3I5U - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF AN O-METHYLTRANSFERASE (NCSB1) FROM NEOCARZINOSTATIN BIOSYNTHESIS IN COMPLEX WITH S-ADENOSYLMETHIONINE (SAM) AND 2-HYDROXY-5-METHYL NAPHTHOIC ACID (MNA)

Authors :   H. A. Cooke, S. D. Bruner

Date :   06 Jul 09 (Deposition) - 01 Sep 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Co-Complex, Rossmann-Like Fold, Methyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. A. Cooke, E. L. Guenther, Y. Luo, B. Shen, S. D. Bruner
Molecular Basis Of Substrate Promiscuity For The Sam-Dependent O-Methyltransferase Ncsb1, Involved In The Biosynthesis Of The Enediyne Antitumor Antibiotic Neocarzinostatin.
Biochemistry V. 48 9590 2009
PubMed-ID: 19702337 | Reference-DOI: 10.1021/BI901257Q

Molecule 1 - O-METHYLTRANSFERASE
	Atcc	:	15944
	Chains	:	A, B
	EC Number	:	2.1.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBS5002
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector	:	PET-30XA/LIC
	Expression System Vector Type	:	PLASMID
	Gene	:	NCSB1
	Organism Scientific	:	STREPTOMYCES CARZINOSTATICUS SUBSP. NEOCARZINOSTATICUS
	Organism Taxid	:	167636

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	5NA	2	Ligand/Ion	2-HYDROXY-5-METHYL NAPHTHOIC ACID
2	GOL	2	Ligand/Ion	GLYCEROL
3	SAM	2	Ligand/Ion	S-ADENOSYLMETHIONINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:133 , PHE A:146 , MET A:150 , HIS A:153 , GLY A:177 , GLY A:179 , ASP A:200 , GLY A:226 , SER A:227 , PHE A:228 , PHE A:229 , SER A:242 , ALA A:243 , ASP A:247 , 5NA A:402 , HOH A:523 , HOH A:538 , HOH A:581 , HOH A:582 , HOH A:723	BINDING SITE FOR RESIDUE SAM A 401
2	AC2	SOFTWARE	TRP A:96 , MET A:150 , HIS A:153 , MET A:286 , ARG A:289 , TYR A:293 , PHE A:294 , SAM A:401 , HOH A:593 , ARG B:11	BINDING SITE FOR RESIDUE 5NA A 402
3	AC3	SOFTWARE	LEU A:154 , GLU A:155 , TYR A:158 , THR A:159 , GLY A:160 , HOH A:550	BINDING SITE FOR RESIDUE GOL A 403
4	AC4	SOFTWARE	TRP B:133 , MET B:150 , HIS B:153 , GLY B:177 , GLY B:179 , ASP B:200 , PRO B:204 , GLY B:226 , SER B:227 , PHE B:228 , PHE B:229 , SER B:242 , ALA B:243 , ASP B:247 , 5NA B:402 , HOH B:526 , HOH B:536 , HOH B:537 , HOH B:573 , HOH B:616 , HOH B:722	BINDING SITE FOR RESIDUE SAM B 401
5	AC5	SOFTWARE	ARG A:11 , TRP B:96 , PHE B:146 , MET B:150 , HIS B:153 , MET B:286 , ARG B:289 , TYR B:293 , SAM B:401	BINDING SITE FOR RESIDUE 5NA B 402
6	AC6	SOFTWARE	LEU B:154 , GLU B:155 , TYR B:158 , HOH B:636	BINDING SITE FOR RESIDUE GOL B 404

(no "SS Bond" information available for 3I5U)

(no "Cis Peptide Bond" information available for 3I5U)

(no "SAP(SNP)/Variant" information available for 3I5U)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_OMT_II	PS51683	SAM-dependent O-methyltransferase class II-type profile.	NCSB1_STRCZ	10-332	2	A:10-332 B:10-332

(no "Exon" information available for 3I5U)

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:325
 aligned with NCSB1_STRCZ | Q84HC8 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:328
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324        
          NCSB1_STRCZ     5 AAHIGLRALADLATPMAVRVAATLRVADHIAAGHRTAAEIASAAGAHADSLDRLLRHLVAVGLFTRDGQGVYGLTEFGEQLRDDHAAGKRKWLDMNSAVGRGDLGFVELAHSIRTGQPAYPVRYGTSFWEDLGSDPVLSASFDTLMSHHLELDYTGIAAKYDWAALGHVVDVGGGSGGLLSALLTAHEDLSGTVLDLQGPASAAHRRFLDTGLSGRAQVVVGSFFDPLPAGAGGYVLSAVLHDWDDLSAVAILRRCAEAAGSGGVVLVIEAVAGDEHAGTGMDLRMLTYFGGKERSLAELGELAAQAGLAVRAAHPISYVSIVEMTAL 332
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3i5uA01 A:5-99 'winged helix' repressor DNA binding domain                                     ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhh.eee.....eee..hhhhhh......hhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhh.eeeee....hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh.....eeeee............eeeee.hhhhhhhhhhhhhhhhhhhhhh...eeeeee....---.hhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SAM_OMT_II  PDB: A:10-332 UniProt: 10-332                                                                                                                                                                                                                                                                                           PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i5u A   5 AAHIGLRALADLATPMAVRVAATLRVADHIAAGHRTAAEIASAAGAHADSLDRLLRHLVAVGLFTRDGQGVYGLTEFGEQLRDDHAAGKRKWLDMNSAVGRGDLGFVELAHSIRTGQPAYPVRYGTSFWEDLGSDPVLSASFDTLMSHHLELDYTGIAAKYDWAALGHVVDVGGGSGGLLSALLTAHEDLSGTVLDLQGPASAAHRRFLDTGLSGRAQVVVGSFFDPLPAGAGGYVLSAVLHDWDDLSAVAILRRCAEAAGSGGVVLVIEAVAG---AGTGMDLRMLTYFGGKERSLAELGELAAQAGLAVRAAHPISYVSIVEMTAL 332
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274   |   284       294       304       314       324        
                                                                                                                                                                                                                                                                                                           278 282

