1TW2 - JenaLib

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Title :   CRYSTAL STRUCTURE OF CARMINOMYCIN-4-O-METHYLTRANSFERASE (DNRK) IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEIN (SAH) AND 4-METHOXY-E-RHODOMYCIN T (M-ET)

Authors :   A. Jansson, H. Koskiniemi, P. Mantsala, J. Niemi, G. Schneider, Structural Proteomics In Europe (Spine)

Date :   30 Jun 04 (Deposition) - 14 Sep 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Anthracycline, Methyltransferase, Methylate, Streptomyces, Tailoring Enzyme, Polyketide, S-Adenosyl-L-Homocystein, Structural Proteomics In Europe, Spine, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Jansson, H. Koskiniemi, P. Mantsala, J. Niemi, G. Schneider
Crystal Structure Of A Ternary Complex Of Dnrk, A Methyltransferase In Daunorubicin Biosynthesis, With Bound Products
J. Biol. Chem. V. 279 41149 2004
PubMed-ID: 15273252 | Reference-DOI: 10.1074/JBC.M407081200
(for further references see the PDB file header)

Molecule 1 - CARMINOMYCIN 4-O-METHYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.1.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX4T-3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DNRK
	Organism Scientific	:	STREPTOMYCES PEUCETIUS
	Organism Taxid	:	1950
	Synonym	:	COMT

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	ERT	2	Ligand/Ion	METHYL (4R)-2-ETHYL-2,5,12-TRIHYDROXY-7-METHOXY-6,11-DIOXO-4-{[2,3,6-TRIDEOXY-3-(DIMETHYLAMINO)-BETA-D-RIBO-HEXOPYRANOSYL]OXY}-1H,2H,3H,4H,6H,11H-TETRACENE-1-CARBOXYLATE
2	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:142 , ARG A:152 , LEU A:159 , PHE A:167 , GLY A:186 , GLY A:187 , GLU A:209 , MET A:210 , GLY A:235 , ASP A:236 , PHE A:237 , SER A:251 , PHE A:252 , TRP A:257 , ERT A:600 , HOH A:637	BINDING SITE FOR RESIDUE SAH A 635
2	AC2	SOFTWARE	TRP A:105 , TYR A:142 , PHE A:155 , LEU A:159 , CYS A:161 , ASP A:162 , PHE A:252 , ASN A:256 , GLU A:298 , LEU A:299 , ARG A:302 , PHE A:306 , SAH A:635 , HOH A:662 , HOH A:705	BINDING SITE FOR RESIDUE ERT A 600
3	AC3	SOFTWARE	TYR B:142 , ARG B:152 , LEU B:159 , PHE B:167 , GLY B:186 , GLY B:187 , GLU B:209 , MET B:210 , GLY B:235 , ASP B:236 , PHE B:237 , SER B:251 , PHE B:252 , ASN B:256 , ERT B:1600 , HOH B:1649 , HOH B:1655	BINDING SITE FOR RESIDUE SAH B 1635
4	AC4	SOFTWARE	TRP B:105 , PHE B:155 , LEU B:159 , ALA B:166 , PHE B:252 , ASN B:256 , LEU B:299 , ARG B:302 , MET B:303 , LEU B:343 , SAH B:1635 , HOH B:1703	BINDING SITE FOR RESIDUE ERT B 1600

(no "SS Bond" information available for 1TW2)

(no "Cis Peptide Bond" information available for 1TW2)

(no "SAP(SNP)/Variant" information available for 1TW2)

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.	DNRK_STRPE	20-346	2	A:19-345 B:19-345

(no "Exon" information available for 1TW2)

