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

(-) Description

Title :  CRYSTAL STRUCTURE OF PCRB COMPLEXED WITH PEG FROM STAPHYLOCOCCUS AUREUS SUBSP. AUREUS MU3
 
Authors :  F. Ren, X. Feng, T. P. Ko, C. H. Huang, Y. Hu, H. C. Chan, Y. L. Liu, K. Wang, C X. Pang, M. He, Y. Li, E. Oldfield, R. T. Guo
Date :  17 Oct 12  (Deposition) - 26 Dec 12  (Release) - 31 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.54
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Biosynthesis, Prenyltransferases, Enzyme Catalysis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Ren, X. Feng, T. P. Ko, C. H. Huang, Y. Hu, H. C. Chan, Y. L. Liu, K. Wang, C. C. Chen, X. Pang, M. He, Y. Li, E. Oldfield, R. T. Guo
Insights Into Tim-Barrel Prenyl Transferase Mechanisms: Crystal Structures Of Pcrb From Bacillus Subtilis And Staphylococcus Aureus
Chembiochem V. 14 195 2013
PubMed-ID: 23322418  |  Reference-DOI: 10.1002/CBIC.201200748

(-) Compounds

Molecule 1 - HEPTAPRENYLGLYCERYL PHOSPHATE SYNTHASE
    Chains: A, B
    EC Number: 2.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PCRB
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 418127
    Strain: MU3
    Synonym: PCRB, HEPGP SYNTHASE, GLYCEROL-1-PHOSPHATE HEPTAPRENYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE B:66 , PRO B:82BINDING SITE FOR RESIDUE PGE B 900

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3W01)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3W01)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3W01)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3W01)

(-) Exons   (0, 0)

(no "Exon" information available for 3W01)

(-) Sequences/Alignments

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:230
 aligned with PCRB_STAA1 | A7X435 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:230
                                 1                                                                                                                                                                                                                                
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225
           PCRB_STAA1     - -----MYDIKKWRHIFKLDPAKHISDDDLDAICMSQTDAIMIGGTDDVTEDNVIHLMSKIRRYPLPLVLEISNIESVMPGFDFYFVPTVLNSTDVAFHNGTLLEALKTYGHSIDFEEVIFEGYVVCNADSKVAKHTKANTDLTTEDLEAYAQMVNHMYRLPVMYIEYSGIYGDVSKVQAVSEHLTETQLFYGGGISSEQQATEMAAIADTIIVGDIIYKDIKKALKTVKI 225
               SCOP domains d3w01a_ A: PcrB protein homolog YerE                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..eeeee......hhhhhhhhhh....eeee......hhhhhhhhhhhhh.....eeee............eeeeeee.........hhhhhhhhhhhhhhhhhh.eeeeeeee....hhhhhhh......hhhhhhhhhhhhhhh....eeeee......hhhhhhhhhh.....eeeee....hhhhhhhhhh...eeee.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w01 A  -4 AGAGAMYDIKKWRHIFKLDPAKHISDDDLDAICMSQTDAIMIGGTDDVTEDNVIHLMSKIRRYPLPLVLEISNIESVMPGFDFYFVPTVLNSTDVAFHNGTLLEALKTYGHSIDFEEVIFEGYVVCNADSKVAKHTKANTDLTTEDLEAYAQMVNHMYRLPVMYIEYSGIYGDVSKVQAVSEHLTETQLFYGGGISSEQQATEMAAIADTIIVGDIIYKDIKKALKTVKI 225
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225


Chain B from PDB  Type:PROTEIN  Length:227
 aligned with PCRB_STAA1 | A7X435 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:231
                               1                                                                                                                                                                                                                                   
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227 
           PCRB_STAA1     - ---MYDIKKWRHIFKLDPAKHISDDDLDAICMSQTDAIMIGGTDDVTEDNVIHLMSKIRRYPLPLVLEISNIESVMPGFDFYFVPTVLNSTDVAFHNGTLLEALKTYGHSIDFEEVIFEGYVVCNADSKVAKHTKANTDLTTEDLEAYAQMVNHMYRLPVMYIEYSGIYGDVSKVQAVSEHLTETQLFYGGGISSEQQATEMAAIADTIIVGDIIYKDIKKALKTVKIKES 228
               SCOP domains d3w01b_ B: PcrB protein homolog YerE                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.eeeee......hhhhhhhhhh....eeee.----.hhhhhhhhhhhhh.....eeee..hhhhh.....eeeeeee.........hhhhhhhhhhhh...hhh.eeeeeeee....hhhhhhh......hhhhhhhhhhhhhhh....eeeee......hhhhhhhhhh.....eeeee....hhhhhhhhhh...eeeehhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w01 B  -2 AGAMYDIKKWRHIFKLDPAKHISDDDLDAICMSQTDAIMIG----VTEDNVIHLMSKIRRYPLPLVLEISNIESVMPGFDFYFVPTVLNSTDVAFHNGTLLEALKTYGHSIDFEEVIFEGYVVCNADSKVAKHTKANTDLTTEDLEAYAQMVNHMYRLPVMYIEYSGIYGDVSKVQAVSEHLTETQLFYGGGISSEQQATEMAAIADTIIVGDIIYKDIKKALKTVKIKES 228
                                     7        17        27        37|    |  47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227 
                                                                   38   43
   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)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3W01)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3W01)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PCRB_STAA1 | A7X435)
molecular function
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0002094    polyprenyltransferase activity    Catalysis of the transfer of multiple prenyl groups from one compound (donor) to another (acceptor).
    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:0016765    transferase activity, transferring alkyl or aryl (other than methyl) groups    Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
biological process
    GO:0046474    glycerophospholipid biosynthetic process    The chemical reactions and pathways resulting in the formation of glycerophospholipids, any derivative of glycerophosphate that contains at least one O-acyl, O-alkyl, or O-alkenyl group attached to the glycerol residue.
    GO:0006650    glycerophospholipid metabolic process    The chemical reactions and pathways involving glycerophospholipids, any derivative of glycerophosphate that contains at least one O-acyl, O-alkyl, or O-alkenyl group attached to the glycerol residue.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0008654    phospholipid biosynthetic process    The chemical reactions and pathways resulting in the formation of phospholipids, any lipid containing phosphoric acid as a mono- or diester.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    PGE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3w01)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  3w01
    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
  PCRB_STAA1 | A7X435
    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)
  2.5.1.-
    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
  PCRB_STAA1 | A7X435
    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
        PCRB_STAA1 | A7X435: 3w02

(-) Related Entries Specified in the PDB File

3vzx 3vzy 3vzz 3w00 3w02