 D:40-166                                                                                               ---------------------------------------------------------------------------------------------------------------------------TaqI_C-2np6D03 D:290-405                                                                                            -------- Pfam domains (1)
           Pfam domains (2) -------------------Methyltransf_26-2np6D02 D:40-166                                                                                               ---------------------------------------------------------------------------------------------------------------------------TaqI_C-2np6D04 D:290-405                                                                                            -------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhh......eeeee....hhhhhhhhhhhh...eeeeee...........eeeee...........eeeeee.................hhhhhhhhhhhh.......hhhhhhhhhhhhheeeeeeeeeeee.hhhhhhhhhhhhhhhhhhheeeeeeee.........eeeeeee.....eeeeeeee....eeeeeeeee...........hhhhhhhhhh.ee....eeeee..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
                 2np6 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
                                          
                 2np6 E   1 GTTCGxTGTC  10
                                 |  10
                                 6-3DR

Chain F from PDB  Type:DNA  Length:10
                                          
                 2np6 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_26-2np6D01	D:40-166
1b	Methyltransf_26-2np6D02	D:40-166

Clan: TRD (7)

Family: TaqI_C (3)

Thermus aquaticus (3)

2a	TaqI_C-2np6D03	D:290-405
2b	TaqI_C-2np6D04	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.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2np6)

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	2np6
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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 2ibt 2ih2 2ih4 2ih5 2jg3 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
2ibt	ADENINE-SPECIFIC DNA METHYLTRANSFERASE M.TAQI/2PR-3DR-DNA/ AETA COMPLEX
2ih2	ADENINE-SPECIFIC DNA METHYLTRANSFERASE M.TAQI/5PY-DNA/AETA COMPLEX
2ih4	ADENINE-SPECIFIC DNA METHYLTRANSFERASE M.TAQI/4PC-DNA/AETA COMPLEX
2ih5	ADENINE-SPECIFIC DNA METHYLTRANSFERASE M.TAQI/3DR-DNA/AETA COMPLEX
2np7	ADENINE-SPECIFIC DNA METHYLTRANSFERASE M.TAQI/3DR-4PC-DNA/ AETA COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 11)

Sites (7, 7)

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

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (2, 4)

Pfam Domains (2, 4)

Gene Ontology (10, 10)

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