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Title :   BINARY STRUCTURE OF ESCHERICHIA COLI DNA ADENINE METHYLTRANSFERASE AND S-ADENOSYLHOMOCYSTEINE

Authors :   J. R. Horton, X. Cheng

Date :   02 Feb 07 (Deposition) - 26 Jun 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.99

Chains :   Asym. Unit : D,E,F
Biol. Unit 1: D  (1x)
Biol. Unit 2: E  (1x)
Biol. Unit 3: F  (1x)

Keywords :   Dam Methylation, Gatc Recognition, S-Adenosylhomocysteine Conformation, Bacterial Virulence Factor, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Liebert, J. R. Horton, S. Chahar, M. Orwick, X. Cheng, A. Jeltsch
Two Alternative Conformations Of S-Adenosyl-L-Homocysteine Bound To Escherichia Coli Dna Adenine Methyltransferase And The Implication Of Conformational Changes In Regulating The Catalytic Cycle.
J. Biol. Chem. V. 282 22848 2007
PubMed-ID: 17545164 | Reference-DOI: 10.1074/JBC.M700926200
(for further references see the PDB file header)

Molecule 1 - DNA ADENINE METHYLASE
	Chains	:	D, E, F
	EC Number	:	2.1.1.72
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	HMS174(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DAM
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	DEOXYADENOSYL-METHYLTRANSFERASE, DNA ADENINE METHYLTRANSFERASE, M.ECODAM

		1	2	3
Asymmetric Unit	:	D	E	F
Biological Unit 1 (1x)	:	D
Biological Unit 2 (1x)	:		E
Biological Unit 3 (1x)	:			F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	SAH	3	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
2	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
2	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
2	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO D:83 , ARG F:171	BINDING SITE FOR RESIDUE SO4 F 501
2	AC2	SOFTWARE	TRP D:10 , PRO D:34 , PHE D:35 , ASP D:54 , ILE D:55 , SER D:164 , TYR D:165 , ASP D:181 , PRO D:183 , TYR D:184	BINDING SITE FOR RESIDUE SAH D 301
3	AC3	SOFTWARE	TRP E:10 , ALA E:11 , GLY E:12 , PRO E:34 , PHE E:35 , VAL E:36 , GLY E:37 , ALA E:38 , SER E:40 , ASP E:54 , ILE E:55 , SER E:164 , TYR E:165 , ASP E:181 , PRO E:182 , PRO E:183 , TYR E:184	BINDING SITE FOR RESIDUE SAH E 302
4	AC4	SOFTWARE	TRP F:10 , ALA F:11 , GLY F:13 , LYS F:14 , PRO F:34 , PHE F:35 , VAL F:36 , GLY F:37 , ALA F:38 , GLY F:39 , SER F:40 , ASP F:54 , ILE F:55 , SER F:164 , TYR F:165 , ASP F:181 , PRO F:182 , PRO F:183 , TYR F:184	BINDING SITE FOR RESIDUE SAH F 303

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

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

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

Asymmetric Unit (1, 3)

	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	3	D:178-184 E:178-184 F:178-184

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.	DMA_ECOLI	178-184	1	D:178-184 - -

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.	DMA_ECOLI	178-184	1	- E:178-184 -

Biological Unit 3 (1, 1)

	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	1	- - F:178-184

(no "Exon" information available for 2ORE)

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 D from PDB  Type:PROTEIN  Length:243
 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 d2ored_ D: DNA methylase T4DAM                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhh.....eeee.....hhhhhh....eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhh..eeee..hhhhhhh.....eeeee.......-----------...hhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhh...eeeee.--------------..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------N6_MTAS-------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ore D   3 KNRAFLKWAGGKYPLLDDIKRHLPKGECLVEPFVGAGSVFLNTDFSRYILADINSDLISLYNIVKMRTDEYVQAARELFVPETNCAEVYYQFREEFNKSQDPFRRAVLFLYLNRYGYNGLCRYNLRGEFNVPFGRYKKPYFPEAELYHFAEKAQNAFFYCESYADSMARADDASVVYCDPPYAPL-----------NSFTLEQQAHLAEIAEGLVERHIPVLISNHDTMLTREWYQRAKLHVVK--------------VDELLALYKP 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            261

Chain E 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 d2oree_ E: DNA methylase T4DAM                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhh....eeee.....hhhhhh....eeeee..hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhh...ee..hhhhhhh.....eeeee.......------------..hhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhh...eeeee..------------...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------N6_MTAS-------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ore E   3 KNRAFLKWAGGKYPLLDDIKRHLPKGECLVEPFVGAGSVFLNTDFSRYILADINSDLISLYNIVKMRTDEYVQAARELFVPETNCAEVYYQFREEFNKSQDPFRRAVLFLYLNRYGYNGLCRYNLRGEFNVPFGRYKKPYFPEAELYHFAEKAQNAFFYCESYADSMARADDASVVYCDPPYAPL------------SFTLEQQAHLAEIAEGLVERHIPVLISNHDTMLTREWYQRAKLHVVKV------------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          200                                            247          260

Chain F 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 d2oref_ F: DNA methylase T4DAM                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------MethyltransfD12-2oreF01 F:10-247                                                                                                                                                                                                                           ---------- Pfam domains (1)
           Pfam domains (2) -------MethyltransfD12-2oreF02 F:10-247                                                                                                                                                                                                                           ---------- Pfam domains (2)
           Pfam domains (3) -------MethyltransfD12-2oreF03 F:10-247                                                                                                                                                                                                                           ---------- Pfam domains (3)
         Sec.struct. author ...........hhhhhhhhhhhh....eeee.......hhhhh...eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhh..eeee..hhhhhhhhh...eeeee.......-----------...hhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhh...eeeee..-------------..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------N6_MTAS-------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ore F   3 KNRAFLKWAGGKYPLLDDIKRHLPKGECLVEPFVGAGSVFLNTDFSRYILADINSDLISLYNIVKMRTDEYVQAARELFVPETNCAEVYYQFREEFNKSQDPFRRAVLFLYLNRYGYNGLCRYNLRGEFNVPFGRYKKPYFPEAELYHFAEKAQNAFFYCESYADSMARADDASVVYCDPPYAPL-----------NSFTLEQQAHLAEIAEGLVERHIPVLISNHDTMLTREWYQRAKLHVVKV-------------VDELLALYKP 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                                             247           261

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(

)

Folds(

)

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	d2ored_	D:
1b	d2oree_	E:
1c	d2oref_	F:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: MethyltransfD12 (6)

Escherichia coli (strain K12) (1)

1a	MethyltransfD12-2oreF01	F:10-247
1b	MethyltransfD12-2oreF02	F:10-247
1c	MethyltransfD12-2oreF03	F:10-247

Asymmetric Unit(hide GO term definitions)

Chain D,E,F (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.

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2g1p	STRUCTURE OF E. COLI DNA ADENINE METHYLTRANSFERASE (DAM)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 4)

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