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(-) Description

Title :  T. BRUCEI FARNESYL DIPHOSPHATE SYNTHASE COMPLEXED WITH BISPHOSPHONATE BPH-722
 
Authors :  R. Cao, Y. Gao, H. Robinson, E. Oldfield
Date :  11 Sep 08  (Deposition) - 05 May 09  (Release) - 05 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Bisphosphonate Complex, Isoprene Biosynthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zhang, R. Cao, F. Yin, M. P. Hudock, R. T. Guo, K. Krysiak, S. Mukherjee, Y. G. Gao, H. Robinson, Y. Song, J. H. No, K. Bergan, A. Leon, L. Cass, A. Goddard, T. K. Chang, F. Y. Lin, E. Van Beek, S. Papapoulos, A. H. Wang, T. Kubo, M. Ochi, D. Mukkamala, E. Oldfield
Lipophilic Bisphosphonates As Dual Farnesyl/Geranylgeranyl Diphosphate Synthase Inhibitors: An X-Ray And Nmr Investigation.
J. Am. Chem. Soc. V. 131 5153 2009
PubMed-ID: 19309137  |  Reference-DOI: 10.1021/JA808285E
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FARNESYL PYROPHOSPHATE SYNTHASE
    Chains: A, B
    EC Number: 2.5.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
17222Ligand/Ion1-(2,2-DIPHOSPHONOETHYL)-3-(HEPTYLOXY)PYRIDINIUM
2MG6Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:103 , ASP A:107 , 722 A:3001 , MG A:3004 , HOH A:3023 , HOH A:3121BINDING SITE FOR RESIDUE MG A3002
2AC2SOFTWAREASP A:255 , 722 A:3001 , HOH A:3005 , HOH A:3031 , HOH A:3127BINDING SITE FOR RESIDUE MG A3003
3AC3SOFTWAREASP A:103 , ASP A:107 , 722 A:3001 , MG A:3002 , HOH A:3011 , HOH A:3014 , HOH A:3059BINDING SITE FOR RESIDUE MG A3004
4AC4SOFTWARETYR A:99 , ASP A:103 , MET A:106 , ASP A:107 , ARG A:112 , GLN A:172 , LYS A:212 , THR A:213 , ASP A:255 , LYS A:269 , MG A:3002 , MG A:3003 , MG A:3004 , HOH A:3005 , HOH A:3011 , HOH A:3014 , HOH A:3019 , HOH A:3023 , HOH A:3031 , HOH A:3035 , HOH A:3112 , HOH A:3121 , HOH A:3127 , ASN B:131 , LEU B:134BINDING SITE FOR RESIDUE 722 A3001
5AC5SOFTWAREASP B:103 , ASP B:107 , 722 B:4001 , MG B:4004 , HOH B:4056 , HOH B:4115BINDING SITE FOR RESIDUE MG B4002
6AC6SOFTWAREASP B:255 , 722 B:4001 , HOH B:4010 , HOH B:4116 , HOH B:4128BINDING SITE FOR RESIDUE MG B4003
7AC7SOFTWAREASP B:103 , ASP B:107 , 722 B:4001 , MG B:4002 , HOH B:4012 , HOH B:4038 , HOH B:4124BINDING SITE FOR RESIDUE MG B4004
8AC8SOFTWAREASN A:131 , LEU A:134 , TYR B:99 , GLU B:102 , ASP B:103 , MET B:106 , ASP B:107 , ARG B:112 , GLN B:172 , LYS B:212 , THR B:213 , ASP B:255 , LYS B:269 , MG B:4002 , MG B:4003 , MG B:4004 , HOH B:4010 , HOH B:4012 , HOH B:4016 , HOH B:4038 , HOH B:4056 , HOH B:4080 , HOH B:4115 , HOH B:4116 , HOH B:4128BINDING SITE FOR RESIDUE 722 B4001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3EGT)

(-) 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:358
 aligned with Q86C09_9TRYP | Q86C09 from UniProtKB/TrEMBL  Length:367

