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(-) Description

Title :  CRYSTAL STRUCTURE OF 2C-METHYL-D-ERYTHRITOL 2,4-CLYCODIPHOSPHATE SYNTHASE COMPLEXED WITH LIGAND
 
Authors :  W. N. Hunter, N. L. Ramsden
Date :  19 Nov 08  (Deposition) - 25 Aug 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Mecdp-Synthase, Lyase, Isoprene Biosynthesis, Magnesium, Manganese, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. L. Ramsden, L. Buetow, A. Dawson, L. A. Kemp, V. Ulaganathan, R. Brenk, G. Klebe, W. N. Hunter
A Structure-Based Approach To Ligand Discovery For 2C-Methyl-D-Erythritol-2, 4-Cyclodiphosphate Synthase: A Target For Antimicrobial Therapy
J. Med. Chem. V. 52 2531 2009
PubMed-ID: 19320487  |  Reference-DOI: 10.1021/JM801475N

(-) 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: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ISPF
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Synonym: MECPS, 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
1C6B1Ligand/Ion[(2S,3S,4R,5S)-5-(4-AMINO-2-OXO-PYRIMIDIN-1-YL)-4-HYDROXY-2-(HYDROXYMETHYL)OXOLAN-3-YL] DIHYDROGENPHOSPHATE
2GOL1Ligand/IonGLYCEROL
3GPP1Ligand/IonGERANYL DIPHOSPHATE
4ZN1Ligand/IonZINC ION
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1C6B3Ligand/Ion[(2S,3S,4R,5S)-5-(4-AMINO-2-OXO-PYRIMIDIN-1-YL)-4-HYDROXY-2-(HYDROXYMETHYL)OXOLAN-3-YL] DIHYDROGENPHOSPHATE
2GOL3Ligand/IonGLYCEROL
3GPP3Ligand/IonGERANYL DIPHOSPHATE
4ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:8 , HIS A:10 , HIS A:42BINDING SITE FOR RESIDUE ZN A 900
2AC2SOFTWAREASP A:56 , ILE A:57 , GLY A:58 , ALA A:100 , PRO A:103 , LYS A:104 , MET A:105 , LEU A:106 , ALA A:131 , THR A:132 , THR A:133 , HOH A:183 , HOH A:194BINDING SITE FOR RESIDUE C6B A 901
3AC3SOFTWAREPHE A:7 , GLY A:138 , PHE A:139 , THR A:140 , ARG A:142 , GLU A:149BINDING SITE FOR RESIDUE GPP A 903
4AC4SOFTWAREHIS A:123 , MET A:124 , ASP A:125 , HOH A:182BINDING SITE FOR RESIDUE GOL A 904

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:16 -Pro A:17
2Asp A:65 -Pro A:66
3Ala A:102 -Pro A:103

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ISPFPS01350 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.ISPF_ECOLI35-50  1A:35-50
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ISPFPS01350 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.ISPF_ECOLI35-50  3A:35-50

(-) Exons   (0, 0)

(no "Exon" information available for 3FBA)

(-) 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:158
 aligned with ISPF_ECOLI | P62617 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:158
                              1                                                                                                                                                           
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148        
           ISPF_ECOLI     - --MRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIK 156
               SCOP domains d3fbaa_ A: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF                                                                                           SCOP domains
               CATH domains 3fbaA00 A:-1-156  [code=3.30.1330.50, no name defined]                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeee..eee..eee...eee......hhhhhhhhhhhhhhh...hhhhhh..........hhhhhhhhhhhhhhhh..eeeeeeeeee........hhhhhhhhhhhhh..hhh.eeeeee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fba A  -1 LEMRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIK 156
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148
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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 3FBA)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (ISPF_ECOLI | P62617)
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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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.
    GO:0006744    ubiquinone biosynthetic process    The chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme.

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 Related Entries

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UniProtKB/Swiss-Prot
        ISPF_ECOLI | P62617: 1gx1 1h47 1h48 1jy8 1knj 1knk 1u3l 1u3p 1u40 1u43 1yqn 2amt 2gzl 3elc 3eor 3ern 3esj

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