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Title :   CRYSTAL STRUCTURE OF TYPE I RESTRICTION ENZYME ECOKI M PROTEIN (EC 2.1.1.72) (M.ECOKI)

Authors :   K. R. Rajashankar, R. Kniewel, C. D. Lima, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   18 Aug 05 (Deposition) - 30 Aug 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Structural Genomics; Protein Structure Initiative; Nysgxrc; T824; Q9Pnp0 Restriction Modification Enzyme; Type I Restriction Enzyme Ecoki M Protein; Methyltransferase, Psi, New York Sgx Research Center For Structural Genomics, Transcription, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. R. Rajashankar, R. Kniewel, C. D. Lima
Crystal Structure Of Type I Restriction Enzyme Ecoki M Protein (Ec 2. 1. 1. 72) (M. Ecoki).
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - TYPE I RESTRICTION ENZYME ECOKI M PROTEIN
	Chains	:	A, B
	EC Number	:	2.1.1.72
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET T7
	Expression System Strain	:	B834, DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HSDM, HSM
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	M.ECOKI

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 28)

No.	Name	Count	Type	Full Name
1	MSE	18	Mod. Amino Acid	SELENOMETHIONINE
2	UNX	10	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 1 (2, 19)

No.	Name	Count	Type	Full Name
1	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
2	UNX	10	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 2 (1, 9)

No.	Name	Count	Type	Full Name
1	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
2	UNX	-1	Ligand/Ion	UNKNOWN ATOM OR ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	UNX A:1002	BINDING SITE FOR RESIDUE UNX A 1001
2	AC2	SOFTWARE	ARG A:519 , UNX A:1001 , UNX A:1004	BINDING SITE FOR RESIDUE UNX A 1002
3	AC3	SOFTWARE	TRP A:13 , ARG B:519	BINDING SITE FOR RESIDUE UNX A 1003
4	AC4	SOFTWARE	TYR A:26 , UNX A:1002	BINDING SITE FOR RESIDUE UNX A 1004
5	AC5	SOFTWARE	UNX A:1008	BINDING SITE FOR RESIDUE UNX A 1006
6	AC6	SOFTWARE	ARG A:519 , UNX A:1009	BINDING SITE FOR RESIDUE UNX A 1007
7	AC7	SOFTWARE	UNX A:1006	BINDING SITE FOR RESIDUE UNX A 1008
8	AC8	SOFTWARE	ARG A:519 , UNX A:1007 , ARG B:519	BINDING SITE FOR RESIDUE UNX A 1009

(no "SS Bond" information available for 2AR0)

(no "Cis Peptide Bond" information available for 2AR0)

(no "SAP(SNP)/Variant" information available for 2AR0)

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.	T1MK_ECOLI	263-269	2	A:265-271 B:265-271

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.	T1MK_ECOLI	263-269	1	A:265-271 -

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.	T1MK_ECOLI	263-269	1	- B:265-271

(no "Exon" information available for 2AR0)

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:485
 aligned with T1MK_ECOLI | P08957 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:524
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523    
           T1MK_ECOLI     4 NDLVAKLWKLCDNLRDGGVSYQNYVNELASLLFLKMCKETGQEAEYLPEGYRWDDLKSRIGQEQLQFYRKMLVHLGEDDKKLVQAVFHNVSTTITEPKQITALVSNMDSLDWYNGAHGKSRDDFGDMYEGLLQKNANETKSGAGQYFTPRPLIKTIIHLLKPQPREVVQDPAAGTAGFLIEADRYVKSQTNDLDDLDGDTQDFQIHRAFIGLELVPGTRRLALMNCLLHDIEGNLDHGGAIRLGNTLGSDGENLPKAHIVATNPPFGSAAGTNITRTFVHPTSNKQLCFMQHIIETLHPGGRAAVVVPDNVLFEGGKGTDIRRDLMDKCHLHTILRLPTGIFYAQGVKTNVLFFTKGTVANPNQDKNCTDDVWVYDLRTNMPSFGKRTPFTDEHLQPFERVYGEDPHGLSPRTEGEWSFNAEETEVADSEENKNTDQHLATSRWRKFSREWIRTAKSDSLDISWLKDKDSIDADSLPEPDVLAAEAMGELVQALSELDALMRELGASDEADLQRQLLEEAFGGV 527
               SCOP domains d2ar0a1 A:6-529 M.EcoKI                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhh.......hhhhhhhhhhhhhh...--------------------------------....hhhhhhhhhhhhh......eee.....hhhhhhhhhhhhh........hhhhhhhhhhh.eeeee.hhhhhhhhhhhhhh.....hhhhh..eee....hhhhhh...eeeeee.....................hhhhhhhhhhhhheeeeeeeeeeeehhhhhh.hhhhhhhhhhhhheeeeeeee............eeeeeeee..............eeeeee..............hhhhhhhhhhhhh.....................ee..hhhhh....hhhhh.eeeeehhhhhhh.........ee...-------.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------N6_MTAS------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ar0 A   6 NDLVAKLWKLCDNLRDGGVSYQNYVNELASLLFLKmCKETGQEAEYLPEGYRWDDLKSRIGQEQLQFYRKmLVHLGEDDKKLVQAVFHNVSTTITEPKQITALVSNmDSLDW--------------------------------QYFTPRPLIKTIIHLLKPQPREVVQDPAAGTAGFLIEADRYVKSQTNDLDDLDGDTQDFQIHRAFIGLELVPGTRRLALmNCLLHDIEGNLDHGGAIRLGNTLGSDGENLPKAHIVATNPPFGSAAGTNITRTFVHPTSNKQLCFmQHIIETLHPGGRAAVVVPDNVLFEGGKGTDIRRDLmDKCHLHTILRLPTGIFYAQGVKTNVLFFTKGTVANPNQDKNCTDDVWVYDLRTNmPSFGKRTPFTDEHLQPFERVYGEDPHGLSPRTEGEWSFNAEETEVADSEENKNTDQHLATSRWRKFSREWIRTAKSDSLDISWLKDKD-------PEPDVLAAEAmGELVQALSELDALmRELGASDEADLQRQLLEEAFGGV 529
                                    15        25        35     |  45        55        65        75|       85        95       105      |115 |       -         -         -    |  155       165       175       185       195       205       215       225   |   235       245       255       265       275       285       295       305       315       325     | 335       345       355       365       375       385|      395       405       415       425       435       445       455       465        |-      |485      |495       505|      515       525    
                                                              41-MSE                             76-MSE                             112-MSE7                              150                                                                            229-MSE                                                           295-MSE                             331-MSE                                                386-MSE                                                                                 474     482       492-MSE       506-MSE

