1NW6 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF THE BETA CLASS N6-ADENINE DNA METHYLTRANSFERASE RSRI BOUND TO SINEFUNGIN

Authors :   C. B. Thomas, R. D. Scavetta, R. I. Gumport, M. E. A. Churchill

Date :   05 Feb 03 (Deposition) - 29 Jul 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.94

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

Keywords :   Adenine Dna Methyltransferase, Sinefungin, Rossmann Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. B. Thomas, R. D. Scavetta, R. I. Gumport, M. E. A. Churchill
Structures Of Liganded And Unliganded Rsri N6-Adenine Dna Methyltransferase: A Distinct Orientation For Active Cofactor Binding
J. Biol. Chem. V. 278 26094 2003
PubMed-ID: 12732637 | Reference-DOI: 10.1074/JBC.M303751200

Molecule 1 - MODIFICATION METHYLASE RSRI
	Chains	:	A
	EC Number	:	2.1.1.72
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	RSRIM
	Organism Scientific	:	RHODOBACTER SPHAEROIDES
	Organism Taxid	:	1063
	Synonym	:	ADENINE-SPECIFIC METHYLTRANSFERASE RSRI, M.RSRI, DNA METHYLTRANSFERASE RSRI

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	SFG	1	Ligand/Ion	SINEFUNGIN

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	SFG	1	Ligand/Ion	SINEFUNGIN

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	SFG	2	Ligand/Ion	SINEFUNGIN

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:136 , LEU A:137 , ASN A:206	BINDING SITE FOR RESIDUE CL A 501
2	AC2	SOFTWARE	GLN A:226 , LYS A:227 , SER A:253	BINDING SITE FOR RESIDUE CL A 502
3	AC3	SOFTWARE	ASP A:46 , CYS A:47 , ASP A:65 , PRO A:66 , PRO A:67 , HIS A:223 , THR A:225 , PHE A:249 , PHE A:250 , GLY A:252 , ASP A:271 , ALA A:272 , HOH A:596 , HOH A:634	BINDING SITE FOR RESIDUE SFG A 401

(no "SS Bond" information available for 1NW6)

(no "Cis Peptide Bond" information available for 1NW6)

(no "SAP(SNP)/Variant" information available for 1NW6)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	N6_MTASE	PS00092	N-6 Adenine-specific DNA methylases signature.	MTR1_RHOSH	62-68	1	A:62-68

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.	MTR1_RHOSH	62-68	1	A:62-68

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	N6_MTASE	PS00092	N-6 Adenine-specific DNA methylases signature.	MTR1_RHOSH	62-68	2	A:62-68

(no "Exon" information available for 1NW6)

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:271
 aligned with MTR1_RHOSH | P14751 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:279
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305         
           MTR1_RHOSH    36 GTTRHVYDVCDCLDTLAKLPDDSVQLIICDPPYNIMLADWDDHMDYIGWAKRWLAEAERVLSPTGSIAIFGGLQYQGEAGSGDLISIISHMRQNSKMLLANLIIWNYPNGMSAQRFFANRHEEIAWFAKTKKYFFDLDAVREPYDEETKAAYMKDKRLNPESVEKGRNPTNVWRMSRLNGNSLERVGHPTQKPAAVIERLVRALSHPGSTVLDFFAGSGVTARVAIQEGRNSICTDAAPVFKEYYQKQLTFLQDDGLIDKARSYEIVEGAANFGAALQR 314
               SCOP domains d1nw6a_ A: m.RsrI N6 adenosine-specific DNA methyltransferase                                                                                                                                                                                                                           SCOP domains
               CATH domains 1nw6A00 A:36-314 Vaccinia Virus protein VP39                                                                                                                                                                                                                                            CATH domains
               Pfam domains -----------------------N6_N4_Mtase-1nw6A01 A:59-282                                                                                                                                                                                                    -------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.hhhhhhhh.....eeeeee......hhhhhhh..hhhhhhhhhhhhhhhheeeeeeeeeee...........hhhhhhhhhhhhh..eeeeeeeee..............eeeeeeee........hhhhh...hhhhhhhhhhh...hhhhhhhh.....eee..................hhhhhhhhhhhhh....eeee.....hhhhhhhhhh..eeeeee...hhhhhhhhhhhhhh--------..eeeee.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------N6_MTAS------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nw6 A  36 GTTRHVYDVCDCLDTLAKLPDDSVQLIICDPPYNIMLADWDDHMDYIGWAKRWLAEAERVLSPTGSIAIFGGLQYQGEAGSGDLISIISHMRQNSKMLLANLIIWNYPNGMSAQRFFANRHEEIAWFAKTKKYFFDLDAVREPYDEETKAAYMKDKRLNPESVEKGRNPTNVWRMSRLNGNSLERVGHPTQKPAAVIERLVRALSHPGSTVLDFFAGSGVTARVAIQEGRNSICTDAAPVFKEYYQKQLTFLQ--------RSYEIVEGAANFGAALQR 314
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285  |      - |     305         
                                                                                                                                                                                                                                                                                      288      297

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Vaccinia Virus protein VP39 (378)

Rhodobacter sphaeroides. Organism_taxid: 1063. (4)

1nw6A00

A:36-314

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: N6_N4_Mtase (6)

Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides) (3)

N6_N4_Mtase-1nw6A01

A:59-282

Asymmetric Unit(hide GO term definitions)

Chain A (MTR1_RHOSH | P14751)

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
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SFG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1nw6)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1nw6
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	MTR1_RHOSH \| P14751
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.1.1.72
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	MTR1_RHOSH \| P14751
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	MTR1_RHOSH \| P14751	:	1eg2 1nw5 1nw7 1nw8

1eg2	RSRI METHYLTRANSFERASE CRYSTALLIZED IN THE ABSENCE OF ADDED LIGAND
1nw5	RSRI METHYLTRANSFERASE CRYSTALLIZED WITH BOUND S- ADENOSYLMETHIONINE
1nw7	RSRI METHYLTRANSFERASE CRYSTALLIZED WITH BOUND S- ADENOSYLHOMOCYSTEINE
1nw8	L72P MUTANT OF RSRI METHYLTRANSFERASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (10, 10)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File