Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF FUSED DOCKING DOMAINS FROM THE ERYTHROMYCIN POLYKETIDE SYNTHASE (DEBS), A MODEL FOR THE INTERACTION BETWEEN DEBS2 AND DEBS3: THE B DOMAIN
 
Authors :  R. W. Broadhurst, D. Nietlispach, M. P. Wheatcroft, P. F. Leadlay, K. J. Weissman
Date :  14 Jul 03  (Deposition) - 24 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (7x)
Keywords :  Four Helix Bundle, Homodimer, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. W. Broadhurst, D. Nietlispach, M. P. Wheatcroft, P. F. Leadlay, K. J. Weissman
The Structure Of Docking Domains In Modular Polyketide Synthases.
Chem. Biol. V. 10 723 2003
PubMed-ID: 12954331  |  Reference-DOI: 10.1016/S1074-5521(03)00156-X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ERYTHRONOLIDE SYNTHASE
    ChainsA, B
    EC Number2.3.1.94
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX4T-3
    Expression System StrainBL21-CODONPLUS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 61-120
    GeneERYA
    Organism ScientificSACCHAROPOLYSPORA ERYTHRAEA
    Organism Taxid1836
    Other DetailsC-TERMINAL FRAGMENT OF DEBS2 FUSED TO N- TERMINAL FRAGMENT OF DEBS3
    SynonymORF 2, 6-DEOXYERYTHRONOLIDE B SYNTHASE II, DEBS 2/ORF 3, 6-DEOXYERYTHRONOLIDE B SYNTHASE III, DEBS 3

 Structural Features

(-) Chains, Units

  
NMR Structure (7x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1PZR)

(-) Sites  (0, 0)

(no "Site" information available for 1PZR)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1PZR)

(-) Sequences/Alignments

NMR Structure
   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:60
 aligned with ERYA2_SACER | Q03132 from UniProtKB/Swiss-Prot  Length:3567

    Alignment length:141
                                  1237      1247      1257      1267      1277      1287      1297      1307      1317      1327      1337      1347      1357      1367 
         ERYA2_SACER   1228 AAKTALLAVLDEVLGDRAVEREVYCSSVAGIWGGAGMAAYAAGSAYLDALAEHHRARGRSCTSVAWTPWALPGGAVDDGYLRERGLRSLSADRAMRTWERVLAAGPVSVAVADVDWPVLSEGFAATRPTALFAELAGRGGQ 1368
               SCOP domains d1pzra_ A: Eryt                 hro            nol                    ide    sy nthase                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh-----------------h..------------...--------------------...---...-hhhhhhh------------hhhhh-----hhhhhhh-----------hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1pzr A   61 ASDDELFSMLDQRFG-----------------GGE------------DLL--------------------MSG---DNG-MTEEKLR------------RYLKR-----TVTELDS-----------VTARLREVEHRAGE  120
                                    70    |    -         -  | |    -       |81         -         -| |   | |-|     |  -        95   |   100     |   -       109       119 
                                         75                76 |           79 |                   82 |  85 | |    94           95  99   100   106         107             
                                                             78             81                     84    87 |                                                            
                                                                                                           88                                                            

Chain A from PDB  Type:PROTEIN  Length:60
 aligned with ERYA3_SACER | Q03133 from UniProtKB/Swiss-Prot  Length:3172

    Alignment length:60
                                                 1                                      
                                     -         - |       9        19        29        39
         ERYA3_SACER      - ---------------------MSGDNGMTEEKLRRYLKRTVTELDSVTARLREVEHRAGE   39
               SCOP domains d1pzra_ A: Erythronolide synthase                            SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                1pzr A   61 ASDDELFSMLDQRFGGGEDLLMSGDNGMTEEKLRRYLKRTVTELDSVTARLREVEHRAGE  120
                                    70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:60
 aligned with ERYA2_SACER | Q03132 from UniProtKB/Swiss-Prot  Length:3567

