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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE GERANYLGERANYL PYROPHOSPHATE SYNTHASE FROM CORYNEBACTERIUM GLUTAMICUM
 
Authors :  V. N. Malashkevich, R. Toro, Y. Patskovsky, J. M. Sauder, S. K. Burley, S New York Sgx Research Center For Structural Genomics (Nysgx
Date :  27 Jan 10  (Deposition) - 09 Mar 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics, Protein Structure Initiative, Geranylgeranyl Pyrophosphate Synthase, Isoprene Biosynthesis, Psi-2, Transferase, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. N. Malashkevich, R. Toro, Y. Patskovsky, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Putative Geranylgeranyl Pyrophosphate Synthase From Corynebacterium Glutamicum Atcc 13032
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GERANYLGERANYL PYROPHOSPHATE SYNTHASE
    Chains: A
    EC Number: 2.5.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)CODON+RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CGL2172
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM
    Organism Taxid: 1718
    Strain: ATCC 13032

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:62 , LYS A:63 , ARG A:64 , ILE A:65 , ARG A:66 , GLN A:101 , HOH A:386 , HOH A:411BINDING SITE FOR RESIDUE GOL A 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LK5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LK5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LK5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LK5)

(-) Exons   (0, 0)

(no "Exon" information available for 3LK5)

(-) Sequences/Alignments

Asymmetric 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:333
 aligned with Q8NNM1_CORGL | Q8NNM1 from UniProtKB/TrEMBL  Length:371

    Alignment length:362
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366  
         Q8NNM1_CORGL     7 SSFDAHDLDLDKFPEVVRDRLTQFLDAQELTIADIGAPVTDAVAHLRSFVLNGGKRIRPLYAWAGFLAAQGHKNSSEKLESVLDAAASLEFIQACALIHDDIIDSSDTRRGAPTVHRAVEADHRANNFEGDPEHFGVSVSILAGDMALVWAEDMLQDSGLSAEALARTRDAWRGMRTEVIGGQLLDIYLESHANESVELADSVNRFKTAAYTIARPLHLGASIAGGSPQLIDALLHYGHDIGIAFQLRDDLLGVFGDPAITGKPAGDDIREGKRTVLLALALQRADKQSPEAATAIRAGVGKVTSPEDIAVITEHIRATGAEEEVEQRISQLTESGLAHLDDVDIPDEVRAQLRALAIRSTE 368
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------polyprenyl_synt-3lk5A01 A:143-328                                                                                                                                                         ------------------------------------------ Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------polyprenyl_synt-3lk5A02 A:143-328                                                                                                                                                         ------------------------------------------ Pfam domains (2)
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh.-----------------------------hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lk5 A   9 SSFDAHDLDLDKFPEVVRDRLTQFLDAQELTIADIGAPVTDAVAHLRSFVLNGGKRIRPLYAWAGFLAAQGHKNSSEKLESVLDAAASLEFIQACALIHDDIIDS-----------------------------FGVSVSILAGDmALVWAEDmLQDSGLSAEALARTRDAWRGmRTEVIGGQLLDIYLESHANESVELADSVNRFKTAAYTIARPLHLGASIAGGSPQLIDALLHYGHDIGIAFQLRDDLLGVFGDPAITGKPAGDDIREGKRTVLLALALQRADKQSPEAATAIRAGVGKVTSPEDIAVITEHIRATGAEEEVEQRISQLTESGLAHLDDVDIPDEVRAQLRALAIRSTE 370
                                    18        28        38        48        58        68        78        88        98       108    |    -         -         -    |  148     | 158   |   168       178    |  188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368  
                                                                                                                                  113                           143        154-MSE 162-MSE              183-MSE
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3LK5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LK5)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q8NNM1_CORGL | Q8NNM1)
molecular function
    GO:0004161    dimethylallyltranstransferase activity    Catalysis of the reaction: dimethylallyl diphosphate + isopentenyl diphosphate = diphosphate + geranyl 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: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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