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(-) Description

Title :  ACTIVE CONFORMATION OF FARNESYL PYROPHOSPHATE SYNTHASE BOUND TO ISOPENTYL PYROPHOSPHATE AND DIMETHYLALLYL S-THIOLODIPHOSPHATE
 
Authors :  D. J. Hosfield, Y. Zhang, D. R. Dougan, A. Brooun, L. W. Tari, R. V. Swanson, J. Finn
Date :  05 Dec 03  (Deposition) - 02 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.42
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Isoprenyl Synthase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. J. Hosfield, Y. Zhang, D. R. Dougan, A. Brooun, L. W. Tari, R. V. Swanson, J. Finn
Structural Basis For Bisphosphonate-Mediated Inhibition Of Isoprenoid Biosynthesis
J. Biol. Chem. V. 279 8526 2004
PubMed-ID: 14672944  |  Reference-DOI: 10.1074/JBC.C300511200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GERANYLTRANSTRANSFERASE
    Chains: A, B
    EC Number: 2.5.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ISPA, B0421
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: FARNESYL-DIPHOSPHATE SYNTHASE, FPP SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1DPO1Ligand/IonDIPHOSPHATE
2DST2Ligand/IonDIMETHYLALLYL S-THIOLODIPHOSPHATE
3IPR2Ligand/IonISOPENTYL PYROPHOSPHATE
4MG6Ligand/IonMAGNESIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP B:244 , ASP B:248 , DST B:400 , HOH B:700 , HOH B:701 , HOH B:741BINDING SITE FOR RESIDUE MG B 600
02AC2SOFTWAREASP B:105 , ASP B:111 , DST B:400 , MG B:602 , HOH B:704 , HOH B:705 , HOH B:862BINDING SITE FOR RESIDUE MG B 601
03AC3SOFTWAREASP B:105 , ASP B:111 , DST B:400 , MG B:601 , HOH B:702 , HOH B:703BINDING SITE FOR RESIDUE MG B 602
04AC4SOFTWAREASP A:244 , DST A:401 , HOH A:717 , HOH A:718 , HOH A:734BINDING SITE FOR RESIDUE MG A 603
05AC5SOFTWAREASP A:105 , ASP A:111 , DST A:401 , MG A:605 , HOH A:721 , HOH A:722 , HOH A:738BINDING SITE FOR RESIDUE MG A 604
06AC6SOFTWAREASP A:105 , ASP A:111 , ASP A:113 , DST A:401 , MG A:604 , HOH A:719 , HOH A:720BINDING SITE FOR RESIDUE MG A 605
07AC7SOFTWARESER B:101 , ASP B:105 , ASP B:111 , ARG B:116 , MET B:175 , GLN B:179 , LYS B:202 , ASP B:244 , LYS B:258 , IPR B:500 , MG B:600 , MG B:601 , MG B:602 , HOH B:700 , HOH B:701 , HOH B:702 , HOH B:704BINDING SITE FOR RESIDUE DST B 400
08AC8SOFTWARESER A:101 , LEU A:102 , ASP A:105 , ASP A:111 , ARG A:116 , MET A:175 , GLN A:179 , LYS A:202 , ASP A:244 , LYS A:258 , IPR A:501 , MG A:603 , MG A:604 , MG A:605 , HOH A:717 , HOH A:718 , HOH A:719 , HOH A:720 , HOH A:721 , HOH A:734 , HOH A:738 , HOH A:835BINDING SITE FOR RESIDUE DST A 401
09AC9SOFTWAREGLY B:65 , LYS B:66 , ARG B:69 , HIS B:98 , LEU B:102 , ARG B:117 , PHE B:240 , GLN B:241 , ASP B:244 , DST B:400 , HOH B:706 , HOH B:707 , HOH B:710 , HOH B:711 , HOH B:712 , HOH B:713BINDING SITE FOR RESIDUE IPR B 500
10BC1SOFTWAREGLY A:65 , LYS A:66 , ARG A:69 , HIS A:98 , ARG A:117 , THR A:203 , PHE A:240 , GLN A:241 , ASP A:244 , DST A:401 , HOH A:723 , HOH A:724 , HOH A:727 , HOH A:728 , HOH A:729 , HOH A:730BINDING SITE FOR RESIDUE IPR A 501
11BC2SOFTWAREGLN A:27 , ALA A:30 , CYS A:31 , GLN A:34 , PHE A:71 , TYR A:74 , ALA A:75 , HIS A:78 , HOH A:844 , HOH A:872 , HIS B:189BINDING SITE FOR RESIDUE DPO A 606

