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(-) Description

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)

(-) Compounds

Molecule 1 - 5'-D(*GP*TP*TP*CP*GP*(2PR)P*TP*GP*TP*C)-3'
    ChainsB, E
    EngineeredYES
    Other DetailsSOLID-PHASE DNA SYNTHESIS USING COMMERCIALLY AVAILABLE PHOSPHORAMIDITES
    SyntheticYES
 
Molecule 2 - 5'-D(*GP*AP*CP*AP*(3DR)P*CP*GP*(6MA)P*AP*C)-3'
    ChainsC, F
    EngineeredYES
    Other DetailsSOLID-PHASE DNA SYNTHESIS USING COMMERCIALLY AVAILABLE PHOSPHORAMIDITES
    SyntheticYES
 
Molecule 3 - MODIFICATION METHYLASE TAQI
    ChainsA, D
    EC Number2.1.1.72
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPA1/MTAQ-A49A
    Expression System StrainER2267
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneTAQIM
    Organism ScientificTHERMUS AQUATICUS
    Organism Taxid271
    StrainYT1
    SynonymADENINE-SPECIFIC METHYLTRANSFERASE TAQI, M.TAQI

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)ABC   
Biological Unit 2 (1x)   DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric Unit (5, 15)
No.NameCountTypeFull Name
12PR2Mod. Nucleotide2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5'-MONOPHOSPHATE
23DR2Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
36MA2Mod. NucleotideN6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE
4GOL7Ligand/IonGLYCEROL
5NEA2Ligand/Ion5'-DEOXY-5'-[2-(AMINO)ETHYLTHIO]ADENOSINE
Biological Unit 1 (5, 7)
No.NameCountTypeFull Name
12PR1Mod. Nucleotide2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5'-MONOPHOSPHATE
23DR1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
36MA1Mod. NucleotideN6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE
4GOL3Ligand/IonGLYCEROL
5NEA1Ligand/Ion5'-DEOXY-5'-[2-(AMINO)ETHYLTHIO]ADENOSINE
Biological Unit 2 (5, 8)
No.NameCountTypeFull Name
12PR1Mod. Nucleotide2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5'-MONOPHOSPHATE
23DR1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
36MA1Mod. NucleotideN6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE
4GOL4Ligand/IonGLYCEROL
5NEA1Ligand/Ion5'-DEOXY-5'-[2-(AMINO)ETHYLTHIO]ADENOSINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL 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:3305BINDING SITE FOR RESIDUE NEA A 2001
2AC2SOFTWAREVAL 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:3297BINDING SITE FOR RESIDUE NEA D 2002
3AC3SOFTWAREGLU A:317 , HOH A:3195 , HOH A:3313 , HOH A:3332 , HOH A:3384 , ALA D:233 , GLU D:234 , TYR D:235BINDING SITE FOR RESIDUE GOL A 3001
4AC4SOFTWARETYR A:129 , LEU A:142 , NEA A:2001 , HOH A:3273 , HOH A:3411BINDING SITE FOR RESIDUE GOL A 3002
5AC5SOFTWAREILE D:72 , TYR D:129 , LEU D:142 , NEA D:2002 , HOH D:3165 , HOH D:3359BINDING SITE FOR RESIDUE GOL D 3003
6AC6SOFTWAREARG D:42 , ARG D:66 , GLU D:84 , ILE D:86 , PRO D:95 , HOH D:3072 , HOH D:3222BINDING SITE FOR RESIDUE GOL D 3004
7AC7SOFTWAREHIS A:278 , PRO A:279 , GLU A:321 , PRO D:81 , GOL D:3006BINDING SITE FOR RESIDUE GOL D 3005
8AC8SOFTWARELYS A:277 , ARG D:58 , THR D:63 , TYR D:65 , PHE D:67 , TRP D:82 , GOL D:3005 , HOH D:3228BINDING SITE FOR RESIDUE GOL D 3006
9AC9SOFTWARETYR 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:3440BINDING SITE FOR RESIDUE GOL A 3007

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1N6_MTASEPS00092 N-6 Adenine-specific DNA methylases signature.MTTA_THEAQ102-108
 
  2A:102-108
D:102-108
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1N6_MTASEPS00092 N-6 Adenine-specific DNA methylases signature.MTTA_THEAQ102-108
 
  1A:102-108
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1N6_MTASEPS00092 N-6 Adenine-specific DNA methylases signature.MTTA_THEAQ102-108
 
  1-
D:102-108

(-) Exons   (0, 0)

(no "Exon" information available for 2IBT)

(-) Sequences/Alignments

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: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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric Unit

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MTTA_THEAQ | P143851aqi 1aqj 1g38 2adm 2ibs 2ih2 2ih4 2ih5 2jg3 2np6 2np7

(-) Related Entries Specified in the PDB File

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