3I58 - 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-ADENOSYL-L-HOMOCYSTEINE (SAH) AND 2-HYDROXY-7-METHOXY-5-METHYL NAPHTHOIC ACID (NA)

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

Date :   03 Jul 09 (Deposition) - 01 Sep 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.69

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

Keywords :   Ternary 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	7NA	2	Ligand/Ion	2-HYDROXY-7-METHOXY-5-METHYL NAPHTHOIC ACID
2	GOL	2	Ligand/Ion	GLYCEROL
3	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:133 , MET A:150 , HIS A:153 , GLY A:177 , GLY A:178 , GLY A:179 , ASP A:200 , LEU A:201 , GLY A:226 , SER A:227 , PHE A:228 , SER A:242 , ASP A:247 , HOH A:533 , HOH A:546 , HOH A:576	BINDING SITE FOR RESIDUE SAH A 401
2	AC2	SOFTWARE	TRP A:96 , VAL A:103 , MET A:150 , HIS A:246 , MET A:286 , ARG A:289 , MET A:290 , HOH A:577 , ARG B:11	BINDING SITE FOR RESIDUE 7NA A 402
3	AC3	SOFTWARE	GLY A:219 , HOH A:630 , ASP B:32 , HIS B:33 , HIS B:38	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 , LEU B:201 , GLY B:226 , SER B:227 , PHE B:228 , SER B:242 , ASP B:247 , HOH B:518 , HOH B:536 , HOH B:542	BINDING SITE FOR RESIDUE SAH B 401
5	AC5	SOFTWARE	ARG A:11 , TRP B:96 , VAL B:103 , MET B:150 , ALA B:243 , HIS B:246 , ARG B:289 , MET B:290 , HOH B:554 , HOH B:599	BINDING SITE FOR RESIDUE 7NA B 402
6	AC6	SOFTWARE	HIS A:33 , GLY B:219	BINDING SITE FOR RESIDUE GOL B 404

(no "SS Bond" information available for 3I58)

(no "Cis Peptide Bond" information available for 3I58)

(no "SAP(SNP)/Variant" information available for 3I58)

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 3I58)

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:328
 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 3i58A01 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.hhhhhh.hhhh.eeeee....hhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhh....eeeee............eeeee.hhhhhhhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhh....hhhhhhhhhhh..eeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SAM_OMT_II  PDB: A:10-332 UniProt: 10-332                                                                                                                                                                                                                                                                                           PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i58 A   5 AAHIGLRALADLATPMAVRVAATLRVADHIAAGHRTAAEIASAAGAHADSLDRLLRHLVAVGLFTRDGQGVYGLTEFGEQLRDDHAAGKRKWLDMNSAVGRGDLGFVELAHSIRTGQPAYPVRYGTSFWEDLGSDPVLSASFDTLMSHHLELDYTGIAAKYDWAALGHVVDVGGGSGGLLSALLTAHEDLSGTVLDLQGPASAAHRRFLDTGLSGRAQVVVGSFFDPLPAGAGGYVLSAVLHDWDDLSAVAILRRCAEAAGSGGVVLVIEAVAGDEHAGTGMDLRMLTYFGGKERSLAELGELAAQAGLAVRAAHPISYVSIVEMTAL 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

Chain B from PDB  Type:PROTEIN  Length:328
 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 3i58B01 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.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhh.eeeee....hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh.....eeeee............eeeee.hhhhhhhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhh....hhhhhhhhhhh..eeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SAM_OMT_II  PDB: B:10-332 UniProt: 10-332                                                                                                                                                                                                                                                                                           PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i58 B   5 AAHIGLRALADLATPMAVRVAATLRVADHIAAGHRTAAEIASAAGAHADSLDRLLRHLVAVGLFTRDGQGVYGLTEFGEQLRDDHAAGKRKWLDMNSAVGRGDLGFVELAHSIRTGQPAYPVRYGTSFWEDLGSDPVLSASFDTLMSHHLELDYTGIAAKYDWAALGHVVDVGGGSGGLLSALLTAHEDLSGTVLDLQGPASAAHRRFLDTGLSGRAQVVVGSFFDPLPAGAGGYVLSAVLHDWDDLSAVAILRRCAEAAGSGGVVLVIEAVAGDEHAGTGMDLRMLTYFGGKERSLAELGELAAQAGLAVRAAHPISYVSIVEMTAL 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

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 3I58)

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	3i58A01	A:5-99
1b	3i58B01	B:5-99

(no "Pfam Domain" information available for 3I58)

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
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3i58)

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	3i58
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	2.1.1.-
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UniProtKB/Swiss-Prot
	NCSB1_STRCZ \| Q84HC8	:	3i53 3i5u 3i64

3i53	CRYSTAL STRUCTURE OF AN O-METHYLTRANSFERASE (NCSB1) FROM NEOCARZINOSTATIN BIOSYNTHESIS IN COMPLEX WITH S-ADENOSYL-L- HOMOCYSTEINE (SAH)
3i5u	CRYSTAL STRUCTURE OF AN O-METHYLTRANSFERASE (NCSB1) FROM NEOCARZINOSTATIN BIOSYNTHESIS IN COMPLEX WITH S- ADENOSYLMETHIONINE (SAM) AND 2-HYDROXY-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

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Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SAPs(SNPs)/Variants (0, 0)

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