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(-) Description

Title :  CRYSTAL STRUCTURE OF 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE FROM SHEWANELLA ONEIDENSIS
 
Authors :  S. Ni, H. Robinson, G. C. Marsing, D. E. Bussiere, M. A. Kennedy
Date :  08 Apr 04  (Deposition) - 26 Oct 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Mixed Alpha Beta, Homotrimer, Synthase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ni, H. Robinson, G. C. Marsing, D. E. Bussiere, M. A. Kennedy
Structure Of 2C-Methyl-D-Erythritol-2, 4-Cyclodiphosphate Synthase From Shewanella Oneidensis At 1. 6 A: Identificatio Of Farnesyl Pyrophosphate Trapped In A Hydrophobic Cavity.
Acta Crystallogr. , Sect. D V. 60 1949 2004
PubMed-ID: 15502301  |  Reference-DOI: 10.1107/S0907444904021791

(-) Compounds

Molecule 1 - 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE
    Chains: A, B, C
    EC Number: 4.6.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI K12
    Expression System Plasmid: PET28B
    Expression System Strain: K12
    Expression System Taxid: 83333
    Expression System Vector Type: PLASMID
    Gene: ISPF
    Organism Scientific: SHEWANELLA ONEIDENSIS
    Organism Taxid: 211586
    Strain: MR-1

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric/Biological Unit (4, 16)
No.NameCountTypeFull Name
1CO3Ligand/IonCOBALT (II) ION
2FPP1Ligand/IonFARNESYL DIPHOSPHATE
3MSE9Mod. Amino AcidSELENOMETHIONINE
4ZN3Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:10 , HIS A:12 , HIS A:44 , HOH A:1861 , HOH A:2015BINDING SITE FOR RESIDUE ZN A 661
2AC2SOFTWAREASP A:10 , HOH A:1841 , HOH A:1842 , HOH A:2015 , THR B:134 , HOH B:803BINDING SITE FOR RESIDUE CO A 662
3AC3SOFTWAREASP B:10 , HIS B:12 , HIS B:44 , HOH B:932BINDING SITE FOR RESIDUE ZN B 760
4AC4SOFTWAREASP B:10 , HOH B:771 , THR C:134 , HOH C:893 , HOH C:916BINDING SITE FOR RESIDUE CO B 761
5AC5SOFTWAREASP C:10 , HIS C:12 , HIS C:44 , HOH C:868BINDING SITE FOR RESIDUE ZN C 860
6AC6SOFTWARETHR A:134 , HOH A:1856 , HOH A:1858 , ASP C:10 , HOH C:862BINDING SITE FOR RESIDUE CO C 861
7AC7SOFTWAREPHE A:9 , GLY A:140 , PHE A:141 , THR A:142 , ARG A:144 , ALA A:149 , HOH A:1889 , HOH A:2018 , HOH A:2028 , PHE B:9 , GLY B:140 , PHE B:141 , ARG B:144 , GLY C:140 , PHE C:141 , ARG C:144BINDING SITE FOR RESIDUE FPP A 1831

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T0A)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ala A:104 -Pro A:105
2Ala B:104 -Pro B:105
3Ala C:104 -Pro C:105

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T0A)

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ISPFPS01350 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.ISPF_SHEON37-52
 
 		  3A:37-52
B:37-52
C:37-52

(-) Exons   (0, 0)

(no "Exon" information available for 1T0A)

(-) 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:158
 aligned with ISPF_SHEON | Q8EBR3 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151        
           ISPF_SHEON     2 KIRIGHGFDVHKFGEPRPLILCGVEVPYETGLVAHSDGDVVLHAISDAILGAMALGDIGKHFPDTDAAYKGADSRVLLRHCYALAKAKGFELGNLDVTIIAQAPKMAPHIEDMRQVLAADLNADVADINVKATTTEKLGFTGRKEGIAVEAVVLLSRQ 159
               SCOP domains d1t0aa_ A: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF                                                                                           SCOP domains
               CATH domains 1t0aA00 A:2-159  [code=3.30.1330.50, no name defined]                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee...eee..eee....ee......hhhhhhhhhhhhhhh...hhhhhh...hhhhh..hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhh..hhh.eeeeee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------ISPF            ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t0a A   2 KIRIGHGFDVHKFGEPRPLILCGVEVPYETGLVAHSDGDVVLHAISDAILGAmALGDIGKHFPDTDAAYKGADSRVLLRHCYALAKAKGFELGNLDVTIIAQAPKmAPHIEDmRQVLAADLNADVADINVKATTTEKLGFTGRKEGIAVEAVVLLSRQ 159
                                    11        21        31        41        51  |     61        71        81        91       101     | 111  |    121       131       141       151        
                                                                               54-MSE                                              107-MSE  |                                             
                                                                                                                                          114-MSE                                         


