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Title :   CRYSTAL STRUCTURE OF TYPE I RESTRICTION ENZYME STYSJI M PROTEIN (NP_813429.1) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 2.20 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   16 Jan 07 (Deposition) - 30 Jan 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Np_813429. 1, N-6 Dna Methylase, Type I Restriction Enzyme Stysji M Protein, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Type I Restriction Enzyme Stysji M Protein (Np_813429. 1) From Bacteroides Thetaiotaomicron Vpi-5482 At 2. 20 A Resolution
To Be Published
PubMed: search

Molecule 1 - TYPE I RESTRICTION ENZYME STYSJI M PROTEIN
	Atcc	:	29148
	Chains	:	A, B
	EC Number	:	2.1.1.72
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	SPEEDET
	Expression System Strain	:	HK100
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-444
	Gene	:	NP_813429.1
	Organism Scientific	:	BACTEROIDES THETAIOTAOMICRON VPI-5482
	Organism Taxid	:	226186
	Strain	:	VPI-5482, E50

		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 (5, 28)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	IPA	2	Ligand/Ion	ISOPROPYL ALCOHOL
4	MSE	22	Mod. Amino Acid	SELENOMETHIONINE
5	SAM	2	Ligand/Ion	S-ADENOSYLMETHIONINE

Biological Unit 1 (4, 14)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	IPA	1	Ligand/Ion	ISOPROPYL ALCOHOL
4	MSE	11	Mod. Amino Acid	SELENOMETHIONINE
5	SAM	1	Ligand/Ion	S-ADENOSYLMETHIONINE

Biological Unit 2 (3, 13)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	-1	Ligand/Ion	GLYCEROL
3	IPA	1	Ligand/Ion	ISOPROPYL ALCOHOL
4	MSE	11	Mod. Amino Acid	SELENOMETHIONINE
5	SAM	1	Ligand/Ion	S-ADENOSYLMETHIONINE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:151 , TYR A:152 , PHE A:153 , THR A:154 , ARG A:156 , PRO A:177 , ALA A:178 , CYS A:179 , GLY A:180 , THR A:181 , GLY A:183 , PHE A:184 , ASP A:214 , ASN A:215 , THR A:216 , GLU A:242 , ASP A:243 , SER A:244 , ASN A:259 , PRO A:261 , PHE A:288 , HOH A:536 , HOH A:576	BINDING SITE FOR RESIDUE SAM A 500
2	AC2	SOFTWARE	GLN B:151 , TYR B:152 , PHE B:153 , THR B:154 , ARG B:156 , PRO B:177 , ALA B:178 , CYS B:179 , GLY B:180 , THR B:181 , GLY B:183 , PHE B:184 , ASP B:214 , ASN B:215 , THR B:216 , GLU B:242 , ASP B:243 , SER B:244 , ASN B:259 , PRO B:261 , PHE B:288 , HOH B:525 , HOH B:537 , HOH B:562 , HOH B:628	BINDING SITE FOR RESIDUE SAM B 500
3	AC3	SOFTWARE	HIS A:331 , TYR A:392 , ARG A:395 , HOH A:627	BINDING SITE FOR RESIDUE GOL A 501
4	AC4	SOFTWARE	LEU A:138 , ASN A:141 , GLY A:142 , ALA A:149 , PHE A:153	BINDING SITE FOR RESIDUE IPA A 502
5	AC5	SOFTWARE	ASP B:164 , ARG B:382 , ASP B:386	BINDING SITE FOR RESIDUE IPA B 501

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

Asymmetric Unit

No.	Residues
1	Ser A:198	-	Lys A:199
2	Ser B:196	-	Ala B:197
3	Ser B:198	-	Lys B:199

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

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.	T1M_BACTN	256-262	2	A:256-262 B:256-262

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.	T1M_BACTN	256-262	1	A:256-262 -

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.	T1M_BACTN	256-262	1	- B:256-262

(no "Exon" information available for 2OKC)

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:424
 aligned with T1M_BACTN | Q89Z59 from UniProtKB/Swiss-Prot  Length:472

