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(-) Description

Title :  CRYSTAL STRUCTURE OF A DECAPRENYL DIPHOSPHATE SYNTHASE FROM RHODOBACTER CAPSULATUS
 
Authors :  C. E. Quartararo, Y. Patskovsky, J. B. Bonanno, M. Rutter, K. T. Bain, S. R. Toro, J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research For Structural Genomics (Nysgxrc)
Date :  13 May 10  (Deposition) - 09 Jun 10  (Release) - 24 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Structural Genomics, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. H. Wallrapp, J. J. Pan, G. Ramamoorthy, D. E. Almonacid, B. S. Hillerich, R. Seidel, Y. Patskovsky, P. C. Babbitt, S. C. Almo, M. P. Jacobson, C. D. Poulter
Prediction Of Function For The Polyprenyl Transferase Subgroup In The Isoprenoid Synthase Superfamily.
Proc. Natl. Acad. Sci. Usa V. 110 E1196 2013
PubMed-ID: 23493556  |  Reference-DOI: 10.1073/PNAS.1300632110

(-) Compounds

Molecule 1 - DECAPRENYL DIPHOSPHATE SYNTHASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET26
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: RHODOBACTER CAPSULATUS
    Organism Taxid: 1061

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3MZV)

(-) Sites  (0, 0)

(no "Site" information available for 3MZV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:72 -Pro A:73
2Gly B:72 -Pro B:73

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MZV)

(-) 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:309
 aligned with Q07D00_RHOCA | Q07D00 from UniProtKB/TrEMBL  Length:333

    Alignment length:325
                                    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     
         Q07D00_RHOCA     9 KPHDRLAQALAEDMAAVNALIRERMSSEHAPRIPEVTAHLIEAGGKRLRPMLTLAAARLVGYGGPFHVHLAATVEFIHTATLLHDDVVDESRQRRGRPTANLLWDNKSSVLVGDYLFARSFQLMTDTGNMRVMEILANASAVIAEGEVLQLTAAQNLATTEDIYLRVIRGKTAALFSAATEVGGIIGGAPEDQVQALFDYGDALGIAFQIVDDLLDYGGKSAEIGKNTGDDFRERKLTMPVIKAVALADEAERAFWKRVIEKGDQQDGDLEHAMALMTKHGTLEATRLAAIGWTDTARKALAKLPDHPLRQMLDDLADYVVERVR 333
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh------.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh----------.hhhhhh...hhhhhhhhhh.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mzv A   9 KPHDRLAQALAEDMAAVNALIRERMSSEHAPRIPEVTAHLIEAGGKRLRPMLTLAAARLVGYGGPFHVHLAATVEFIHTATLLHDDV------RRGRPTANLLWDNKSSVLVGDYLFARSFQLMTDTGNMRVMEILANASAVIAEGEVLQLTAAQNLATTEDIYLRVIRGKTAALFSAATEVGGIIGGAPEDQVQALFDYGDALGIAFQIVDDLLDY----------TGDDFRERKLTMPVIKAVALADEAERAFWKRVIEKGDQQDGDLEHAMALMTKHGTLEATRLAAIGWTDTARKALAKLPDHPLRQMLDDLADYVVERVR 333
                                    18        28        38        48        58        68        78        88      |  -   |   108       118       128       138       148       158       168       178       188       198       208       218      |  -       238       248       258       268       278       288       298       308       318       328     
                                                                                                                 95    102                                                                                                                        225        236                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:325
 aligned with Q07D00_RHOCA | Q07D00 from UniProtKB/TrEMBL  Length:333

    Alignment length:325
                                                                                                                                                                                                                                                                                                                                                             333 
                                    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   | 
         Q07D00_RHOCA    10 PHDRLAQALAEDMAAVNALIRERMSSEHAPRIPEVTAHLIEAGGKRLRPMLTLAAARLVGYGGPFHVHLAATVEFIHTATLLHDDVVDESRQRRGRPTANLLWDNKSSVLVGDYLFARSFQLMTDTGNMRVMEILANASAVIAEGEVLQLTAAQNLATTEDIYLRVIRGKTAALFSAATEVGGIIGGAPEDQVQALFDYGDALGIAFQIVDDLLDYGGKSAEIGKNTGDDFRERKLTMPVIKAVALADEAERAFWKRVIEKGDQQDGDLEHAMALMTKHGTLEATRLAAIGWTDTARKALAKLPDHPLRQMLDDLADYVVERVR-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------polyprenyl_synt-3mzvB01 B:41-296                                                                                                                                                                                                                                -------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------polyprenyl_synt-3mzvB02 B:41-296                                                                                                                                                                                                                                -------------------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh....hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh...hhhhhhhhhh.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mzv B  10 PHDRLAQALAEDMAAVNALIRERMSSEHAPRIPEVTAHLIEAGGKRLRPMLTLAAARLVGYGGPFHVHLAATVEFIHTATLLHDDVVDESRQRRGRPTANLLWDNKSSVLVGDYLFARSFQLMTDTGNMRVMEILANASAVIAEGEVLQLTAAQNLATTEDIYLRVIRGKTAALFSAATEVGGIIGGAPEDQVQALFDYGDALGIAFQIVDDLLDYGGKSAEIGKNTGDDFRERKLTMPVIKAVALADEAERAFWKRVIEKGDQQDGDLEHAMALMTKHGTLEATRLAAIGWTDTARKALAKLPDHPLRQMLDDLADYVVERVRE 334
                                    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
   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  (0, 0)

(no "SCOP Domain" information available for 3MZV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: polyprenyl_synt] (86)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q07D00_RHOCA | Q07D00)
molecular function
    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.
biological process
    GO:0008299    isoprenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.

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  Cis Peptide Bonds
    Gly A:72 - Pro A:73   [ RasMol ]  
    Gly B:72 - Pro B:73   [ RasMol ]  
 

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