Chain B from PDB  Type:PROTEIN  Length:158
 aligned with ISPF_SHEON | Q8EBR3 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151        
           ISPF_SHEON     2 KIRIGHGFDVHKFGEPRPLILCGVEVPYETGLVAHSDGDVVLHAISDAILGAMALGDIGKHFPDTDAAYKGADSRVLLRHCYALAKAKGFELGNLDVTIIAQAPKMAPHIEDMRQVLAADLNADVADINVKATTTEKLGFTGRKEGIAVEAVVLLSRQ 159
               SCOP domains d1t0ab_ B: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF                                                                                           SCOP domains
               CATH domains 1t0aB00 B:2-159  [code=3.30.1330.50, no name defined]                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee....ee..ee.....ee......hhhhhhhhhhhhhhh...hhhhhh...hhhhh..hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhh..hhh.eeeeee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------ISPF            ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t0a B   2 KIRIGHGFDVHKFGEPRPLILCGVEVPYETGLVAHSDGDVVLHAISDAILGAmALGDIGKHFPDTDAAYKGADSRVLLRHCYALAKAKGFELGNLDVTIIAQAPKmAPHIEDmRQVLAADLNADVADINVKATTTEKLGFTGRKEGIAVEAVVLLSRQ 159
                                    11        21        31        41        51  |     61        71        81        91       101     | 111  |    121       131       141       151        
                                                                               54-MSE                                              107-MSE  |                                             
                                                                                                                                          114-MSE                                         


Chain C from PDB  Type:PROTEIN  Length:158
 aligned with ISPF_SHEON | Q8EBR3 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151        
           ISPF_SHEON     2 KIRIGHGFDVHKFGEPRPLILCGVEVPYETGLVAHSDGDVVLHAISDAILGAMALGDIGKHFPDTDAAYKGADSRVLLRHCYALAKAKGFELGNLDVTIIAQAPKMAPHIEDMRQVLAADLNADVADINVKATTTEKLGFTGRKEGIAVEAVVLLSRQ 159
               SCOP domains d1t0ac_ C: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF                                                                                           SCOP domains
               CATH domains 1t0aC00 C:2-159  [code=3.30.1330.50, no name defined]                                                                                                          CATH domains
           Pfam domains (1) -YgbB-1t0aC01 C:3-159                                                                                                                                          Pfam domains (1)
           Pfam domains (2) -YgbB-1t0aC02 C:3-159                                                                                                                                          Pfam domains (2)
           Pfam domains (3) -YgbB-1t0aC03 C:3-159                                                                                                                                          Pfam domains (3)
         Sec.struct. author .eeeeeeeeeeeeee....ee..ee.....ee......hhhhhhhhhhhhhhh...hhhhhh...hhhhh..hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhh..hhh.eeeeee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------ISPF            ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t0a C   2 KIRIGHGFDVHKFGEPRPLILCGVEVPYETGLVAHSDGDVVLHAISDAILGAmALGDIGKHFPDTDAAYKGADSRVLLRHCYALAKAKGFELGNLDVTIIAQAPKmAPHIEDmRQVLAADLNADVADINVKATTTEKLGFTGRKEGIAVEAVVLLSRQ 159
                                    11        21        31        41        51  |     61        71        81        91       101     | 111  |    121       131       141       151        
                                                                               54-MSE                                              107-MSE  |                                             
                                                                                                                                          114-MSE
   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, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: YgbB] (24)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (ISPF_SHEON | Q8EBR3)
molecular function
    GO:0008685    2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity    Catalysis of the reaction: 4-CDP-2-C-methyl-D-erythritol 2-phosphate = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + CMP.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0019288    isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway    The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.
    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.
    GO:0016114    terpenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of terpenoids, any member of a class of compounds characterized by an isoprenoid chemical structure.

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