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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN FARNESYL PYROPHOSPHATE SYNTHASE (Y204F) MUTANT COMPLEXED WITH MG, RISEDRONATE AND ISOPENTENYL PYROPHOSPHATE
 
Authors :  B. L. Barnett, M. K. Tsoumpra, J. R. C. Muniz, R. L. Walter
Date :  13 May 13  (Deposition) - 30 Apr 14  (Release) - 30 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Isoprene Biosynthesis, Lipid Synthesis, Steroid Biosynthesis, Transferase, Dimethylallyl Pyrophosphate, Isoprenoid Pathway, Cholesterol Synthesis, Bisphosphonates (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. K. Tsoumpra, J. R. C. Muniz, B. L. Barnett, E. Pilka, A. Kwaasi, K. L. Kavanagh, A. G. Evdokimov, R. L. Walter, F. H. Ebetino, U. Oppermann, R. G. G. Russell, J. E. Dunford
Crystal Structure Of Human Farnesyl Pyrophosphate Synthase (Y204F) Mutant Complexed With Mg, Risedronate And Isopentenyl Pyrophosphate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - FARNESYL PYROPHOSPHATE SYNTHASE
    Chains: A
    EC Number: 2.5.1.10, 2.5.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 11 DERIVATIVE
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 67-419
    Gene: FDPS, FPS, KIAA1293
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: FPP SYNTHASE, FPS, (2E,6E)-FARNESYL DIPHOSPHATE SYNTHASE, DIMETHYLALLYLTRANSTRANSFERASE, FARNESYL DIPHOSPHATE SYNTHASE, GERANYLTRANSTRANSFERASE

 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, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1IPE1Ligand/Ion3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
2MG3Ligand/IonMAGNESIUM ION
3RIS1Ligand/Ion1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1IPE2Ligand/Ion3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3RIS2Ligand/Ion1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:103 , ASP A:107 , MG A:403 , RIS A:405 , HOH A:582 , HOH A:583 , HOH A:611BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWAREASP A:243 , RIS A:405 , HOH A:577 , HOH A:578 , HOH A:579 , HOH A:632BINDING SITE FOR RESIDUE MG A 402
3AC3SOFTWAREASP A:103 , ASP A:107 , MG A:401 , RIS A:405 , HOH A:573 , HOH A:574 , HOH A:575BINDING SITE FOR RESIDUE MG A 403
4AC4SOFTWAREGLY A:56 , LYS A:57 , ARG A:60 , GLN A:96 , ARG A:113 , THR A:201 , PHE A:204 , SER A:205 , PHE A:239 , GLN A:240 , ARG A:351 , RIS A:405 , HOH A:571 , HOH A:584 , HOH A:585 , HOH A:586 , HOH A:589 , HOH A:605 , HOH A:615 , HOH A:616BINDING SITE FOR RESIDUE IPE A 404
5AC5SOFTWAREASP A:103 , ASP A:107 , ARG A:112 , GLN A:171 , LYS A:200 , THR A:201 , ASP A:243 , LYS A:257 , MG A:401 , MG A:402 , MG A:403 , IPE A:404 , HOH A:573 , HOH A:575 , HOH A:576 , HOH A:577 , HOH A:578 , HOH A:579 , HOH A:581 , HOH A:582 , HOH A:583 , HOH A:611 , HOH A:632BINDING SITE FOR RESIDUE RIS A 405

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:334 -Pro A:335

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KPD)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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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:341
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kpd A   9 VYAQEKQDFVQHFSQIVRVLTEHPEIGDAIARLKEVLEYNAIGGKYNRGLTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLIELFLQSSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKTAFFSFYLPIAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIGTDIQDNKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELDLPAVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYKRRK 353
                                    18        28 ||     42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352 
                                                30|                                                                                                                                                                                                                                                                                                                              
                                                 35
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  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 4KPD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

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  Cis Peptide Bonds
    Ala A:334 - Pro A:335   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        FPPS_HUMAN | P14324: 1yq7 1yv5 1zw5 2f7m 2f89 2f8c 2f8z 2f92 2f94 2f9k 2opm 2opn 2qis 2rah 2vf6 3b7l 3cp6 3n1v 3n1w 3n3l 3n45 3n46 3n49 3n5h 3n5j 3n6k 3rye 3s4j 4dem 4ga3 4h5c 4h5d 4h5e 4jvj 4kfa 4kpj 4kq5 4kqs 4kqu 4l2x 4lfv 4lpg 4lph 4n1z 4n9u 4nfi 4nfj 4nfk 4ng6 4nke 4nkf 4nua 4ogu 4p0v 4p0w 4p0x 4pvx 4pvy 4q23 4qpf 4qxs 4rxa 4xqr 4xqs 4xqt 5cg5 5cg6 5dgm 5dgn 5dgs 5diq 5djp 5djr 5djv 5ja0 5juz 5jv0 5jv1 5jv2 5ksx

(-) Related Entries Specified in the PDB File

4kfa 4kpj 4kq5 4kqs 4kqu