2G1P | PD0787 - JenaLib

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Title :   STRUCTURE OF E. COLI DNA ADENINE METHYLTRANSFERASE (DAM)

Authors :   J. R. Horton, K. Liebert, M. Bekes, A. Jeltsch, X. Cheng

Date :   14 Feb 06 (Deposition) - 21 Nov 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.89

Chains :   Asym./Biol. Unit : A,B,F,G

Keywords :   Dam Methylation; Gatc Recognition; Base Flipping; Bacterial Virulence Factor, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. R. Horton, K. Liebert, M. Bekes, A. Jeltsch, X. Cheng
Structure And Substrate Recognition Of The Escherichia Coli Dna Adenine Methyltransferase.
J. Mol. Biol. V. 358 559 2006
PubMed-ID: 16524590 | Reference-DOI: 10.1016/J.JMB.2006.02.028

*Molecule 1 - 5'-D(TPCPTPAPGPAPTPCPTPAPGPA)-3'*
	Chains	:	F, G
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - DNA ADENINE METHYLASE
	Chains	:	A, B
	EC Number	:	2.1.1.72
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	HMS174(DE3)
	Expression System Taxid	:	562
	Gene	:	DAM
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	DEOXYADENOSYL-METHYLTRANSFERASE, DNA ADENINE METHYLTRANSFERASE, M.ECODAM

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	F	G

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:10 , LYS A:14 , PRO A:34 , PHE A:35 , VAL A:36 , GLY A:37 , ALA A:38 , GLY A:39 , SER A:40 , ASP A:54 , ILE A:55 , SER A:164 , TYR A:165 , ASP A:181 , PRO A:183 , HOH A:403 , HOH A:409 , HOH A:448	BINDING SITE FOR RESIDUE SAH A 401
2	AC2	SOFTWARE	TRP B:10 , LYS B:14 , PRO B:34 , PHE B:35 , VAL B:36 , GLY B:37 , ALA B:38 , GLY B:39 , SER B:40 , ASP B:54 , ILE B:55 , SER B:164 , TYR B:165 , ASP B:181 , HOH B:404 , HOH B:410 , HOH B:429 , HOH B:457 , HOH B:518	BINDING SITE FOR RESIDUE SAH B 402
3	AC3	SOFTWARE	TRP B:10 , ALA B:11 , GLY B:121 , LEU B:122 , CYS B:123 , HOH B:429 , HOH B:479	BINDING SITE FOR RESIDUE GOL B 397

(no "SS Bond" information available for 2G1P)

(no "Cis Peptide Bond" information available for 2G1P)

(no "SAP(SNP)/Variant" information available for 2G1P)

Asymmetric/Biological 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_ECOLI	178-184	2	A:178-184 B:178-184

(no "Exon" information available for 2G1P)

Asymmetric/Biological 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:244
 aligned with DMA_ECOLI | P0AEE8 from UniProtKB/Swiss-Prot  Length:278

    Alignment length:268
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262        
            DMA_ECOLI     3 KNRAFLKWAGGKYPLLDDIKRHLPKGECLVEPFVGAGSVFLNTDFSRYILADINSDLISLYNIVKMRTDEYVQAARELFVPETNCAEVYYQFREEFNKSQDPFRRAVLFLYLNRYGYNGLCRYNLRGEFNVPFGRYKKPYFPEAELYHFAEKAQNAFFYCESYADSMARADDASVVYCDPPYAPLSATANFTAYHTNSFTLEQQAHLAEIAEGLVERHIPVLISNHDTMLTREWYQRAKLHVVKVRRSISSNGGTRKKVDELLALYKP 270
               SCOP domains d2g1pa_ A: DNA methylase T4DAM                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhh....eeee.....hhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhh..eeeee.hhhhhhh.....eeeee.......-----------...hhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhh...eeeee.-------------...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------N6_MTAS-------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g1p A   3 KNRAFLKWAGGKYPLLDDIKRHLPKGECLVEPFVGAGSVFLNTDFSRYILADINSDLISLYNIVKMRTDEYVQAARELFVPETNCAEVYYQFREEFNKSQDPFRRAVLFLYLNRYGYNGLCRYNLRGEFNVPFGRYKKPYFPEAELYHFAEKAQNAFFYCESYADSMARADDSSVVYCDPPYAPL-----------NSFTLEQQAHLAEIAEGLVERHIPVLISNHDTMLTREWYQRAKLHVVK-------------KVDELLALYKP 270
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182    |    -      |202       212       222       232       242   |     -       262        
                                                                                                                                                                                                                  187         199                                            246           260

