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Title :   CRYSTAL STRUCTURE OF ACLACINOMYCIN-10-HYDROXYLASE (RDMB) IN COMPLEX WITH S-ADENOSYL-L-METHIONINE (SAM) AND 11-DEOXY-BETA-RHODOMYCIN (DBRA)

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

Date :   08 Sep 04 (Deposition) - 23 Nov 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Anthracycline; Hydroxylase; S-Adenosyl-L-Methionine; Streptomyces; Polyketide Antibiotics; Divergent Evolution, Structural Proteomics In Europe, Spine, Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Jansson, H. Koskiniemi, A. Erola, J. Wang, G. Schneider, J. Niemi
Aclacinomycin 10-Hydroxylase Is A Novel Substrate-Assisted Hydroxylase Requiring S-Adenosyl-L-Methionine As Cofactor
J. Biol. Chem. V. 280 3636 2005
PubMed-ID: 15548527 | Reference-DOI: 10.1074/JBC.M412095200
(for further references see the PDB file header)

Molecule 1 - PROTEIN RDMB
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRDM16 FROM PGEX4T-3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RDMB
	Organism Scientific	:	STREPTOMYCES PURPURASCENS
	Organism Taxid	:	1924

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 16)

No.	Name	Count	Type	Full Name
1	DRA	2	Ligand/Ion	11-DEOXY-BETA-RHODOMYCIN
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
3	SAM	2	Ligand/Ion	S-ADENOSYLMETHIONINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:146 , GLY A:190 , GLY A:191 , GLU A:213 , LEU A:214 , PRO A:217 , GLY A:239 , ASP A:240 , PHE A:241 , SER A:255 , PHE A:256 , ASN A:260 , DRA A:5600 , HOH A:5640 , HOH A:5649 , HOH A:5654 , HOH A:5674 , HOH A:5688	BINDING SITE FOR RESIDUE SAM A 5635
2	AC2	SOFTWARE	GLY B:190 , GLY B:191 , GLU B:213 , PRO B:217 , ASP B:240 , PHE B:241 , SER B:255 , PHE B:256 , ASN B:260 , TRP B:261 , DRA B:9600 , HOH B:9644 , HOH B:9647 , HOH B:9671 , HOH B:9690	BINDING SITE FOR RESIDUE SAM B 9635
3	AC3	SOFTWARE	TRP A:109 , VAL A:116 , PHE A:145 , PHE A:159 , MSE A:163 , MSE A:196 , PHE A:256 , ASN A:260 , LEU A:304 , ARG A:307 , MSE A:308 , MSE A:312 , PHE A:346 , SAM A:5635	BINDING SITE FOR RESIDUE DRA A 5600
4	AC4	SOFTWARE	TRP B:109 , VAL B:116 , PHE B:145 , PHE B:159 , MSE B:163 , ALA B:173 , PRO B:174 , PHE B:256 , ASN B:260 , MSE B:308 , PHE B:311 , MSE B:312 , LEU B:344 , PHE B:346 , PHE B:348 , SAM B:9635 , HOH B:9688	BINDING SITE FOR RESIDUE DRA B 9600

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

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

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

(no "PROSITE Motif" information available for 1XDS)

(no "Exon" information available for 1XDS)

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:336
 aligned with RDMB_STREF | Q54527 from UniProtKB/Swiss-Prot  Length:374

    Alignment length:348
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349        
           RDMB_STREF    10 LEPTDQDLDVLLKNLGNLVTPMALRVAATLRLVDHLLAGADTLAGLADRTDTHPQALSRLVRHLTVVGVLEGGEKQGRPLRPTRLGMLLADGHPAQQRAWLDLNGAVSHADLAFTGLLDVVRTGRPAYAGRYGRPFWEDLSADVALADSFDALMSCDEDLAYEAPADAYDWSAVRHVLDVGGGNGGMLAAIALRAPHLRGTLVELAGPAERARRRFADAGLADRVTVAEGDFFKPLPVTADVVLLSFVLLNWSDEDALTILRGCVRALEPGGRLLVLDRADVEGDGADRFFSTLLDLRMLTFMGGRVRTRDEVVDLAGSAGLALASERTSGSTTLPFDFSILEFTAVS 357
               SCOP domains d1xdsa1 A:10-101 Aclacinomycin-10-hydroxylase RdmB                                          d1xdsa2 A:102-357 Aclacinomycin-10-hydroxylase RdmB                                                                                                                                                                                                              SCOP domains
               CATH domains 1xdsA01 A:10-112 'winged helix' repressor DNA binding domain                                           ------------------------------------------------------         -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..ee...---...ee.hhhhhhh.....hhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhh..---------.........eeeee....hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh....eeeee..........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeee.........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeeeeee......eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xds A  10 LEPTDQDLDVLLKNLGNLVTPmALRVAATLRLVDHLLAGADTLAGLADRTDTHPQALSRLVRHLTVVGVLEGGE---RPLRPTRLGmLLADGHPAQQRAWLDLNGAVSHADLAFTGLLDVVRTGRPAYAGRYGRPFWEDLSADVALADSFDALmSCD---------DAYDWSAVRHVLDVGGGNGGmLAAIALRAPHLRGTLVELAGPAERARRRFADAGLADRVTVAEGDFFKPLPVTADVVLLSFVLLNWSDEDALTILRGCVRALEPGGRLLVLDRADVEGDGADRFFSTLLDLRmLTFmGGRVRTRDEVVDLAGSAGLALASERTSGSTTLPFDFSILEFTAVS 357
                                    19        29 |      39        49        59        69        79   |   |89      | 99       109       119       129       139       149       159   |  |  -      |179       189      |199       209       219       229       239       249       259       269       279       289       299       309  |    319       329       339       349        
                                                31-MSE                                              83  87       96-MSE                                                            163-MSE      176                 196-MSE                                                                                                         308-MSE                                             
                                                                                                                                                                                      166                                                                                                                                               312-MSE

