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(-) Description

Title :  STRUCTURE OF THE COMPLEX OF TRYPANOSOMA CRUZI FARNESYL DIPHOSPHATE SYNTHASE WITH RISEDRONATE, DMAPP AND MG+2
 
Authors :  S. B. Gabelli, J. S. Mclellan, A. Montalvetti, E. Oldfield, R. Docampo,
Date :  09 Jan 05  (Deposition) - 20 Dec 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Farnesyl Diphosphate Synthase, Bisphosphonate, Dimethyl Allyl Pyrophosphate Sulfate, Fpps, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. B. Gabelli, J. S. Mclellan, A. Montalvetti, E. Oldfield, R. Docampo L. M. Amzel
Structure And Mechanism Of The Farnesyl Diphosphate Synthas From Trypanosoma Cruzi: Implications For Drug Design.
Proteins V. 62 80 2005
PubMed-ID: 16288456  |  Reference-DOI: 10.1002/PROT.20754

(-) Compounds

Molecule 1 - FARNESYL PYROPHOSPHATE SYNTHASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PET28
    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  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1DMA1Ligand/IonDIMETHYLALLYL DIPHOSPHATE
2MG3Ligand/IonMAGNESIUM ION
3RIS1Ligand/Ion1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID
4SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1DMA2Ligand/IonDIMETHYLALLYL DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3RIS2Ligand/Ion1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID
4SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:98 , ASP A:102 , RIS A:1400 , MG A:1403 , HOH A:1407 , HOH A:1408BINDING SITE FOR RESIDUE MG A 1401
2AC2SOFTWAREASP A:250 , RIS A:1400 , HOH A:1410 , HOH A:1411 , HOH A:1533BINDING SITE FOR RESIDUE MG A 1402
3AC3SOFTWAREASP A:98 , ASP A:102 , RIS A:1400 , MG A:1401 , HOH A:1406 , HOH A:1409 , HOH A:1532BINDING SITE FOR RESIDUE MG A 1403
4AC4SOFTWAREHIS A:141 , HOH A:1501 , HOH A:1647BINDING SITE FOR RESIDUE SO4 A 1405
5AC5SOFTWAREGLY A:47 , LYS A:48 , TYR A:49 , PHE A:50 , ARG A:51 , GLN A:91 , ARG A:108 , TYR A:211 , PHE A:246 , LYS A:264 , LYS A:362 , RIS A:1400 , HOH A:1415 , HOH A:1424 , HOH A:1574BINDING SITE FOR RESIDUE DMA A 1301
6AC6SOFTWARELEU A:95 , ASP A:98 , ASP A:102 , ARG A:107 , GLN A:167 , LYS A:207 , THR A:208 , TYR A:211 , ASP A:250 , LYS A:264 , DMA A:1301 , MG A:1401 , MG A:1402 , MG A:1403 , HOH A:1407 , HOH A:1408 , HOH A:1409 , HOH A:1410 , HOH A:1411 , HOH A:1440 , HOH A:1455 , HOH A:1533 , HOH A:1663BINDING SITE FOR RESIDUE RIS A 1400

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YHL)

(-) 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 Q8WS26_TRYCR | Q8WS26 from UniProtKB/TrEMBL  Length:425

    Alignment length:362
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423  
         Q8WS26_TRYCR    64 MASMERFLSVYDEVQAFLLDQLQSKYEIDPNRARYLRIMMDTTCLGGKYFRGMTVVNVAEGFLAVTQHDEATKERILHDACVGGWMIEFLQAHYLVEDDIMDGSVMRRGKPCWYRFPGVTTQCAINDGIILKSWTQIMAWHYFADRPFLKDLLCLFQKVDYATAVGQMYDVTSMCDSNKLDPEVAQPMTTDFAEFTPAIYKRIVKYKTTFYTYLLPLVMGLLVSEAAASVEMNLVERVAHLIGEYFQVQDDVMDCFTPPEQLGKVGTDIEDAKCSWLAVTFLGKANAAQVAEFKANYGEKDPAKVAVVKRLYSKANLQADFAAYEAEVVREVESLIEQLKVKSPTFAESVAVVWEKTHKRKK 425
               SCOP domains d1yhla_ A: automated matches                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1yhlA00 A:1-362 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------polyprenyl_synt-1yhlA01 A:35-323                                                                                                                                                                                                                                                                 --------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yhl 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  (1, 1)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q8WS26_TRYCR | Q8WS26)
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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 Related Entries

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

UniProtKB/TrEMBL
        Q8WS26_TRYCR | Q8WS26: 1yhk 1yhm

(-) Related Entries Specified in the PDB File

1yhk