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(-) Description

Title :  CRYSTAL STRUCTURE OF GERANYLGERANYL DIPHOSPHATE SYNTHASE SUB1274 (TARGET EFI-509455) FROM STREPTOCOCCUS UBERIS 0140J WITH BOUND MAGNESIUM AND ISOPENTYL DIPHOSPHATE, PARTIALLY LIGANDED COMPLEX;
 
Authors :  Y. Patskovsky, R. Toro, R. Bhosle, B. Hillerich, R. D. Seidel, E. Washin A. Scott Glenn, S. Chowdhury, B. Evans, J. Hammonds, H. J. Imker, N. Al M. Stead, J. Love, C. D. Poulter, J. A. Gerlt, S. C. Almo, Enzyme Functi Initiative (Efi)
Date :  26 Jun 13  (Deposition) - 10 Jul 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Isoprenoid Synthase, Enzyme Function Initiative, Efi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, R. Toro, R. Bhosle, B. Hillerich, R. D. Seidel, E. Washington, A. Scott Glenn, S. Chowdhury, B. Evans, J. Hammonds, H. J. Imker, N. Al Obaidi, M. Stead, J. Love, C. D. Poulter, J. A. Gerlt, S. C. Almo
Crystal Structure Of Geranylgeranyl Diphosphate Synthase From Streptococcus Uberis 0140J
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GERANYLGERANYL DIPHOSPHATE SYNTHASE
    Chains: A, B
    EC Number: 2.5.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3) RIL
    Expression System Taxid: 469008
    Gene: FPS, SUB1274
    Organism Scientific: STREPTOCOCCUS UBERIS
    Organism Taxid: 218495
    Strain: 0140J

 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
1IPE3Ligand/Ion3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
2MG5Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:74 , LEU A:75 , ASP A:78 , ASP A:84 , ARG A:89 , LYS A:172 , MG A:302 , MG A:303 , HOH A:403 , HOH A:415 , HOH A:417 , HOH A:419 , HOH A:452 , HOH A:454 , HOH A:467 , HOH A:489BINDING SITE FOR RESIDUE IPE A 301
2AC2SOFTWAREASP A:78 , ASP A:84 , IPE A:301 , MG A:303 , HOH A:436 , HOH A:454 , HOH A:471BINDING SITE FOR RESIDUE MG A 302
3AC3SOFTWAREASP A:78 , ASP A:84 , IPE A:301 , MG A:302 , HOH A:419 , HOH A:452BINDING SITE FOR RESIDUE MG A 303
4AC4SOFTWAREASP B:78 , ASP B:84 , ARG B:89 , LYS B:172 , THR B:173 , GLN B:210 , ASP B:213 , LYS B:227 , IPE B:302 , MG B:303 , MG B:304 , MG B:305 , HOH B:409 , HOH B:420 , HOH B:431 , HOH B:436 , HOH B:474 , HOH B:484 , HOH B:496BINDING SITE FOR RESIDUE IPE B 301
5AC5SOFTWAREGLY B:37 , LYS B:38 , ARG B:41 , HIS B:71 , LEU B:75 , ARG B:90 , THR B:173 , PHE B:209 , GLN B:210 , ASP B:213 , IPE B:301 , HOH B:402 , HOH B:404 , HOH B:406 , HOH B:423 , HOH B:430 , HOH B:518BINDING SITE FOR RESIDUE IPE B 302
6AC6SOFTWAREASP B:213 , IPE B:301 , HOH B:416 , HOH B:420 , HOH B:436BINDING SITE FOR RESIDUE MG B 303
7AC7SOFTWAREASP B:78 , ASP B:84 , IPE B:301 , MG B:305 , HOH B:419 , HOH B:458 , HOH B:496BINDING SITE FOR RESIDUE MG B 304
8AC8SOFTWAREASP B:78 , ASP B:84 , IPE B:301 , MG B:304 , HOH B:431 , HOH B:474BINDING SITE FOR RESIDUE MG B 305

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LFE)

(-) 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:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4lfea_ A: automated matches                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhh....hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lfe A   0 SMDKLKKIDQTIHAFYCEKAVISEKLNEAVLYSINAGGKRIRPILFLEVIEALQIPLTESHFKAAAALEMIHTGSLIHDDLPAMDNDDYRRGQLTNHKKFDEATAILAGDSLFLDAFGMLAETDFPTDVTVDLVRSLSSASGTFGMVGGQMLDMAAEGKKLNLKNLQLIHRHKTGQLLAYPFWAAARVAQLDENLLATFLEIGMIIGLAFQVRDDILDITAKMTYPHLLGLNESYQILDESLDQAEAILRKLSDEIAFAPQKILSLIERLRLDA 289
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219||     245       255       265       275       285    
                                                                                                                                                                                                                                                      220|                                                    
                                                                                                                                                                                                                                                       237                                                    


Chain B from PDB  Type:PROTEIN  Length:288
                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4lfeb_ B: automated matches                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh........ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lfe B   2 DKLKKIDQTIHAFYCEKAVISEKLNEAVLYSINAGGKRIRPILFLEVIEALQIPLTESHFKAAAALEMIHTGSLIHDDLPAMDNDDYRRGQLTNHKKFDEATAILAGDSLFLDAFGMLAETDFPTDVTVDLVRSLSSASGTFGMVGGQMLDMAAEGKKLNLKNLQLIHRHKTGQLLAYPFWAAARVAQLDENLLATFLEIGMIIGLAFQVRDDILDITANFEEIGKTPKKDVMAEKMTYPHLLGLNESYQILDESLDQAEAILRKLSDEIAFAPQKILSLIERLRLDA 289
                                    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
   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        B9DUT7_STRU0 | B9DUT7: 4lfg

(-) Related Entries Specified in the PDB File

4lfg RELATED ID: EFI-509455 RELATED DB: TARGETTRACK