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(-) Description

Title :  ISPF WITH MG AND CDP
 
Authors :  S. Steinbacher, J. Kaiser, J. Wungsintaweekul, S. Hechst, W. Eisenrei S. Gerhardt, A. Bacher, F. Rohdich
Date :  22 Jul 04  (Deposition) - 31 Aug 04  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Lyase, Mep Pathway, Terpene Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Steinbacher, J. Kaiser, J. Wungsintaweekul, S. Hechst, W. Eisenreich, S. Gerhardt, A. Bacher, F. Rohdich
Structure Of 2C-Methyl-D-Erythritol-2, 4-Cyclodiphosphate Synthase Involved In Mevalonate Independent Biosynthesis Of Isoprenoids
J. Mol. Biol. V. 316 79 2002
PubMed-ID: 11829504  |  Reference-DOI: 10.1006/JMBI.2001.5341

(-) 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 Taxid: 562
    Gene: ISPF
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: MECPS, MECDP-SYNTHASE, ISPF

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1CDP1Ligand/IonCYTIDINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1CDP3Ligand/IonCYTIDINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:63 , GLU A:135 , CDP A:669BINDING SITE FOR RESIDUE MG A 700
2AC2SOFTWAREASP A:8 , HIS A:10 , HIS A:42 , CDP A:669BINDING SITE FOR RESIDUE ZN A 701
3AC3SOFTWAREASP A:8 , HIS A:10 , HIS A:42 , ASP A:56 , GLY A:58 , ASP A:63 , ALA A:100 , PRO A:103 , LYS A:104 , MET A:105 , LEU A:106 , ALA A:131 , THR A:132 , THR A:133 , GLU A:135 , MG A:700 , ZN A:701BINDING SITE FOR RESIDUE CDP A 669

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U3L)

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U3L)

(-) 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 1U3L)

(-) 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:155
 aligned with ISPF_ECOLI | P62617 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150     
           ISPF_ECOLI     1 MRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLI 155
               SCOP domains d1u3la_ A: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF                                                                                        SCOP domains
               CATH domains 1u3lA00 A:1-155  [code=3.30.1330.50, no name defined]                                                                                                       CATH domains
               Pfam domains YgbB-1u3lA01 A:1-155                                                                                                                                        Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee..eee..eee...eee......hhhhhhhhhhhhhhhh..hhhhhh...hhhhh..hhhhhhhhhhhhhhhh..eeeeeeeeee.....hhhhhhhhhhhhhhhh..hhh.eeeeee....hhhhhh..eeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------ISPF            --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u3l A   1 MRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLI 155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

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

(-) 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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  1u3l
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  ISPF_ECOLI | P62617
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  4.6.1.12
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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

(-) Related Entries Specified in the PDB File

1jy8 ISPF WITH CMP AND 2C-METHYL-D-ERYTHRITOL 2,4- CYCLODIPHOSPHATE
1u3p ISPF NATIVE
1u40 ISPF WITH 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL
1u43 ISPF WITH 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL 2- PHOSPHATE