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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SHIGELLA FLEXNERI FARNESYL PYROPHOSPHATE SYNTHASE COMPLEX WITH AN ISOPENTENYL PYROPHOSPHATE
 
Authors :  G. Minasov, J. S. Brunzelle, L. Shuvalova, F. R. Collart, A. Joachimiak W. F. Anderson, Midwest Center For Structural Genomics (Mcsg)
Date :  13 Jan 06  (Deposition) - 31 Jan 06  (Release) - 05 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Bisphosphonate; Isoprenyl Synthase, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Minasov, J. S. Brunzelle, L. Shuvalova, F. R. Collart, W. F. Anderso
Crystal Structure Of The Shigella Flexneri Farnesyl Pyrophosphate Synthase Complex With An Isopentenyl Pyrophosphate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GERANYLTRANSTRANSFERASE
    Chains: A, B
    EC Number: 2.5.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21-DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AAP15892
    Organism Scientific: SHIGELLA FLEXNERI
    Organism Taxid: 623
    Strain: 301
    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  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1IPR2Ligand/IonISOPENTYL PYROPHOSPHATE
2PO47Ligand/IonPHOSPHATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:44 , LYS A:45 , HIS A:77 , ARG A:96 , PO4 A:301 , HOH A:438 , HOH A:439 , HOH A:440BINDING SITE FOR RESIDUE PO4 A 300
2AC2SOFTWAREARG A:48 , HIS A:77 , PO4 A:300 , HOH A:442 , HOH A:443 , HOH A:454BINDING SITE FOR RESIDUE PO4 A 301
3AC3SOFTWAREASP A:161 , LYS A:181 , LYS A:247 , HOH A:444 , HOH A:445BINDING SITE FOR RESIDUE PO4 A 302
4AC4SOFTWAREGLY B:44 , LYS B:45 , HIS B:77 , ARG B:96 , PO4 B:301 , IPR B:302 , HOH B:463 , HOH B:465 , HOH B:468 , HOH B:469BINDING SITE FOR RESIDUE PO4 B 300
5AC5SOFTWAREARG B:48 , HIS B:77 , PO4 B:300 , HOH B:453 , HOH B:467 , HOH B:468 , HOH B:481BINDING SITE FOR RESIDUE PO4 B 301
6AC6SOFTWAREARG A:176 , ARG A:179 , HIS A:180 , PO4 A:304BINDING SITE FOR RESIDUE PO4 A 303
7AC7SOFTWAREARG A:187 , PO4 A:303BINDING SITE FOR RESIDUE PO4 A 304
8AC8SOFTWARELYS A:45 , LEU A:47 , ARG A:48 , ASP A:223 , ARG A:297 , HOH A:437 , HOH A:440 , HOH A:442 , HOH A:443 , HOH A:454BINDING SITE FOR RESIDUE IPR A 305
9AC9SOFTWARELYS B:45 , LEU B:47 , ARG B:48 , HIS B:77 , ARG B:95 , PO4 B:300 , HOH B:456 , HOH B:465 , HOH B:467 , HOH B:468 , HOH B:481BINDING SITE FOR RESIDUE IPR B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FOR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2FOR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FOR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2FOR)

(-) Exons   (0, 0)

(no "Exon" information available for 2FOR)

(-) 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:283
 aligned with Q83M58_SHIFL | Q83M58 from UniProtKB/TrEMBL  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        
         Q83M58_SHIFL     2 DFPQQLEACVKQANQALSRFIAPLPFQNTPVVETMQYGALLGGKRLRPFLVYATGHMFGVSTNTLDAPAAAVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDANMPEVSDRDRISMISELASASGIAGMCGGQALDLDAEGKHVPLDALERIHRHKTGALIRAAVRLGALSAGDKGRRALPVLDKYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALLGLEQARKKARDLIDDARQALKQLAEQSLDTSALEALADYIIQRNK 299
               SCOP domains d2fora_ A: automated matches                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2forA00 A:2-299 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh........ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh---------------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2for A   2 DFPQQLEACVKQANQALSRFIAPLPFQNTPVVETMQYGALLGGKRLRPFLVYATGHMFGVSTNTLDAPAAAVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDANMPEVSDRDRISMISELASASGIAGMCGGQALDLDAEGKHVPLDALERIHRHKTGALIRAAVRLGALSAGDKGRRALPVLDKYAESIGLAFQVQDDILDVVG---------------GKSTYPALLGLEQARKKARDLIDDARQALKQLAEQSLDTSALEALADYIIQRNK 299
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221        |-         -    |  251       261       271       281       291        
                                                                                                                                                                                                                                                              230             246                                                     


Chain B from PDB  Type:PROTEIN  Length:281
 aligned with Q83M58_SHIFL | Q83M58 from UniProtKB/TrEMBL  Length:299

    Alignment length:298
                                    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        
         Q83M58_SHIFL     1 MDFPQQLEACVKQANQALSRFIAPLPFQNTPVVETMQYGALLGGKRLRPFLVYATGHMFGVSTNTLDAPAAAVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDANMPEVSDRDRISMISELASASGIAGMCGGQALDLDAEGKHVPLDALERIHRHKTGALIRAAVRLGALSAGDKGRRALPVLDKYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALLGLEQARKKARDLIDDARQALKQLAEQSLDTSALEALADYIIQRN 298
               SCOP domains d2forb_ B: automated matches                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2forB00 B:1-298 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.......ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-----------------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2for B   1 MDFPQQLEACVKQANQALSRFIAPLPFQNTPVVETMQYGALLGGKRLRPFLVYATGHMFGVSTNTLDAPAAAVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDANMPEVSDRDRISMISELASASGIAGMCGGQALDLDAEGKHVPLDALERIHRHKTGALIRAAVRLGALSAGDKGRRALPVLDKYAESIGLAFQVQDDILDVV-----------------KSTYPALLGLEQARKKARDLIDDARQALKQLAEQSLDTSALEALADYIIQRN 298
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220        |-         -      |250       260       270       280       290        
                                                                                                                                                                                                                                                              229               247
   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 2FOR)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q83M58_SHIFL | Q83M58)
molecular function
    GO:0004337    geranyltranstransferase activity    Catalysis of the reaction: geranyl diphosphate + isopentenyl diphosphate = 2-trans,6-trans-farnesyl diphosphate + diphosphate.
    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: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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