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(-) Description

Title :  CRYSTAL STRUCTURE OF A FARNESYL DIPHOSPHATE SYNTHASE FROM ROSEOBACTER DENITRIFICANS OCH 114, TARGET EFI-509393, WITH TWO IPP AND CALCIUM BOUND IN ACTIVE SITE
 
Authors :  J. Kim, R. Toro, R. Bhosle, N. F. Al Obaidi, L. L. Morisco, S. R. Wasserma S. Sojitra, E. Washington, A. Scott Glenn, S. Chowdhury, B. Evans, J. B. Hillerich, J. Love, R. D. Seidel, H. J. Imker, M. Stead, J. A. Gerlt, S Enzyme Function Initiative
Date :  09 Jul 13  (Deposition) - 24 Jul 13  (Release) - 24 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Enzyme Function Initiative, Polyprenyl Synthetase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Kim, R. Toro, R. Bhosle, N. F. Al Obaidi, L. L. Morisco, S. R. Wasserman, S. Sojitra, E. Washington, A. Scott Glenn, S. Chowdhury, B. Evans, J. Hammonds, B. Hillerich, J. Love, R. D. Seidel, H. J. Imker, M. Stead, J. A. Gerlt, S. C. Almo
Crystal Structure Of A Farnesyl Diphosphate Synthase From Roseobacter Denitrificans Och 114, Target Efi-509393, With Two Ipp And Calcium Bound In Active Site
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GERANYLTRANSTRANSFERASE
    Chains: A, B
    EC Number: 2.5.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSGC-HIS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ISPA, RD1_0549
    Organism Scientific: ROSEOBACTER DENITRIFICANS
    Organism Taxid: 375451
    Strain: ATCC 33942 / OCH 114
    Synonym: FARNESYL DIPHOSPHATE SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2IPE4Ligand/Ion3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:40 , LYS A:41 , ARG A:44 , HIS A:73 , LEU A:77 , ARG A:92 , THR A:179 , PHE A:212 , ASP A:216 , IPE A:302 , HOH A:404 , HOH A:409 , HOH A:410 , HOH A:423 , HOH A:424 , HOH A:436BINDING SITE FOR RESIDUE IPE A 301
02AC2SOFTWARESER A:76 , ASP A:80 , ASP A:86 , ARG A:91 , MET A:149 , LYS A:178 , ASP A:216 , LYS A:230 , IPE A:301 , CA A:303 , CA A:304 , HOH A:457 , HOH A:464 , HOH A:537 , HOH A:538 , HOH A:540BINDING SITE FOR RESIDUE IPE A 302
03AC3SOFTWAREASP A:216 , IPE A:302 , HOH A:458 , HOH A:472 , HOH A:489BINDING SITE FOR RESIDUE CA A 303
04AC4SOFTWAREASP A:80 , ASP A:86 , IPE A:302 , HOH A:462 , HOH A:538BINDING SITE FOR RESIDUE CA A 304
05AC5SOFTWAREASP A:86 , ASP A:156 , GLU A:160 , HOH A:457 , HOH A:464 , HOH A:527 , HOH A:528BINDING SITE FOR RESIDUE CA A 305
06AC6SOFTWAREGLY B:40 , LYS B:41 , ARG B:44 , HIS B:73 , LEU B:77 , ARG B:92 , THR B:179 , PHE B:212 , ASP B:216 , IPE B:302 , HOH B:410 , HOH B:420 , HOH B:430 , HOH B:439 , HOH B:446 , HOH B:456BINDING SITE FOR RESIDUE IPE B 301
07AC7SOFTWARELEU B:77 , ASP B:80 , ASP B:86 , ARG B:91 , LYS B:178 , ASP B:216 , LYS B:230 , IPE B:301 , CA B:303 , CA B:304 , HOH B:519 , HOH B:538 , HOH B:545 , HOH B:546BINDING SITE FOR RESIDUE IPE B 302
08AC8SOFTWAREASP B:80 , ASP B:86 , IPE B:302 , HOH B:497 , HOH B:537BINDING SITE FOR RESIDUE CA B 303
09AC9SOFTWAREASP B:216 , IPE B:302 , HOH B:443 , HOH B:451 , HOH B:514BINDING SITE FOR RESIDUE CA B 304
10BC1SOFTWAREASP B:86 , ASP B:156 , HOH B:519 , HOH B:520 , HOH B:521 , HOH B:539BINDING SITE FOR RESIDUE CA B 305

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4LLT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LLT)

(-) 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
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4llta_ A: automated matches                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.......ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4llt A -10 DLGTENLYFQSMFTQRLDAAAAAVQAHFDKVLAAFEPLPIVEAMAHATSGGKRLRGFLVLETARLHDIAAGEAIWSATAIEALHAYSLVHDDLPCMDNDDMRRGQPTVHKKWDDATAVLAGDALQTLAFELVTHPGASASAEVRADLALSLARASGAQGMVLGQALDIAAETARAPLSLDEITRLQQGKTGALIGWSAQAGARLAQADTAALKRYAQALGLAFQIADDILDVTGDSAQVGKAVGKDASAGKATFVSLLGLDAARARAMSLIDEACDSLATYGAKADTLRETARFVVRRTH 289
                                    -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


Chain B from PDB  Type:PROTEIN  Length:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4lltb_ B: automated matches                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh........ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4llt B   0 SMFTQRLDAAAAAVQAHFDKVLAAFEPLPIVEAMAHATSGGKRLRGFLVLETARLHDIAAGEAIWSATAIEALHAYSLVHDDLPCMDNDDMRRGQPTVHKKWDDATAVLAGDALQTLAFELVTHPGASASAEVRADLALSLARASGAQGMVLGQALDIAAETARAPLSLDEITRLQQGKTGALIGWSAQAGARLAQADTAALKRYAQALGLAFQIADDILDVTGDSAQVGKAVGKDASAGKATFVSLLGLDAARARAMSLIDEACDSLATYGAKADTLRETARFVVRRTH 289
                                     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
   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, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        Q16CN9_ROSDO | Q16CN9: 4lls

(-) Related Entries Specified in the PDB File

4lls FARNESYL DIPHOSPHATE SYNTHASE WITH IPP AND GSPP BOUND RELATED ID: EFI-509393 RELATED DB: TARGETTRACK