Chain B from PDB  Type:PROTEIN  Length:483
 aligned with T1MK_ECOLI | P08957 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:522
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523  
           T1MK_ECOLI     4 NDLVAKLWKLCDNLRDGGVSYQNYVNELASLLFLKMCKETGQEAEYLPEGYRWDDLKSRIGQEQLQFYRKMLVHLGEDDKKLVQAVFHNVSTTITEPKQITALVSNMDSLDWYNGAHGKSRDDFGDMYEGLLQKNANETKSGAGQYFTPRPLIKTIIHLLKPQPREVVQDPAAGTAGFLIEADRYVKSQTNDLDDLDGDTQDFQIHRAFIGLELVPGTRRLALMNCLLHDIEGNLDHGGAIRLGNTLGSDGENLPKAHIVATNPPFGSAAGTNITRTFVHPTSNKQLCFMQHIIETLHPGGRAAVVVPDNVLFEGGKGTDIRRDLMDKCHLHTILRLPTGIFYAQGVKTNVLFFTKGTVANPNQDKNCTDDVWVYDLRTNMPSFGKRTPFTDEHLQPFERVYGEDPHGLSPRTEGEWSFNAEETEVADSEENKNTDQHLATSRWRKFSREWIRTAKSDSLDISWLKDKDSIDADSLPEPDVLAAEAMGELVQALSELDALMRELGASDEADLQRQLLEEAFG 525
               SCOP domains d2ar0b_ B: M.EcoKI                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhh.......hhhhhhhhhhhhhh...--------------------------------....hhhhhhhhhhhhh......eee.....hhhhhhhhhhhhh........hhhhhhhhhhh.eeeee.hhhhhhhhhhhhhh.....hhhhh..eee....hhhhhh...eeeeee.....................hhhhhhhhhhhhheeeeeeeeeeeehhhhhh.hhhhhhhhhhhhheeeeeeee............eeeeeeee..............eeeeee..............hhhhhhhhhhhhh.....................ee..hhhhh....hhhhh.eeeeehhhhhhh.........ee...-------.hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------N6_MTAS---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ar0 B   6 NDLVAKLWKLCDNLRDGGVSYQNYVNELASLLFLKmCKETGQEAEYLPEGYRWDDLKSRIGQEQLQFYRKmLVHLGEDDKKLVQAVFHNVSTTITEPKQITALVSNmDSLDW--------------------------------QYFTPRPLIKTIIHLLKPQPREVVQDPAAGTAGFLIEADRYVKSQTNDLDDLDGDTQDFQIHRAFIGLELVPGTRRLALmNCLLHDIEGNLDHGGAIRLGNTLGSDGENLPKAHIVATNPPFGSAAGTNITRTFVHPTSNKQLCFmQHIIETLHPGGRAAVVVPDNVLFEGGKGTDIRRDLmDKCHLHTILRLPTGIFYAQGVKTNVLFFTKGTVANPNQDKNCTDDVWVYDLRTNmPSFGKRTPFTDEHLQPFERVYGEDPHGLSPRTEGEWSFNAEETEVADSEENKNTDQHLATSRWRKFSREWIRTAKSDSLDISWLKDKD-------PEPDVLAAEAmGELVQALSELDALmRELGASDEADLQRQLLEEAFG 527
                                    15        25        35     |  45        55        65        75|       85        95       105      |115 |       -         -         -    |  155       165       175       185       195       205       215       225   |   235       245       255       265       275       285       295       305       315       325     | 335       345       355       365       375       385|      395       405       415       425       435       445       455       465        |-      |485      |495       505|      515       525  
                                                              41-MSE                             76-MSE                             112-MSE7                              150                                                                            229-MSE                                                           295-MSE                             331-MSE                                                386-MSE                                                                                 474     482       492-MSE       506-MSE

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: N-6 DNA Methylase-like (3)

Protein domain: M.EcoKI (1)

Escherichia coli [TaxId: 562] (1)

1a	d2ar0a1	A:6-529
1b	d2ar0b_	B:

(no "CATH Domain" information available for 2AR0)

(no "Pfam Domain" information available for 2AR0)

Asymmetric Unit(hide GO term definitions)

Chain A,B (T1MK_ECOLI | P08957)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0008170	N-methyltransferase activity	Catalysis of the transfer of a methyl group to the nitrogen atom of an acceptor molecule.
	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:0006306	DNA methylation	The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
	GO:0032775	DNA methylation on adenine	The covalent transfer of a methyl group to N-6 of adenine in a DNA molecule.
	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.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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(no "Cis Peptide Bonds" information available for 2ar0)

Biological Units
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Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 28)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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