    Alignment length:141
                                  1237      1247      1257      1267      1277      1287      1297      1307      1317      1327      1337      1347      1357      1367 
         ERYA2_SACER   1228 AAKTALLAVLDEVLGDRAVEREVYCSSVAGIWGGAGMAAYAAGSAYLDALAEHHRARGRSCTSVAWTPWALPGGAVDDGYLRERGLRSLSADRAMRTWERVLAAGPVSVAVADVDWPVLSEGFAATRPTALFAELAGRGGQ 1368
               SCOP domains d1pzrb_ B: Eryt                 hro            nol                    ide    sy nthase                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh-----------------h..------------...--------------------...---...-hhhhhhh------------hhhhh-----hhhhhhh-----------hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1pzr B   61 ASDDELFSMLDQRFG-----------------GGE------------DLL--------------------MSG---DNG-MTEEKLR------------RYLKR-----TVTELDS-----------VTARLREVEHRAGE  120
                                    70    |    -         -  | |    -       |81         -         -| |   | |-|     |  -        95   |   100     |   -       109       119 
                                         75                76 |           79 |                   82 |  85 | |    94           95  99   100   106         107             
                                                             78             81                     84    87 |                                                            
                                                                                                           88                                                            

Chain B from PDB  Type:PROTEIN  Length:60
 aligned with ERYA3_SACER | Q03133 from UniProtKB/Swiss-Prot  Length:3172

    Alignment length:60
                                                 1                                      
                                     -         - |       9        19        29        39
         ERYA3_SACER      - ---------------------MSGDNGMTEEKLRRYLKRTVTELDSVTARLREVEHRAGE   39
               SCOP domains d1pzrb_ B: Erythronolide synthase                            SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                1pzr B   61 ASDDELFSMLDQRFGGGEDLLMSGDNGMTEEKLRRYLKRTVTELDSVTARLREVEHRAGE  120
                                    70        80        90       100       110       120

   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  (1, 2)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1PZR)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 22)

NMR Structure(hide GO term definitions)
Chain A,B   (ERYA3_SACER | Q03133)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0048037    cofactor binding    Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
    GO:0047879    erythronolide synthase activity    Catalysis of the reaction: 6 malonyl-CoA + propionyl-CoA = 7 CoA + 6-deoxyerythronolide B.
    GO:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    GO:0031177    phosphopantetheine binding    Interacting selectively and non-covalently with phosphopantetheine, the vitamin pantetheine 4'-(dihydrogen phosphate).
    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.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
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:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0033068    macrolide biosynthetic process    The chemical reactions and pathways leading to the formation of macrolides, any of a large group of polyketide compounds that contain a large lactone ring with few or no double bonds and no nitrogen atoms, linked glycosidically to one or more sugar groups. The macrolides include the carbomycins, the erythromycins, oleandomycin, oligomycins, and the spiramycins, and act as antibiotics, mainly against Gram-positive bacteria.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

Chain A,B   (ERYA2_SACER | Q03132)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0048037    cofactor binding    Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
    GO:0047879    erythronolide synthase activity    Catalysis of the reaction: 6 malonyl-CoA + propionyl-CoA = 7 CoA + 6-deoxyerythronolide B.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0031177    phosphopantetheine binding    Interacting selectively and non-covalently with phosphopantetheine, the vitamin pantetheine 4'-(dihydrogen phosphate).
    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.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
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:0033068    macrolide biosynthetic process    The chemical reactions and pathways leading to the formation of macrolides, any of a large group of polyketide compounds that contain a large lactone ring with few or no double bonds and no nitrogen atoms, linked glycosidically to one or more sugar groups. The macrolides include the carbomycins, the erythromycins, oleandomycin, oligomycins, and the spiramycins, and act as antibiotics, mainly against Gram-positive bacteria.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

 Visualization

(-) Interactive Views

NMR Structure
  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
(no "Ligands, Modified Residues, Ions" information available for 1pzr)
 
  Sites
(no "Sites" information available for 1pzr)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1pzr)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1pzr
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ERYA2_SACER | Q03132
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  ERYA3_SACER | Q03133
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.3.1.94
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  ERYA2_SACER | Q03132
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  ERYA3_SACER | Q03133
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ERYA2_SACER | Q031321pzq 2qo3 3el6
        ERYA3_SACER | Q031331kez 1mo2 2hg4 5d3k 5d3z

(-) Related Entries Specified in the PDB File

1pzq STRUCTURE OF FUSED DOCKING DOMAINS FROM THE ERYTHROMYCIN POLYKETIDE SYNTHASE (DEBS), A MODEL FOR THE INTERACTION BETWEEN DEBS 2 AND DEBS 3: THE A DOMAIN