    Alignment length:367
                                    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       
         Q86C09_9TRYP     1 MPMQMFMQVYDEIQMFLLEELELKFDMDPNRVRYLRKMMDTTCLGGKYNRGLTVIDVAESLLSLSPNNNGEEDDGARRKRVLHDACVCGWMIEFLQAHYLVEDDIMDNSVTRRGKPCWYRHPDVTVQCAINDGLLLKSWTHMMAMHFFADRPFLQDLLCRFNRVDYTTAVGQLYDVTSMFDSNKLDPDVSQPTTTDFAEFTLSNYKRIVKYKTAYYTYLLPLVMGLIVSEALPTVDMGVTEELAMLMGEYFQVQDDVMDCFTPPERLGKVGTDIQDAKCSWLAVTFLAKASSAQVAEFKANYGSGDSEKVATVRRLYEEADLQGDYVAYEAAVAEQVKELIEKLRLCSPGFAASVETLWGKTYKRQK 367
               SCOP domains d3egta_ A: automated matches                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 3egtA00 A:1-367 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..---------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3egt A   1 MPMQMFMQVYDEIQMFLLEELELKFDMDPNRVRYLRKMMDTTCLGGKYNRGLTVIDVAESLLSL---------DGARRKRVLHDACVCGWMIEFLQAHYLVEDDIMDNSVTRRGKPCWYRHPDVTVQCAINDGLLLKSWTHMMAMHFFADRPFLQDLLCRFNRVDYTTAVGQLYDVTSMFDSNKLDPDVSQPTTTDFAEFTLSNYKRIVKYKTAYYTYLLPLVMGLIVSEALPTVDMGVTEELAMLMGEYFQVQDDVMDCFTPPERLGKVGTDIQDAKCSWLAVTFLAKASSAQVAEFKANYGSGDSEKVATVRRLYEEADLQGDYVAYEAAVAEQVKELIEKLRLCSPGFAASVETLWGKTYKRQK 367
                                    10        20        30        40        50        60   |     -   |    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       
                                                                                          64        74                                                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:359
 aligned with Q86C09_9TRYP | Q86C09 from UniProtKB/TrEMBL  Length:367

    Alignment length:367
                                    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       
         Q86C09_9TRYP     1 MPMQMFMQVYDEIQMFLLEELELKFDMDPNRVRYLRKMMDTTCLGGKYNRGLTVIDVAESLLSLSPNNNGEEDDGARRKRVLHDACVCGWMIEFLQAHYLVEDDIMDNSVTRRGKPCWYRHPDVTVQCAINDGLLLKSWTHMMAMHFFADRPFLQDLLCRFNRVDYTTAVGQLYDVTSMFDSNKLDPDVSQPTTTDFAEFTLSNYKRIVKYKTAYYTYLLPLVMGLIVSEALPTVDMGVTEELAMLMGEYFQVQDDVMDCFTPPERLGKVGTDIQDAKCSWLAVTFLAKASSAQVAEFKANYGSGDSEKVATVRRLYEEADLQGDYVAYEAAVAEQVKELIEKLRLCSPGFAASVETLWGKTYKRQK 367
               SCOP domains d3egtb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 3egtB00 B:1-367 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...--------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3egt B   1 MPMQMFMQVYDEIQMFLLEELELKFDMDPNRVRYLRKMMDTTCLGGKYNRGLTVIDVAESLLSL--------DDGARRKRVLHDACVCGWMIEFLQAHYLVEDDIMDNSVTRRGKPCWYRHPDVTVQCAINDGLLLKSWTHMMAMHFFADRPFLQDLLCRFNRVDYTTAVGQLYDVTSMFDSNKLDPDVSQPTTTDFAEFTLSNYKRIVKYKTAYYTYLLPLVMGLIVSEALPTVDMGVTEELAMLMGEYFQVQDDVMDCFTPPERLGKVGTDIQDAKCSWLAVTFLAKASSAQVAEFKANYGSGDSEKVATVRRLYEEADLQGDYVAYEAAVAEQVKELIEKLRLCSPGFAASVETLWGKTYKRQK 367
                                    10        20        30        40        50        60   |     -  |     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       
                                                                                          64       73
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q86C09_9TRYP | Q86C09)
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
        Q86C09_9TRYP | Q86C09: 2ewg 2i19 2ogd 2p1c 3dyf 3dyg 3dyh 3efq 4rxc 4rxd 4rxe 4ryp 5ael 5afx 5ahu

(-) Related Entries Specified in the PDB File

2ewg 2i19 3dyf 3dyg 3dyh 3efq