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(-) Description

Title :  CRYSTAL STRUCTURE OF 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE PV003920 FROM PLASMODIUM VIVAX
 
Authors :  A. K. Wernimont, J. Lew, I. Kozieradzki, Y. H. Lin, X. Sun, C. Khuu, Y. Zhao, M. Schapira, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, A. Bochkarev, R. Hui, J. D. Artz, T. Xiao, Structural Genomics Consortium (Sgc)
Date :  29 Oct 07  (Deposition) - 20 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.26
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Malaria Isoprenoid Biosynthesis And Prenylation Pathways Ispf, Isoprene Biosynthesis, Lyase, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Wernimont, J. Lew, I. Kozieradzki, Y. H. Lin, X. Sun, C. Khuu, Y. Zhao, M. Schapira, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, A. Bochkarev, R. Hui, J. D. Artz, T. Xiao
Crystal Structure Of 2C-Methyl-D-Erythritol 2, 4-Cyclodiphosphate Synthase Pv003920 From Plasmodium Vivax.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE
    Chains: A
    EC Number: 4.6.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15-MHL-LIC
    Expression System Strain: DH5A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 102-287
    Gene: PV003920, PVX_003920
    Organism Scientific: PLASMODIUM VIVAX SAI-1
    Organism Taxid: 126793
    Strain: SALVADOR I

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:12 , HIS A:14 , HIS A:62 , HIS A:70BINDING SITE FOR RESIDUE ZN A 1157

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3B6N)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:130 -Pro A:131
2Lys A:185 -Gln A:186

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3B6N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3B6N)

(-) Exons   (0, 0)

(no "Exon" information available for 3B6N)

(-) 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:150
 aligned with A5KBP6_PLAVS | A5KBP6 from UniProtKB/TrEMBL  Length:287

    Alignment length:183
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283   
         A5KBP6_PLAVS   104 GVRIGQGYDIHQIRVGPPEDIVADTTADTAANTADPNKQSFKRLTIGGVPVETISVLSHSDGDVIFHALVDALLGGMSCSDLGTLFPDGSPKYKNKNSLSFLRYARLLLYKRNYAIANVDIIVIAEVPKISPIREEIVRNISSALGISESQVSLKGKTHEQLGPVGQKKAIECFANALLIRKQ 286
               SCOP domains d3b6na_ A: automate                  d matches                                                                                                                                          SCOP domains
               CATH domains 3b6nA00 A:4-186  [c                  ode=3.30.1330.50, no name defined]                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee.....------------------..eeeeeee..eeeeeeeeee....hhhhhhhhhhhhhhh...---------------..hhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhh.eeeeee....hhhhhh..eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b6n A   4 GVRIGQGYDIHQIRVGPPE------------------KQSFKRLTIGGVPVETISVLSHSDGDVIFHALVDALLGGMSCS---------------KNSLSFLRYARLLLYKRNYAIANVDIIVIAEVPKISPIREEIVRNISSALGISESQVSLKGKTHEQLGPVGQKKAIECFANALLIRKQ 186
                                    13        |-         -       |43        53        63        73        83         -     | 103       113       123       133       143       153       163       173       183   
                                             22                 41                                        83              99
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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  (1, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3B6N)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (A5KBP6_PLAVS | A5KBP6)
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: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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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