Chain B from PDB  Type:PROTEIN  Length:330
 aligned with RDMB_STREF | Q54527 from UniProtKB/Swiss-Prot  Length:374

    Alignment length:349
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348         
           RDMB_STREF     9 PLEPTDQDLDVLLKNLGNLVTPMALRVAATLRLVDHLLAGADTLAGLADRTDTHPQALSRLVRHLTVVGVLEGGEKQGRPLRPTRLGMLLADGHPAQQRAWLDLNGAVSHADLAFTGLLDVVRTGRPAYAGRYGRPFWEDLSADVALADSFDALMSCDEDLAYEAPADAYDWSAVRHVLDVGGGNGGMLAAIALRAPHLRGTLVELAGPAERARRRFADAGLADRVTVAEGDFFKPLPVTADVVLLSFVLLNWSDEDALTILRGCVRALEPGGRLLVLDRADVEGDGADRFFSTLLDLRMLTFMGGRVRTRDEVVDLAGSAGLALASERTSGSTTLPFDFSILEFTAVS 357
               SCOP domains -d1xdsb1 B:10-101 Aclacinomycin-10-hyd         roxylase RdmB                                 d1xdsb2 B:102-357 Aclacinomycin-10-hydroxylase RdmB                                                                                                                                                                                                              SCOP domains
               CATH domains 1xdsB01 B:9-112 'winged helix' repress         or DNA binding domain                                    ----------------------------------------------------       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh...hhhhhhhhhhhh.hhhhhh.---------......hhhhhhhhhhhhhhh..ee...---...ee.hhhhhhh.....hhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhh.-------hhhhhhhhhhhh.eeeee....hhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhh.....eee............eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeee.........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeeeee........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xds B   9 PLEPTDQDLDVLLKNLGNLVTPmALRVAATLRLVDHLL---------ADRTDTHPQALSRLVRHLTVVGVLEGGE---RPLRPTRLGmLLADGHPAQQRAWLDLNGAVSHADLAFTGLLDVVRTGRPAYAGRYGRPFWEDLSADVALADSFDALmS-------EAPADAYDWSAVRHVLDVGGGNGGmLAAIALRAPHLRGTLVELAGPAERARRRFADAGLADRVTVAEGDFFKPLPVTADVVLLSFVLLNWSDEDALTILRGCVRALEPGGRLLVLDRADVEGDGADRFFSTLLDLRmLTFmGGRVRTRDEVVDLAGSAGLALASERTSGSTTLPFDFSILEFTAVS 357
                                    18        28  |     38       | -       |58        68        78    |   88       |98       108       118       128       138       148       158    ||   -   |   178       188       198       208       218       228       238       248       258       268       278       288       298       308   |   318       328       338       348         
                                                 31-MSE         46        56                         83  87       96-MSE                                                            163-MSE  172                     196-MSE                                                                                                         308-MSE                                             
                                                                                                                                                                                     164                                                                                                                                                 312-MSE

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( (-)

)

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)

Streptomyces purpurascens. Organism_taxid: 1924. (4)

1a	1xdsB01	B:9-112
1b	1xdsA01	A:10-112

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (RDMB_STREF | Q54527)

molecular function
	GO:0008171	O-methyltransferase activity	Catalysis of the transfer of a methyl group to the oxygen atom of an acceptor molecule.
	GO:0016831	carboxy-lyase activity	Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
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 1xds)

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	1xds
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	RDMB_STREF \| Q54527
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	RDMB_STREF \| Q54527
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UniProtKB/Swiss-Prot
	RDMB_STREF \| Q54527	:	1qzz 1r00 1xdu

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	CRYSTAL STRUCTURE OF CARMINOMYCIN-4-O-METHYLTRANSFERASE (DNRK) IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEIN (SAH) AND EPSILON-RHODOMYCIN T (ET)
1xdu	RELATED ID: ST_02 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 16)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (2, 4)

CATH Domains (1, 2)

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Gene Ontology (6, 6)

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