Chain B from PDB  Type:PROTEIN  Length:325
 aligned with NCSB1_STRCZ | Q84HC8 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:328
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324        
          NCSB1_STRCZ     5 AAHIGLRALADLATPMAVRVAATLRVADHIAAGHRTAAEIASAAGAHADSLDRLLRHLVAVGLFTRDGQGVYGLTEFGEQLRDDHAAGKRKWLDMNSAVGRGDLGFVELAHSIRTGQPAYPVRYGTSFWEDLGSDPVLSASFDTLMSHHLELDYTGIAAKYDWAALGHVVDVGGGSGGLLSALLTAHEDLSGTVLDLQGPASAAHRRFLDTGLSGRAQVVVGSFFDPLPAGAGGYVLSAVLHDWDDLSAVAILRRCAEAAGSGGVVLVIEAVAGDEHAGTGMDLRMLTYFGGKERSLAELGELAAQAGLAVRAAHPISYVSIVEMTAL 332
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3i5uB01 B:5-99 'winged helix' repressor DNA binding domain                                     ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhh.eee.....eee..hhhhhh......hhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhh.eeeee....hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh.....eeeee............eeeee.hhhhhhhhhhhhhhhhhhhhhh...eeeeee....---.hhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SAM_OMT_II  PDB: B:10-332 UniProt: 10-332                                                                                                                                                                                                                                                                                           PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i5u B   5 AAHIGLRALADLATPMAVRVAATLRVADHIAAGHRTAAEIASAAGAHADSLDRLLRHLVAVGLFTRDGQGVYGLTEFGEQLRDDHAAGKRKWLDMNSAVGRGDLGFVELAHSIRTGQPAYPVRYGTSFWEDLGSDPVLSASFDTLMSHHLELDYTGIAAKYDWAALGHVVDVGGGSGGLLSALLTAHEDLSGTVLDLQGPASAAHRRFLDTGLSGRAQVVVGSFFDPLPAGAGGYVLSAVLHDWDDLSAVAILRRCAEAAGSGGVVLVIEAVAG---AGTGMDLRMLTYFGGKERSLAELGELAAQAGLAVRAAHPISYVSIVEMTAL 332
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274   |   284       294       304       314       324        
                                                                                                                                                                                                                                                                                                           278 282

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 "SCOP Domain" information available for 3I5U)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: 'winged helix' repressor DNA binding domain (507)

Neocarzinostaticus (Streptomyces carzinostaticus subsp) (4)

1a	3i5uA01	A:5-99
1b	3i5uB01	B:5-99

(no "Pfam Domain" information available for 3I5U)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (NCSB1_STRCZ | Q84HC8)

molecular function
	GO:0008171	O-methyltransferase activity	Catalysis of the transfer of a methyl group to the oxygen atom of an acceptor molecule.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	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:0017000	antibiotic biosynthetic process	The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.

Asymmetric/Biological 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
		5NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SAM	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3i5u)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites 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
	3i5u
		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
	NCSB1_STRCZ \| Q84HC8
		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.-
		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
	NCSB1_STRCZ \| Q84HC8
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	NCSB1_STRCZ \| Q84HC8	:	3i53 3i58 3i64

3i53	CRYSTAL STRUCTURE OF AN O-METHYLTRANSFERASE (NCSB1) FROM NEOCARZINOSTATIN BIOSYNTHESIS IN COMPLEX WITH S-ADENOSYL-L- HOMOCYSTEINE (SAH)
3i58	CRYSTAL STRUCTURE OF AN O-METHYLTRANSFERASE (NCSB1) FROM NEOCARZINOSTATIN BIOSYNTHESIS IN COMPLEX WITH S-ADENOSYL-L- HOMOCYSTEINE (SAH) AND 2-HYDROXY-7-METHOXY-5-METHYL NAPHTHOIC ACID
3i64	CRYSTAL STRUCTURE OF AN O-METHYLTRANSFERASE (NCSB1) FROM NEOCARZINOSTATIN BIOSYNTHESIS IN COMPLEX WITH S-ADENOSYL-L- HOMOCYSTEINE (SAH) AND 1,4-DIHYDROXY-2-NAPHTHOIC ACID (DHN)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

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