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(-) Description

Title :  CRYSTAL STRUCTURE OF TRYPANOSOME CRUZI FARNESYL DIPHOSPHATE SYNTHASE IN COMPLEX WITH [2-(N-HEXYLAMINO)ETHANE-1,1-DIYL]BISPHOSPHONIC ACID AND MG2+
 
Authors :  S. Aripirala, L. M. Amzel, S. B. Gabelli
Date :  06 Mar 12  (Deposition) - 16 Jan 13  (Release) - 17 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Geranyl Transferase, Farnesyl Pyrophosphate Synthase, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Aripirala, S. H. Szajnman, J. Jakoncic, J. B. Rodriguez, R. Docampo S. B. Gabelli, L. M. Amzel
Design, Synthesis, Calorimetry, And Crystallographic Analysis Of 2-Alkylaminoethyl-1, 1-Bisphosphonates As Inhibitors Of Trypanosoma Cruzi Farnesyl Diphosphate Synthase.
J. Med. Chem. V. 55 6445 2012
PubMed-ID: 22715997  |  Reference-DOI: 10.1021/JM300425Y

(-) Compounds

Molecule 1 - FARNESYL PYROPHOSPHATE SYNTHASE
    Chains: A
    EC Number: 2.5.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: FPPS
    Organism Scientific: TRYPANOSOMA CRUZI
    Organism Taxid: 5693
    Synonym: FPPS, FARNESYL DIPHOSPHATE SYNTHASE

 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
10MW1Ligand/Ion[2-(HEXYLAMINO)ETHANE-1,1-DIYL]BIS(PHOSPHONIC ACID)
2IPE1Ligand/Ion3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
3MG3Ligand/IonMAGNESIUM ION
4NA1Ligand/IonSODIUM ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
10MW2Ligand/Ion[2-(HEXYLAMINO)ETHANE-1,1-DIYL]BIS(PHOSPHONIC ACID)
2IPE2Ligand/Ion3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4NA-1Ligand/IonSODIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:250 , 0MW A:404 , HOH A:511 , HOH A:512BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWAREASP A:98 , ASP A:102 , MG A:403 , 0MW A:404 , HOH A:507BINDING SITE FOR RESIDUE MG A 402
3AC3SOFTWAREASP A:98 , ASP A:102 , ASP A:170 , MG A:402 , 0MW A:404 , HOH A:508 , HOH A:509 , HOH A:510BINDING SITE FOR RESIDUE MG A 403
4AC4SOFTWARETYR A:94 , ASP A:98 , ASP A:102 , ARG A:107 , GLN A:167 , LYS A:207 , GLN A:247 , ASP A:250 , LYS A:264 , MG A:401 , MG A:402 , MG A:403 , IPE A:405 , HOH A:507 , HOH A:508 , HOH A:509 , HOH A:511 , HOH A:512BINDING SITE FOR RESIDUE 0MW A 404
5AC5SOFTWAREGLY A:47 , LYS A:48 , ARG A:51 , GLN A:91 , ARG A:108 , TYR A:211 , PHE A:246 , GLN A:247 , ASP A:250 , LYS A:264 , 0MW A:404BINDING SITE FOR RESIDUE IPE A 405
6AC6SOFTWAREHIS A:141 , HOH A:514BINDING SITE FOR RESIDUE NA A 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E1E)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:262 -Gly A:263

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E1E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4E1E)

(-) Exons   (0, 0)

(no "Exon" information available for 4E1E)

(-) 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:361
 aligned with Q95WL3_TRYCR | Q95WL3 from UniProtKB/TrEMBL  Length:362

    Alignment length:361
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361 
         Q95WL3_TRYCR     2 ASMERFLSVYDEVQAFLLDQLQSKYEIDPNRARYLRIMMDTTCLGGKYFRGMTVVNVAEGFLAVTQHDEATKERILHDACVGGWMIEFLQAHYLVEDDIMDGSVMRRGKPCWYRFPGVTTQCAINDGIILKSWTQIMAWHYFADRPFLKDLLCLFQKVDYATAVGQMYDVTSMCDSNKLDPEVAQPMTTDFAEFTPAIYKRIVKYKTTFYTYLLPLVMGLFVSEAAASVEMNLVERVAHLIGEYFQVQDDVMDCFTPPEQLGKVGTDIEDAKCSWLAVTFLGKANAAQVAEFKANYGDKDPAKVAVVKRLYSEANLQADFAAYEAEVVREVESLIEQLKVKSPTFAESVAVVWEKTHKRKK 362
               SCOP domains d4e1ea_ A: automated matches                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e1e A   2 ASMERFLSVYDEVQAFLLDQLQSKYEIDPNRARYLRIMMDTTCLGGKYFRGMTVVNVAEGFLAVTQHDEATKERILHDACVGGWMIEFLQAHYLVEDDIMDGSVMRRGKPCWYRFPGVTTQCAINDGIILKSWTQIMAWHYFADRPFLKDLLCLFQKVDYATAVGQMYDVTSMCDSNKLDPEVAQPMTTDFAEFTPAIYKRIVKYKTTFYTYLLPLVMGLFVSEAAASVEMNLVERVAHLIGEYFQVQDDVMDCFTPPEQLGKVGTDIEDAKCSWLAVTFLGKANAAQVAEFKANYGDKDPAKVAVVKRLYSEANLQADFAAYEAEVVREVESLIEQLKVKSPTFAESVAVVWEKTHKRKK 362
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361
   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  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4E1E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E1E)

(-) Gene Ontology  (2, 2)

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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q95WL3_TRYCR | Q95WL3: 3id0
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        Q95WL3_TRYCR | Q95WL3: 3iba 3ick 3icm 3icn 3icz 4dwb 4dwg 4dxj 4dzw

(-) Related Entries Specified in the PDB File

1yhk 1yhl 1yhm 3iba 3ick 3icm 3icn 3icz 4dwb 4dwg 4dxj 4dzw