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:338
 aligned with DNRK_STRPE | Q06528 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:338
                                    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       334       344        
           DNRK_STRPE    15 DALRTLIRLGSLHTPMVVRTAATLRLVDHILAGARTVKALAARTDTRPEALLRLIRHLVAIGLLEEDAPGEFVPTEVGELLADDHPAAQRAWHDLTQAVARADISFTRLPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAYDWTNVRHVLDVGGGKGGFAAAIARRAPHVSATVLEMAGTVDTARSYLKDEGLSDRVDVVEGDFFEPLPRKADAIILSFVLLNWPDHDAVRILTRCAEALEPGGRILIHERDDLHENSFNEQFTELDLRMLVFLGGALRTREKWDGLAASAGLVVEEVRQLPSPTIPYDLSLLVLAPA 352
               SCOP domains d1tw2a1 A:14-98 Carminomycin 4-O-methyltransferase                                   d1tw2a2 A:99-351 Carminomycin 4-O-methyltransferase                                                                                                                                                                                                           SCOP domains
               CATH domains 1tw2A01 A:14-108 'winged helix' repressor DNA binding domain                                   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eee..hhhhhh.....hhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhh......hhhhhhh.......eeeee....hhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeee..........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeee.........hhhhhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeeeeee......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SAM_OMT_II  PDB: A:19-345 UniProt: 20-346                                                                                                                                                                                                                                                                                              ------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tw2 A  14 DALRTLIRLGSLHTPMVVRTAATLRLVDHILAGARTVKALAARTDTRPEALLRLIRHLVAIGLLEEDAPGEFVPTEVGELLADDHPAAQRAWHDLTQAVARADISFTRLPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAYDWTNVRHVLDVGGGKGGFAAAIARRAPHVSATVLEMAGTVDTARSYLKDEGLSDRVDVVEGDFFEPLPRKADAIILSFVLLNWPDHDAVRILTRCAEALEPGGRILIHERDDLHENSFNEQFTELDLRMLVFLGGALRTREKWDGLAASAGLVVEEVRQLPSPTIPYDLSLLVLAPA 351
                                    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

Chain B from PDB  Type:PROTEIN  Length:350
 aligned with DNRK_STRPE | Q06528 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:350
                                    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
           DNRK_STRPE     4 EPTVAARPQQIDALRTLIRLGSLHTPMVVRTAATLRLVDHILAGARTVKALAARTDTRPEALLRLIRHLVAIGLLEEDAPGEFVPTEVGELLADDHPAAQRAWHDLTQAVARADISFTRLPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAYDWTNVRHVLDVGGGKGGFAAAIARRAPHVSATVLEMAGTVDTARSYLKDEGLSDRVDVVEGDFFEPLPRKADAIILSFVLLNWPDHDAVRILTRCAEALEPGGRILIHERDDLHENSFNEQFTELDLRMLVFLGGALRTREKWDGLAASAGLVVEEVRQLPSPTIPYDLSLLVLAPAA 353
               SCOP domains d1tw2b1 B:3-98 Carminomycin 4-O-methyltransferase                                               d1tw2b2 B:99-352 Carminomycin 4-O-methyltransferase                                                                                                                                                                                                            SCOP domains
               CATH domains 1tw2B01 B:3-108 'winged helix' repressor DNA binding domain                                               ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eee..hhhhhh.....hhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhh......hhhhhhh.......eeeee....hhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeee..........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeee..hhhhh.hhhhhhhhhhhhhhhh......hhhhhhhhhh.eeeeeeeee........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------SAM_OMT_II  PDB: B:19-345 UniProt: 20-346                                                                                                                                                                                                                                                                                              ------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tw2 B   3 EPTVAARPQQIDALRTLIRLGSLHTPMVVRTAATLRLVDHILAGARTVKALAARTDTRPEALLRLIRHLVAIGLLEEDAPGEFVPTEVGELLADDHPAAQRAWHDLTQAVARADISFTRLPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAYDWTNVRHVLDVGGGKGGFAAAIARRAPHVSATVLEMAGTVDTARSYLKDEGLSDRVDVVEGDFFEPLPRKADAIILSFVLLNWPDHDAVRILTRCAEALEPGGRILIHERDDLHENSFNEQFTELDLRMLVFLGGALRTREKWDGLAASAGLVVEEVRQLPSPTIPYDLSLLVLAPAA 352
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352

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/Biological Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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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)

Streptomyces peucetius. Organism_taxid: 1950. (2)

1a	1tw2A01	A:14-108
1b	1tw2B01	B:3-108

(no "Pfam Domain" information available for 1TW2)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (DNRK_STRPE | Q06528)

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:1901771	daunorubicin biosynthetic process	The chemical reactions and pathways resulting in the formation of daunorubicin.
	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 1tw2)

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	1tw2
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	2.1.1.-
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	DNRK_STRPE \| Q06528
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	DNRK_STRPE \| Q06528	:	1tw3 4wxh 5eeg 5eeh 5jr3

1qzz	CRYSTAL STRUCTURE OF ACLACINOMYCIN-10-HYDROXYLASE (RDMB) IN COMPLEX WITH S-ADENOSYL-L-METHIONINE (SAM)
1r00	CRYSTAL STRUCTURE OF ACLACINOMYCIN-10-HYDROXYLASE (RDMB) IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEIN (SAH)
1tw3	CARMINOMYCIN-4-O-METHYLTRANSFERASE (DNRK) IN COMPLEX WITH S -ADENOSYL-L-HOMOCYSTEIN (SAH)AND 4-METHOXY-E-RHODOMYCIN T (M-ET) AT 2.35 A RELATED ID: ST_04 RELATED DB: TARGETDB

Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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