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(-) Description

Title :  TRYPANOSOMA CRUZI FARNESYL DIPHOSPHATE SYNTHASE HOMODIMER IN COMPLEX WITH 3-FLUORO-1-(2-HYDROXY-2,2-BISPHOSPHONO-ETHYL) PYRIDINIUM
 
Authors :  L. M. Amzel, C. H. Huang, S. B. Gabelli, E. Oldfield
Date :  19 Jul 09  (Deposition) - 09 Feb 10  (Release) - 09 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.81
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Farnesyl Diphosphate Synthase, Fpps, Bisphosphonate, Zoledronate, Risedronate, Minodronate, Chagas Disease, Isoprene Biosynthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. H. Huang, S. B. Gabelli, E. Oldfield, L. M. Amzel
Binding Of Nitrogen-Containing Bisphosphonates (N-Bps) To The Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer.
Proteins V. 78 888 2010
PubMed-ID: 19876942  |  Reference-DOI: 10.1002/PROT.22614

(-) Compounds

Molecule 1 - FARNESYL PYROPHOSPHATE SYNTHASE
    Chains: A
    EC Number: 2.5.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FPPS
    Organism Scientific: TRYPANOSOMA CRUZI
    Organism Taxid: 5693

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION
2NI91Ligand/Ion3-FLUORO-1-(2-HYDROXY-2,2-DIPHOSPHONOETHYL)PYRIDINIUM
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2NI92Ligand/Ion3-FLUORO-1-(2-HYDROXY-2,2-DIPHOSPHONOETHYL)PYRIDINIUM
3SO44Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:94 , ASP A:98 , ASP A:102 , ARG A:107 , GLN A:167 , LYS A:207 , THR A:208 , GLN A:247 , ASP A:250 , LYS A:264 , MG A:401 , MG A:402 , MG A:403BINDING SITE FOR RESIDUE NI9 A 363
2AC2SOFTWAREASP A:98 , ASP A:102 , NI9 A:363BINDING SITE FOR RESIDUE MG A 401
3AC3SOFTWAREASP A:250 , ASP A:251 , ASP A:268 , NI9 A:363BINDING SITE FOR RESIDUE MG A 402
4AC4SOFTWAREASP A:98 , ASP A:102 , ASP A:170 , NI9 A:363BINDING SITE FOR RESIDUE MG A 403
5AC5SOFTWARELYS A:25 , HIS A:141 , LYS A:158BINDING SITE FOR RESIDUE SO4 A 405
6AC6SOFTWAREGLY A:47 , LYS A:48 , TYR A:49 , PHE A:50 , ARG A:51 , GLN A:91 , ARG A:108 , HOH A:364 , HOH A:365 , HOH A:396BINDING SITE FOR RESIDUE SO4 A 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ID0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ID0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ID0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ID0)

(-) Exons   (0, 0)

(no "Exon" information available for 3ID0)

(-) 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:362
 aligned with Q8WS25_TRYCR | Q8WS25 from UniProtKB/TrEMBL  Length:316

    Alignment length:362
                                                                          1                                                                                                                                                                                                                                                                                                                           
                                     -         -         -         -      |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314  
         Q8WS25_TRYCR     - ----------------------------------------------GKYFRGMTVVNVAEGFLAVTQHDEATKERILHDACVGGWMIEFLQAHYLVEDDIMDGSVMRRGKPCWYRFPGVTTQCAINDGIILKSWTQIMAWHYFADRPFLKDLLCLFQKVDYATAVGQMYDVTSMCDSNKLDPEVAQPMTTDFAEFTPAIYKRIVKYKTTFYTYLLPLVMGLFVSEAAASVEMNLVERVAHLIGEYFQVQDDVMDCFTPPEQLGKVGTDIEDAKCSWLAVTFLGKANAAQVAEFKANYGDKDPAKVAVVKRLYSEANLQADFAAYEAEVVREVESLIEQLKVKSPTFAESVAVVWEKTHKRKK 316
               SCOP domains d3id0a_ A: automated matches                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 3id0A00 A:1-362 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh..hhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3id0 A   1 MASMERFLSVYDEVQAFLLDQLQSKYEIDPNRARYLRIMMDTTCLGGKYFRGMTVVNVAEGFLAVTQHDEATKERILHDACVGGWMIEFLQAHYLVEDDIMDGSVMRRGKPCWYRFPGVTTQCAINDGIILKSWTQIMAWHYFADRPFLKDLLCLFQKVDYATAVGQMYDVTSMCDSNKLDPEVAQPMTTDFAEFTPAIYKRIVKYKTTFYTYLLPLVMGLFVSEAAASVEMNLVERVAHLIGEYFQVQDDVMDCFTPPEQLGKVGTDIEDAKCSWLAVTFLGKANAAQVAEFKANYGDKDPAKVAVVKRLYSEANLQADFAAYEAEVVREVESLIEQLKVKSPTFAESVAVVWEKTHKRKK 362
                                    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       330       340       350       360  


Chain A from PDB  Type:PROTEIN  Length:362
 aligned with Q95WL3_TRYCR | Q95WL3 from UniProtKB/TrEMBL  Length:362

    Alignment length:362
                                    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       330       340       350       360  
         Q95WL3_TRYCR     1 MASMERFLSVYDEVQAFLLDQLQSKYEIDPNRARYLRIMMDTTCLGGKYFRGMTVVNVAEGFLAVTQHDEATKERILHDACVGGWMIEFLQAHYLVEDDIMDGSVMRRGKPCWYRFPGVTTQCAINDGIILKSWTQIMAWHYFADRPFLKDLLCLFQKVDYATAVGQMYDVTSMCDSNKLDPEVAQPMTTDFAEFTPAIYKRIVKYKTTFYTYLLPLVMGLFVSEAAASVEMNLVERVAHLIGEYFQVQDDVMDCFTPPEQLGKVGTDIEDAKCSWLAVTFLGKANAAQVAEFKANYGDKDPAKVAVVKRLYSEANLQADFAAYEAEVVREVESLIEQLKVKSPTFAESVAVVWEKTHKRKK 362
               SCOP domains d3id0a_ A: automated matches                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 3id0A00 A:1-362 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh..hhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3id0 A   1 MASMERFLSVYDEVQAFLLDQLQSKYEIDPNRARYLRIMMDTTCLGGKYFRGMTVVNVAEGFLAVTQHDEATKERILHDACVGGWMIEFLQAHYLVEDDIMDGSVMRRGKPCWYRFPGVTTQCAINDGIILKSWTQIMAWHYFADRPFLKDLLCLFQKVDYATAVGQMYDVTSMCDSNKLDPEVAQPMTTDFAEFTPAIYKRIVKYKTTFYTYLLPLVMGLFVSEAAASVEMNLVERVAHLIGEYFQVQDDVMDCFTPPEQLGKVGTDIEDAKCSWLAVTFLGKANAAQVAEFKANYGDKDPAKVAVVKRLYSEANLQADFAAYEAEVVREVESLIEQLKVKSPTFAESVAVVWEKTHKRKK 362
                                    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       330       340       350       360
   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, 1)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ID0)

(-) Gene Ontology  (3, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q95WL3_TRYCR | Q95WL3)
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.

Chain A   (Q8WS25_TRYCR | Q8WS25)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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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 Related Entries

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

UniProtKB/TrEMBL
        Q95WL3_TRYCR | Q95WL3: 3iba 3ick 3icm 3icn 3icz 4dwb 4dwg 4dxj 4dzw 4e1e

(-) Related Entries Specified in the PDB File

1yhk 1yhl 1yhm 3iba 3ick 3icm 3icn 3icz