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(-) Description

Title :  STRUCTURE OF 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE FROM THE ISOPRENOID BIOSYNTHETIC PATHWAY OF ARABIDOPSIS THALIANA
 
Authors :  B. M. Calisto, J. Perez-Gil, J. Querol-Audi, I. Fita, S. Imperial
Date :  23 Apr 07  (Deposition) - 18 Sep 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Plant Enzymes, Arabidopsis Thaliana, Mep Pathway, Isoprenoid-Binding Proteins, Cmp, Zinc Ions, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. M. Calisto, J. Perez-Gil, M. Bergua, J. Querol-Audi, I. Fita, S. Imperial
Biosynthesis Of Isoprenoids In Plants: Structure Of The 2C-Methyl-D-Erithrytol 2, 4-Cyclodiphosphate Synthase From Arabidopsis Thaliana. Comparison With The Bacterial Enzymes
Protein Sci. V. 16 2082 2007
PubMed-ID: 17660251  |  Reference-DOI: 10.1110/PS.072972807

(-) Compounds

Molecule 1 - 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE
    ChainsA
    EC Number4.6.1.12
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET23B
    Expression System StrainBL21 (DE3) [PLYSS]
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentISPF
    GeneISPF
    Organism CommonTHALE CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    StrainECOTYPE COLUMBIA 0
    SynonymMECPS, MECDP-SYNTHASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (3x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1C5P1Ligand/IonCYTIDINE-5'-MONOPHOSPHATE
2CL1Ligand/IonCHLORIDE ION
3PO41Ligand/IonPHOSPHATE ION
4ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1C5P3Ligand/IonCYTIDINE-5'-MONOPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3PO43Ligand/IonPHOSPHATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:11 , HIS A:13 , HIS A:45 , HOH A:704BINDING SITE FOR RESIDUE ZN A 500
2AC2SOFTWAREASP A:141 , LEU A:143 , HOH A:749 , HOH A:757BINDING SITE FOR RESIDUE PO4 A 701
3AC3SOFTWAREGLN A:104 , ARG A:105BINDING SITE FOR RESIDUE CL A 702
4AC4SOFTWAREASP A:59 , ILE A:60 , GLY A:61 , LEU A:103 , PRO A:106 , LYS A:107 , ILE A:108 , SER A:109 , ALA A:134 , LYS A:135 , THR A:136 , HOH A:748 , HOH A:765 , HOH A:766BINDING SITE FOR RESIDUE C5P A 700

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PMP)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Arg A:105 -Pro A:106

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PMP)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ISPFPS01350 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.ISPF_ARATH109-124  1A:38-53
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ISPFPS01350 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.ISPF_ARATH109-124  3A:38-53

(-) Exons   (0, 0)

(no "Exon" information available for 2PMP)

(-) 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:160
 aligned with ISPF_ARATH | Q9CAK8 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:160
                                    81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
           ISPF_ARATH    72 TLPFRIGHGFDLHRLEPGYPLIIGGIVIPHDRGCEAHSDGDVLLHCVVDAILGALGLPDIGQIFPDSDPKWKGAASSVFIKEAVRLMDEAGYEIGNLDATLILQRPKISPHKETIRSNLSKLLGADPSVVNLKAKTHEKVDSLGENRSIAAHTVILLMKK 231
               SCOP domains d2pmpa_ A: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF                                                                                             SCOP domains
               CATH domains 2pmpA00 A:1-160  [code=3.30.1330.50, no name defined]                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeeee....ee..ee....eee......hhhhhhhhhhhhhhhh..hhhhhh..........hhhhhhhhhhhhhhhhheeeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhh.eeeeee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------ISPF            ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pmp A   1 TLPFRIGHGFDLHRLEPGYPLIIGGIVIPHDRGCEAHSDGDVLLHCVVDAILGALGLPDIGQIFPDSDPKWKGAASSVFIKEAVRLMDEAGYEIGNLDATLILQRPKISPHKETIRSNLSKLLGADPSVVNLKAKTHEKVDSLGENRSIAAHTVILLMKK 160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

   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, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2PMP)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (ISPF_ARATH | Q9CAK8)
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:0016117    carotenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of carotenoids, tetraterpenoid compounds in which two units of 4 isoprenoid residues joined head-to-tail are themselves joined tail-to-tail.
    GO:0015995    chlorophyll biosynthetic process    The chemical reactions and pathways resulting in the formation of chlorophyll, any compound of magnesium complexed in a porphyrin (tetrapyrrole) ring and which functions as a photosynthetic pigment, from less complex precursors.
    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.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009570    chloroplast stroma    The space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes and some temporary products of photosynthesis.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

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 Related Entries

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(-) Related Entries Specified in the PDB File

1gx1 HOMOLOGUE PROTEIN
1iv1 HOMOLOGUE PROTEIN
1jn1 HOMOLOGUE PROTEIN