Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF ACLACINOMYCIN-10-HYDROXYLASE (RDMB) IN COMPLEX WITH S-ADENSYL-L-METHIONINE (SAM)
 
Authors :  A. Jansson, J. Niemi, Y. Lindqvist, P. Mantsala, G. Schneider, Structu Proteomics In Europe (Spine)
Date :  19 Sep 03  (Deposition) - 25 Nov 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Anthracycline, Hydroxylase, Methyltransferase, Polyketide, Streptomyces, Tailoring Enzymes, Structural Proteomics In Europe, Spine, Structural Genomics, Oxidoreductase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Jansson, J. Niemi, Y. Lindqvist, P. Mantsala, G. Schneider
Crystal Structure Of Aclacinomycin-10-Hydroxylase, A S-Adenosyl-L-Methionine-Dependent Methyltransferase Homolog Involved In Anthracycline Biosynthesis In Streptomyces Purpurascens.
J. Mol. Biol. V. 334 269 2003
PubMed-ID: 14607118  |  Reference-DOI: 10.1016/J.JMB.2003.09.061
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ACLACINOMYCIN-10-HYDROXYLASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRDM16
    Expression System Strain: XL2-BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PGEX 4T-3
    Gene: RDMB
    Organism Scientific: STREPTOMYCES PURPURASCENS
    Organism Taxid: 1924
    Synonym: RDMB

 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  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2SAM2Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:171 , ASP A:188 , GLY A:191 , GLY A:194 , GLY A:195 , MET A:196 , LEU A:197 , SER A:255 , SAM A:635BINDING 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 , SER A:255 , PHE A:256 , ASN A:260 , TRP A:261 , ACT A:421 , HOH A:642 , HOH A:767 , HOH A:844 , HOH A:861 , HOH A:869BINDING SITE FOR RESIDUE SAM A 635

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1QZZ)

(-) 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 d1qzza1 A:10-101 Aclacinomycin-10-hydroxylase RdmB                                          d1qzza2 A:102-357 Aclacinomycin-10-hydroxylase RdmB                                                                                                                                                                                                              SCOP domains
               CATH domains 1qzzA01 A:10-112 'winged helix' repressor DNA binding domain                                           --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------       -------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..ee....-....ee..hhhhhh.....hhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh.......eeeee....hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh.....eeeee..........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeee.-------hhhhhhhhhhhhhhhhhh....hhhhhhhhhhh..eeeeeeeee........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qzz 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        
                                                                                                     84 |                                                                                                                                                                                                       288     296                                                             
                                                                                                       86
   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 '|'

 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 1QZZ)

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SAM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1qzz)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1qzz
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  RDMB_STREF | Q54527
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  RDMB_STREF | Q54527
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1r00 CRYSTAL STRUCTURE OF ACLACINOMYCIN-10-HYDROXYLASE (RDMB) IN COMPLEX WITH S-ADENSYL-L-HOMOCYSTEIN (SAH) RELATED ID: ST_02 RELATED DB: TARGETDB