Chain B from PDB  Type:PROTEIN  Length:246
 aligned with DMA_ECOLI | P0AEE8 from UniProtKB/Swiss-Prot  Length:278

    Alignment length:268
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262        
            DMA_ECOLI     3 KNRAFLKWAGGKYPLLDDIKRHLPKGECLVEPFVGAGSVFLNTDFSRYILADINSDLISLYNIVKMRTDEYVQAARELFVPETNCAEVYYQFREEFNKSQDPFRRAVLFLYLNRYGYNGLCRYNLRGEFNVPFGRYKKPYFPEAELYHFAEKAQNAFFYCESYADSMARADDASVVYCDPPYAPLSATANFTAYHTNSFTLEQQAHLAEIAEGLVERHIPVLISNHDTMLTREWYQRAKLHVVKVRRSISSNGGTRKKVDELLALYKP 270
               SCOP domains d2g1pb_ B: DNA methylase T4DAM                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhh....eeee.....hhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhh..eeeee.hhhhhhh.....eeeee.......----------....hhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhh...eeeee..------------...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------N6_MTAS-------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g1p B   3 KNRAFLKWAGGKYPLLDDIKRHLPKGECLVEPFVGAGSVFLNTDFSRYILADINSDLISLYNIVKMRTDEYVQAARELFVPETNCAEVYYQFREEFNKSQDPFRRAVLFLYLNRYGYNGLCRYNLRGEFNVPFGRYKKPYFPEAELYHFAEKAQNAFFYCESYADSMARADDSSVVYCDPPYAPL----------TNSFTLEQQAHLAEIAEGLVERHIPVLISNHDTMLTREWYQRAKLHVVKV------------KVDELLALYKP 270
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182    |    -     | 202       212       222       232       242    |    -       262        
                                                                                                                                                                                                                  187        198                                              247          260

Chain F from PDB  Type:DNA  Length:12
                                            
                 2g1p F   1 TCTAGATCTAGA  12
                                    10

Chain G from PDB  Type:DNA  Length:12
                                            
                 2g1p G   1 TCTAGATCTAGA  12
                                    10

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/Biological Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: S-adenosyl-L-methionine-dependent methyltransferases (533)

Superfamily: S-adenosyl-L-methionine-dependent methyltransferases (533)

Family: N6 adenine-specific DNA methylase, DAM (13)

Protein domain: DNA methylase T4DAM (7)

Escherichia coli [TaxId: 562] (2)

1a	d2g1pa_	A:
1b	d2g1pb_	B:

(no "CATH Domain" information available for 2G1P)

(no "Pfam Domain" information available for 2G1P)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (DMA_ECOLI | P0AEE8)

molecular function
	GO:1904047	S-adenosyl-L-methionine binding	Interacting selectively and non-covalently with S-adenosyl-L-methionine.
	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:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
	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:0006261	DNA-dependent DNA replication	A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.
	GO:1902328	bacterial-type DNA replication initiation	Any DNA replication initiation that is involved in bacterial-type DNA replication.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0006298	mismatch repair	A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.

Asymmetric/Biological Unit
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	2g1p
		Family and Domain Information	:	ProDom \| SYSTERS
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	DMA_ECOLI \| P0AEE8
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	2.1.1.72
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1fy3	BACTERIOPHAGE T4DAM-ADOHCY-13-MER DNA
1q0s	BACTERIOPHAGE T4DAM-ADOHCY
1q0t	BACTERIOPHAGE T4DAM-ADOHY-DNA (NON-SPECIFIC)
1yfj	BACTERIOPHAGE T4DAM-ADOHCY-15-MER DNA
1yfl	BACTERIOPHAGE T4DAM-SINEFUNGIN-16-MER DNA

Description

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Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

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