    Alignment length:425
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428     
            T1M_BACTN     9 QSLTKKVWNLATTLAGQGIGFTDYITQLTYLLFLKMDAENVEMFGEESAIPTGYQWADLIAFDGLDLVKQYEETLKLLSELDNLIGTIYTKAQNKIDKPVYLKKVITMIDEEQWLIMDGDVKGAIYESILEKNGQDKKSGAGQYFTPRPLIQAMVDCINPQMGETVCDPACGTGGFLLTAYDYMKGQSASKEKRDFLRDKALHGVDNTPLVVTLASMNLYLHGIGTDRSPIVCEDSLEKEPSTLVDVILANPPFGTRPAGSVDINRPDFYVETKNNQLNFLQHMMLMLKTGGRAAVVLPDNVLFEAGAGETIRKRLLQDFNLHTILRLPTGIFYAQGVKANVLFFSKGQPTKEIWFYDYRTDIKHTLATNKLERHHLDDFVSCYNNRVEIYDAENNPQGRWRKYPVDEIIARDKTSLDITWIKPG 433
               SCOP domains d2okca1 A:9-433 Type I restriction enzyme StySJI M protein                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhh........hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.....hhhhh.hhhhhhhhhhhhh......eee.....hhhhhhhhhhhhh..-.hhhhhhhhhh.eeeee.hhhhhhhhhhhhhhh........eee...........eeeeee........................hhhhhhhhhhhhheeeeeeeeeeeehhhhhh.hhhhhhhhhhhhheeeeeeee............eeeeeeee.....eeeeee..............hhhhhhhhhhhhhh..............eeeeehhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------N6_MTAS--------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2okc A   9 QSLTKKVWNLATTLAGQGIGFTDYITQLTYLLFLKmDAENVEmFGEESAIPTGYQWADLIAFDGLDLVKQYEETLKLLSELDNLIGTIYTKAQNKIDKPVYLKKVITmIDEEQWLImDGDVKGAIYESILEKNGQDKKSGAGQYFTPRPLIQAmVDCINPQmGETVCDPACGTGGFLLTAYDYmKGQS-SKEKRDFLRDKALHGVDNTPLVVTLASmNLYLHGIGTDRSPIVCEDSLEKEPSTLVDVILANPPFGTRPAGSVDINRPDFYVETKNNQLNFLQHmmLmLKTGGRAAVVLPDNVLFEAGAGETIRKRLLQDFNLHTILRLPTGIFYAQGVKANVLFFSKGQPTKEIWFYDYRTDIKHTLATNKLERHHLDDFVSCYNNRVEIYDAENNPQGRWRKYPVDEIIARDKTSLDITWIKPG 433
                                    18        28        38     |  48  |     58        68        78        88        98       108       118      |128       138       148       158   |   168 |     178       188   |   198       208       218      |228       238       248       258       268       278       288   || |298       308       318       328       338       348       358       368       378       388       398       408       418       428     
                                                              44-MSE 51-MSE                                                          116-MSE  125-MSE                              162-MSE 170-MSE               192-MSE |                        225-MSE                                                            292-MSE                                                                                                                                         
                                                                                                                                                                                                                       198                                                                                            293-MSE                                                                                                                                        
                                                                                                                                                                                                                                                                                                                        295-MSE

Chain B from PDB  Type:PROTEIN  Length:426
 aligned with T1M_BACTN | Q89Z59 from UniProtKB/Swiss-Prot  Length:472

    Alignment length:426
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426      
            T1M_BACTN     7 TEQSLTKKVWNLATTLAGQGIGFTDYITQLTYLLFLKMDAENVEMFGEESAIPTGYQWADLIAFDGLDLVKQYEETLKLLSELDNLIGTIYTKAQNKIDKPVYLKKVITMIDEEQWLIMDGDVKGAIYESILEKNGQDKKSGAGQYFTPRPLIQAMVDCINPQMGETVCDPACGTGGFLLTAYDYMKGQSASKEKRDFLRDKALHGVDNTPLVVTLASMNLYLHGIGTDRSPIVCEDSLEKEPSTLVDVILANPPFGTRPAGSVDINRPDFYVETKNNQLNFLQHMMLMLKTGGRAAVVLPDNVLFEAGAGETIRKRLLQDFNLHTILRLPTGIFYAQGVKANVLFFSKGQPTKEIWFYDYRTDIKHTLATNKLERHHLDDFVSCYNNRVEIYDAENNPQGRWRKYPVDEIIARDKTSLDITWIKP 432
               SCOP domains d2okcb_ B: Type I restriction enzyme StySJI M protein                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhh........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhh......eee.....hhhhhhhhhhhhh....hhhhhhhhhh.eeeee.hhhhhhhhhhhhhhh........eee...........eeeeee........................hhhhhhhhhhhhheeeeeeeeeeeehhhhhh.hhhhhhhhhhhhheeeeeeee............eeeeeeee.....eeeeee..............hhhhhhhhhhhhhh..............eeeeehhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------N6_MTAS-------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2okc B   7 TEQSLTKKVWNLATTLAGQGIGFTDYITQLTYLLFLKmDAENVEmFGEESAIPTGYQWADLIAFDGLDLVKQYEETLKLLSELDNLIGTIYTKAQNKIDKPVYLKKVITmIDEEQWLImDGDVKGAIYESILEKNGQDKKSGAGQYFTPRPLIQAmVDCINPQmGETVCDPACGTGGFLLTAYDYmKGQSASKEKRDFLRDKALHGVDNTPLVVTLASmNLYLHGIGTDRSPIVCEDSLEKEPSTLVDVILANPPFGTRPAGSVDINRPDFYVETKNNQLNFLQHmmLmLKTGGRAAVVLPDNVLFEAGAGETIRKRLLQDFNLHTILRLPTGIFYAQGVKANVLFFSKGQPTKEIWFYDYRTDIKHTLATNKLERHHLDDFVSCYNNRVEIYDAENNPQGRWRKYPVDEIIARDKTSLDITWIKP 432
                                    16        26        36       |46    |   56        66        76        86        96       106       116       126       136       146       156     | 166   |   176       186     | 196       206       216       226       236       246       256       266       276       286     ||296       306       316       326       336       346       356       366       376       386       396       406       416       426      
                                                                44-MSE 51-MSE                                                          116-MSE  125-MSE                              162-MSE 170-MSE               192-MSE                          225-MSE                                                            292-MSE                                                                                                                                        
                                                                                                                                                                                                                                                                                                                        293-MSE                                                                                                                                       
                                                                                                                                                                                                                                                                                                                          295-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 '\|'

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (T1M_BACTN | Q89Z59)

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.

Asymmetric Unit
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	Cis Peptide Bonds
		Ser A:198 - Lys A:199	[ RasMol ]
		Ser B:196 - Ala B:197	[ RasMol ]
		Ser B:198 - Lys B:199	[ RasMol ]

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SS Bonds (0, 0)

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