1TW3 - 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

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

Method :   X-RAY DIFFRACTION

Resolution :   2.35

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

Keywords :   Anthracycline, Methyltransferase, Methylate, Streptomyces, Tailoring Enzyme, Polyketide, S-Adenosyl-L-Homocystein (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:645 , HOH A:681 , HOH A:697 , HOH A:739	BINDING SITE FOR RESIDUE SAH A 635
2	AC2	SOFTWARE	TRP A:105 , PHE A:155 , LEU A:159 , 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:650 , HOH A:693	BINDING SITE FOR RESIDUE ERT A 600
3	AC3	SOFTWARE	TYR B:142 , ARG B:152 , PHE B:167 , GLY B:186 , GLU B:209 , MET B:210 , GLY B:235 , ASP B:236 , PHE B:237 , SER B:251 , PHE B:252 , ASN B:256 , TRP B:257 , ERT B:1600 , HOH B:1637 , HOH B:1695 , HOH B:1699	BINDING SITE FOR RESIDUE SAH B 1635
4	AC4	SOFTWARE	TRP B:105 , TYR B:142 , PHE B:155 , LEU B:159 , ASP B:162 , ALA B:166 , PHE B:252 , ASN B:256 , GLU B:298 , LEU B:299 , ARG B:302 , PHE B:306 , SAH B:1635 , HOH B:1719 , HOH B:1720	BINDING SITE FOR RESIDUE ERT B 1600

(no "SS Bond" information available for 1TW3)

(no "Cis Peptide Bond" information available for 1TW3)

(no "SAP(SNP)/Variant" information available for 1TW3)

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 1TW3)

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:340
 aligned with DNRK_STRPE | Q06528 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:340
                                    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
           DNRK_STRPE    13 QIDALRTLIRLGSLHTPMVVRTAATLRLVDHILAGARTVKALAARTDTRPEALLRLIRHLVAIGLLEEDAPGEFVPTEVGELLADDHPAAQRAWHDLTQAVARADISFTRLPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAYDWTNVRHVLDVGGGKGGFAAAIARRAPHVSATVLEMAGTVDTARSYLKDEGLSDRVDVVEGDFFEPLPRKADAIILSFVLLNWPDHDAVRILTRCAEALEPGGRILIHERDDLHENSFNEQFTELDLRMLVFLGGALRTREKWDGLAASAGLVVEEVRQLPSPTIPYDLSLLVLAPA 352
               SCOP domains --d1tw3a1 A:14-98 Carminomycin 4-O-methyltransferase                                   d1tw3a2 A:99-351 Carminomycin 4-O-methyltransferase                                                                                                                                                                                                           SCOP domains
               CATH domains 1tw3A01 A:12-108 'winged helix' repressor DNA binding domain                                     --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eeeee..eeee..hhhhhh.....hhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhh......hhhhhhhh......eeeee....hhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeee..........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeee...hhhhh.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
                 1tw3 A  12 QIDALRTLIRLGSLHTPMVVRTAATLRLVDHILAGARTVKALAARTDTRPEALLRLIRHLVAIGLLEEDAPGEFVPTEVGELLADDHPAAQRAWHDLTQAVARADISFTRLPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAYDWTNVRHVLDVGGGKGGFAAAIARRAPHVSATVLEMAGTVDTARSYLKDEGLSDRVDVVEGDFFEPLPRKADAIILSFVLLNWPDHDAVRILTRCAEALEPGGRILIHERDDLHENSFNEQFTELDLRMLVFLGGALRTREKWDGLAASAGLVVEEVRQLPSPTIPYDLSLLVLAPA 351
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351

Chain B from PDB  Type:PROTEIN  Length:340
 aligned with DNRK_STRPE | Q06528 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:340
                                    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
           DNRK_STRPE    13 QIDALRTLIRLGSLHTPMVVRTAATLRLVDHILAGARTVKALAARTDTRPEALLRLIRHLVAIGLLEEDAPGEFVPTEVGELLADDHPAAQRAWHDLTQAVARADISFTRLPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAYDWTNVRHVLDVGGGKGGFAAAIARRAPHVSATVLEMAGTVDTARSYLKDEGLSDRVDVVEGDFFEPLPRKADAIILSFVLLNWPDHDAVRILTRCAEALEPGGRILIHERDDLHENSFNEQFTELDLRMLVFLGGALRTREKWDGLAASAGLVVEEVRQLPSPTIPYDLSLLVLAPA 352
               SCOP domains --d1tw3b1 B:14-98 Carminomycin 4-O-methyltransferase                                   d1tw3b2 B:99-351 Carminomycin 4-O-methyltransferase                                                                                                                                                                                                           SCOP domains
               CATH domains 1tw3B01 B:12-108 '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.hhhhhhhhhhhhh......eeeee....hhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeee..........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeee...hhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeeeee........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------SAM_OMT_II  PDB: B:19-345 UniProt: 20-346                                                                                                                                                                                                                                                                                              ------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tw3 B  12 QIDALRTLIRLGSLHTPMVVRTAATLRLVDHILAGARTVKALAARTDTRPEALLRLIRHLVAIGLLEEDAPGEFVPTEVGELLADDHPAAQRAWHDLTQAVARADISFTRLPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAYDWTNVRHVLDVGGGKGGFAAAIARRAPHVSATVLEMAGTVDTARSYLKDEGLSDRVDVVEGDFFEPLPRKADAIILSFVLLNWPDHDAVRILTRCAEALEPGGRILIHERDDLHENSFNEQFTELDLRMLVFLGGALRTREKWDGLAASAGLVVEEVRQLPSPTIPYDLSLLVLAPA 351
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351

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(

)

Architectures( (-)

)

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	1tw3A01	A:12-108
1b	1tw3B01	B:12-108

(no "Pfam Domain" information available for 1TW3)

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 1tw3)

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	1tw3
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	2.1.1.-
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	DNRK_STRPE \| Q06528	:	1tw2 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)
1wt2	CARMINOMYCIN-4-O-METHYLTRANSFERASE (DNRK) IN COMPLEX WITH S -ADENOSYL-L-HOMOCYSTEIN (SAH) AND 4-METHOXY-E-RHODOMYCIN T (M-ET) AT 2.5 A

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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