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(-) Description

Title :  CRYSTAL STRUCTURE OF ACLACINOMYCIN-10-HYDROXYLASE (RDMB) IN COMPLEX WITH SINEFUNGIN (SFG)
 
Authors :  A. Jansson, H. Koskiniemi, A. Erola, J. Wang, P. Mantsala, G. Schneider
Date :  08 Sep 04  (Deposition) - 23 Nov 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Anthracycline; Hydroxylase; S-Adenosyl-L-Methionine Analogue; Sinefungin; Streptomyces; Polyketide Antibiotics; Divergent Evolution, 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

(-) Compounds

Molecule 1 - PROTEIN RDMB
    Chains: A
    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

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2MSE6Mod. Amino AcidSELENOMETHIONINE
3SFG1Ligand/IonSINEFUNGIN
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2MSE6Mod. Amino AcidSELENOMETHIONINE
3SFG1Ligand/IonSINEFUNGIN
Biological Unit 2 (3, 16)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2MSE12Mod. Amino AcidSELENOMETHIONINE
3SFG2Ligand/IonSINEFUNGIN

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:236 , HOH A:5661BINDING SITE FOR RESIDUE ACT A 421
2AC2SOFTWARETRP A:146 , TYR A:171 , GLY A:190 , GLY A:191 , GLY A:192 , GLU A:213 , LEU A:214 , PRO A:217 , GLY A:239 , ASP A:240 , PHE A:241 , PHE A:242 , SER A:255 , PHE A:256 , ASN A:260 , TRP A:261BINDING SITE FOR RESIDUE SFG A 5635

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1XDU)

(-) Sequences/Alignments

Asymmetric 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 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 d1xdua1 A:10-101 Aclacinomycin-10-hydroxylase RdmB                                          d1xdua2 A:102-357 Aclacinomycin-10-hydroxylase RdmB                                                                                                                                                                                                              SCOP domains
               CATH domains 1xduA01 A:10-112 'winged helix' repressor DNA binding domain                                           --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------       -------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...hhhhhhhh...hhhhhhhhhhhhhhh..ee....-....ee.hhhhhhh.....hhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh......eeeee....hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh.....eeeee..........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeee.-------hhhhhhhhhhhhhhhhhh....hhhhhhhhhhh..eeeeeeeee........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xdu A  10 LEPTDQDLDVLLKNLGNLVTPmALRVAATLRLVDHLLAGADTLAGLADRTDTHPQALSRLVRHLTVVGVLEGGEK-GRPLRPTRLGmLLADGHPAQQRAWLDLNGAVSHADLAFTGLLDVVRTGRPAYAGRYGRPFWEDLSADVALADSFDALmSCDEDLAYEAPADAYDWSAVRHVLDVGGGNGGmLAAIALRAPHLRGTLVELAGPAERARRRFADAGLADRVTVAEGDFFKPLPVTADVVLLSFVLLNWSDEDALTILRGCVRALEPGGRLLVLDR-------ADRFFSTLLDLRmLTFmGGRVRTRDEVVDLAGSAGLALASERTSGSTTLPFDFSILEFTAVS 357
                                    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        |-      |299       309  |    319       329       339       349        
                                                31-MSE                                               84 |        96-MSE                                                            163-MSE                          196-MSE                                                                                     288     296         308-MSE                                             
                                                                                                       86                                                                                                                                                                                                                               312-MSE
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (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.

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  1xdu
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  RDMB_STREF | Q54527
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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

(-) Related Entries Specified in the PDB File

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)
1xds