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(-) Description

Title :  CRYSTAL STRUCTURE OF GERANYLGERANYL PYROPHOSPHATE SYNTHASE FROM BACTEROIDES THETAIOTAOMICRON
 
Authors :  Y. Patskovsky, R. Toro, J. M. Sauder, C. D. Poulter, J. A. Gerlt, S. K. Bur S. C. Almo, Enzyme Function Initiative (Efi), New York Sgx Rese Center For Structural Genomics (Nysgxrc)
Date :  20 Apr 11  (Deposition) - 11 May 11  (Release) - 24 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Protein Structure Initiative, Isoprene Biosynthesis, Transferase, New York Sgx Research Center For Structural Genomics, Nysgxrc, Enzyme Function Initiative, Efi, Psi-2 (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 - OCTAPRENYL-DIPHOSPHATE SYNTHASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)CODON+RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BT_3261
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON
    Organism Taxid: 818
    Strain: VPI-5482

 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 3RMG)

(-) Sites  (0, 0)

(no "Site" information available for 3RMG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3RMG)

(-) 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:299
 aligned with Q8A2P4_BACTN | Q8A2P4 from UniProtKB/TrEMBL  Length:324

    Alignment length:324
                             1                                                                                                                                                                                                                                                                                                                                  
                             |       9        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    
         Q8A2P4_BACTN     - -MDSISLIKTPIEAELEDFKALFDTPLSDSNALLDSVITHIRKRNGKMMRPILVLLVARLYGAVTPATLHAAVSLELLHTASLVHDDVVDESTERRGQLSVNAIFNNKVSVLAGDYLLATSLVHAEQTNNYEIIRLVSSLGQKLAEGELLQLSNVSNHSFSEEVYFDVIRKKTAALFAACAEAAALSVQVGEEEVAFARLLGEYIGICFQIKDDIFDYFDSKKIGKPTGNDMLEGKLTLPALYALNTTKDAWAEQIAFKVKEGTATPDEIVRLIEFTKDNGGIEYACRTIEQYKKKAFDLLAALPDSNICLALRTYLDYVVARE 323
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhh.hhhhhhhhhhhh.----..hhhhhhhhhhh.----.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh---------hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...--.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh....------.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3rmg A  -1 SLDSISLIKTPIEAELEDFKALFD----DSNALLDSVITHIR----KMMRPILVLLVARLYGAVTPATLHAAVSLELLHTASLVHDDVVD---------SVNAIFNNKVSVLAGDYLLATSLVHAEQTNNYEIIRLVSSLGQKLAEGELLQLSNVSN--FSEEVYFDVIRKKTAALFAACAEAAALSVQVGEEEVAFARLLGEYIGICFQIKDDIFDYFDS------TGNDMLEGKLTLPALYALNTTKDAWAEQIAFKVKEGTATPDEIVRLIEFTKDNGGIEYACRTIEQYKKKAFDLLAALPDSNICLALRTYLDYVVARE 323
                                     8        18   |    28        38 |    | 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    
                                                  22   27           40   46                                         89        99                                                      156  |                                                          220    227                                                                                                
                                                                                                                                                                                         159                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:297
 aligned with Q8A2P4_BACTN | Q8A2P4 from UniProtKB/TrEMBL  Length:324

    Alignment length:322
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320  
         Q8A2P4_BACTN     1 MDSISLIKTPIEAELEDFKALFDTPLSDSNALLDSVITHIRKRNGKMMRPILVLLVARLYGAVTPATLHAAVSLELLHTASLVHDDVVDESTERRGQLSVNAIFNNKVSVLAGDYLLATSLVHAEQTNNYEIIRLVSSLGQKLAEGELLQLSNVSNHSFSEEVYFDVIRKKTAALFAACAEAAALSVQVGEEEVAFARLLGEYIGICFQIKDDIFDYFDSKKIGKPTGNDMLEGKLTLPALYALNTTKDAWAEQIAFKVKEGTATPDEIVRLIEFTKDNGGIEYACRTIEQYKKKAFDLLAALPDSNICLALRTYLDYVVAR 322
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------       -----polypreny  l_synt-3rmgB01 B:36-275                                                                                                                                                                                                              ----------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------       -----polypreny  l_synt-3rmgB02 B:36-275                                                                                                                                                                                                              ----------------------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhh.hhhhhhhhhhhhh-------hhhhhhhhhhhhhh--hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh-------------hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.....--......hhhhh..hhhhhhhh...-hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rmg B   0 LDSISLIKTPIEAELEDFKALFD-------ALLDSVITHIRKRN--MMRPILVLLVARLYGAVTPATLHAAVSLELLHTASLVHDDVV-------------AIFNNKVSVLAGDYLLATSLVHAEQTNNYEIIRLVSSLGQKLAEGELLQLSNVSNHSFSEEVYFDVIRKKTAALFAACAEAAALSVQVGEEEVAFARLLGEYIGICFQIKDDIFDYFDSK--GKPTGNDMLEGKLTLPALYALNTT-DAWAEQIAFKVKEGTATPDEIVRLIEFTKDNGGIEYACRTIEQYKKKAFDLLAALPDSNICLALRTYLDYVVAR 322
                                     9        19  |      -|       40   |  | 50        60        70        80       | -         - |     110       120       130       140       150       160       170       180       190       200       210       220|  |   230       240      |250       260       270       280       290       300       310       320  
                                                 22      31           44 47                                       88           102                                                                                                                    221  |                    247 |                                                                         
                                                                                                                                                                                                                                                         224                      249
   Legend:   → Mismatch (orange background)
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  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 3RMG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8A2P4_BACTN | Q8A2P4)
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.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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