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1POLYPRENYL_SYNTHASE_1PS00723 Polyprenyl synthases signature 1.ISPA_ECOLI81-97
 		  2A:102-118
B:102-118
2POLYPRENYL_SYNTHASE_2PS00444 Polyprenyl synthases signature 2.ISPA_ECOLI215-227
 		  2A:236-248
B:236-248

(-) Exons   (0, 0)

(no "Exon" information available for 1RQI)

(-) 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:300
 aligned with ISPA_ECOLI | P22939 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:300
                             1                                                                                                                                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299
           ISPA_ECOLI     - -MDFPQQLEACVKQANQALSRFIAPLPFQNTPVVETMQYGALLGGKRLRPFLVYATGHMFGVSTNTLDAPAAAVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDADMPEVSDRDRISMISELASASGIAGMCGGQALDLDAEGKHVPLDALERIHRHKTGALIRAAVRLGALSAGDKGRRALPVLDKYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALLGLEQARKKARDLIDDARQSLKQLAEQSLDTSALEALADYIIQRNK 299
               SCOP domains d1rqia_ A: Farnesyl diphosphate synthase (geranyltranstransferase)                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1rqiA00 A:21-320 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh........ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------POLYPRENYL_SYNTHA---------------------------------------------------------------------------------------------------------------------POLYPRENYL_SY------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rqi A  21 AMDFPQQLEACVKQANQALSRFIAPLPFQNTPVVETMQYGALLGGKRLRPFLVYATGHMFGVSTNTLDAPAAAVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDADMPEVSDRDRISMISELASASGIAGMCGGQALDLDAEGKHVPLDALERIHRHKTGALIRAAVRLGALSAGDKGRRALPVLDKYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALLGLEQARKKARDLIDDARQSLKQLAEQSLDTSALEALADYIIQRNK 320
                                    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


Chain B from PDB  Type:PROTEIN  Length:298
 aligned with ISPA_ECOLI | P22939 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:298
                                    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        
           ISPA_ECOLI     2 DFPQQLEACVKQANQALSRFIAPLPFQNTPVVETMQYGALLGGKRLRPFLVYATGHMFGVSTNTLDAPAAAVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDADMPEVSDRDRISMISELASASGIAGMCGGQALDLDAEGKHVPLDALERIHRHKTGALIRAAVRLGALSAGDKGRRALPVLDKYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALLGLEQARKKARDLIDDARQSLKQLAEQSLDTSALEALADYIIQRNK 299
               SCOP domains d1rqib_ B: Farnesyl diphosphate synthase (geranyltranstransferase)                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1rqiB00 B:23-320 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                             CATH domains
           Pfam domains (1) ------------------------------polyprenyl_synt-1rqiB01 B:53-316                                                                                                                                                                                                                                        ---- Pfam domains (1)
           Pfam domains (2) ------------------------------polyprenyl_synt-1rqiB02 B:53-316                                                                                                                                                                                                                                        ---- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh........ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------POLYPRENYL_SYNTHA---------------------------------------------------------------------------------------------------------------------POLYPRENYL_SY------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rqi B  23 DFPQQLEACVKQANQALSRFIAPLPFQNTPVVETMQYGALLGGKRLRPFLVYATGHMFGVSTNTLDAPAAAVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDADMPEVSDRDRISMISELASASGIAGMCGGQALDLDAEGKHVPLDALERIHRHKTGALIRAAVRLGALSAGDKGRRALPVLDKYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALLGLEQARKKARDLIDDARQSLKQLAEQSLDTSALEALADYIIQRNK 320
                                    32        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
   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  (1, 2)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ISPA_ECOLI | P22939)
molecular function
    GO:0004161    dimethylallyltranstransferase activity    Catalysis of the reaction: dimethylallyl diphosphate + isopentenyl diphosphate = diphosphate + geranyl diphosphate.
    GO:0004337    geranyltranstransferase activity    Catalysis of the reaction: geranyl diphosphate + isopentenyl diphosphate = 2-trans,6-trans-farnesyl diphosphate + diphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0045337    farnesyl diphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of farnesyl diphosphate.
    GO:0033384    geranyl diphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of geranyl diphosphate.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  ISPA_ECOLI | P22939
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  2.5.1.10
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 Related Entries

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

UniProtKB/Swiss-Prot
        ISPA_ECOLI | P22939: 1rqj

(-) Related Entries Specified in the PDB File

1rqj 1rtr