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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE FARNESYL DIPHOSPHATE SYNTHASE FROM RHODOBACTER CAPSULATUS
 
Authors :  V. N. Malashkevich, R. Toro, J. M. Sauder, S. K. Burley, S. C. Almo, New Y Research Center For Structural Genomics (Nysgxrc)
Date :  03 Mar 10  (Deposition) - 31 Mar 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Protein Structure Initiative, Nysgxrc, Isoprene Biosynthesis, Transferase, Psi-2, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. N. Malashkevich, R. Toro, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Putative Farnesyl Diphosphate Synthase From Rhodobacter Capsulatus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - FARNESYL DIPHOSPHATE SYNTHASE
    Chains: A, B
    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: 8272412
    Organism Common: RHODOPSEUDOMONAS CAPSULATA
    Organism Scientific: RHODOBACTER CAPSULATUS
    Organism Taxid: 1061

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 14)

Asymmetric/Biological Unit (1, 14)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3M0G)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M0G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3M0G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M0G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3M0G)

(-) Exons   (0, 0)

(no "Exon" information available for 3M0G)

(-) 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:264
 aligned with Q9KWR7_RHOCA | Q9KWR7 from UniProtKB/TrEMBL  Length:288

    Alignment length:285
                                    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     
         Q9KWR7_RHOCA     1 MFSERLKEVQDGVEAAMAAAIGRLPAGDLRDAMAYAAQGGKRLRAFLAIESAAIHGISMEQAMPAALAVEALHAYSLVHDDMPCMDNDDLRRGLPTVHRKWDEATAVLAGDALQTLAFELCTDPVLGSAENRVALVAALAQASGAEGMVYGQALDIAAETAAVPLTLDEIIRLQAGKTGALISFAAQAGAIIAGADRALLAAYATALGLAFQIADDILDVEGDEEAAGKRLGKDAEAHKATFVSLLGLPGAKARAADLVAEAEAALAPYGEAAATLRACARYVIE 285
               SCOP domains d3m0ga_ A: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh........ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...---------------------.hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m0g A   2 SLSERLKEVQDAVETAmAAAIGRLPAGDLRDAmAYAAQGGKRLRAFLAIESAAIHGISmAQAmPAALAVEALHAYSLVHDDmPCmDNDDLRRGLPTVHKKWDDATAVLAGDALQTLAFELCTDPVLGSAENRVALVAALAQASGAEGmVYGQALDIAAETAAVPLTLDEIIRLQAGKTGALISFAAQAGAILAGADRGPLTAYATALGLAFQIADDIL---------------------ATFVSLLGLAGAKSRAADLVAEAEAALAPYGEAASTLRACARYVIE 286
                                    11      | 21        31  |     41        51        61  |     71        81 |  |   91       101       111       121       131       141       151       161       171       181       191       201       211       | -         -       241       251       261       271       281     
                                           18-MSE          34-MSE                    60-MSE                 83-MSE                                                           149-MSE                                                               219                   241                                             
                                                                                         64-MSE                86-MSE                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:268
 aligned with Q9KWR7_RHOCA | Q9KWR7 from UniProtKB/TrEMBL  Length:288

    Alignment length:286
                                    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      
         Q9KWR7_RHOCA     1 MFSERLKEVQDGVEAAMAAAIGRLPAGDLRDAMAYAAQGGKRLRAFLAIESAAIHGISMEQAMPAALAVEALHAYSLVHDDMPCMDNDDLRRGLPTVHRKWDEATAVLAGDALQTLAFELCTDPVLGSAENRVALVAALAQASGAEGMVYGQALDIAAETAAVPLTLDEIIRLQAGKTGALISFAAQAGAIIAGADRALLAAYATALGLAFQIADDILDVEGDEEAAGKRLGKDAEAHKATFVSLLGLPGAKARAADLVAEAEAALAPYGEAAATLRACARYVIER 286
               SCOP domains d3m0gb_ B: automated matches                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------polyprenyl_synt-3m0gB01 B:30-282                                                                                                                                                                                                                             ----- Pfam domains (1)
           Pfam domains (2) ----------------------------polyprenyl_synt-3m0gB02 B:30-282                                                                                                                                                                                                                             ----- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh........ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.------------------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m0g B   2 SLSERLKEVQDAVETAmAAAIGRLPAGDLRDAmAYAAQGGKRLRAFLAIESAAIHGISmAQAmPAALAVEALHAYSLVHDDmPCmDNDDLRRGLPTVHKKWDDATAVLAGDALQTLAFELCTDPVLGSAENRVALVAALAQASGAEGmVYGQALDIAAETAAVPLTLDEIIRLQAGKTGALISFAAQAGAILAGADRGPLTAYATALGLAFQIADDILDV------------------KATFVSLLGLAGAKSRAADLVAEAEAALAPYGEAASTLRACARYVIER 287
                                    11      | 21        31  |     41        51        61  |     71        81 |  |   91       101       111       121       131       141       151       161       171       181       191       201       211       221         -       241       251       261       271       281      
                                           18-MSE          34-MSE                    60-MSE                 83-MSE                                                           149-MSE                                                                 221                240                                               
                                                                                         64-MSE                86-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 3M0G)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9KWR7_RHOCA | Q9KWR7)
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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 Related Entries

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        Q9KWR7_RHOCA | Q9KWR7: 3lvs

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