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(-) Description

Title :  2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE FROM SALMONELLA TYPHIMURIUM
 
Authors :  J. Osipiuk, M. Gu, S. Peterson, W. F. Anderson, A. Joachimiak, Center F Structural Genomics Of Infectious Diseases (Csgid)
Date :  04 Mar 09  (Deposition) - 17 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.03
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Structural Genomics, Idp01038, 2-C-Methyl-D-Erythritol 2, 4- Cyclodiphosphate Synthase, Isoprene Biosynthesis, Lyase, Metal- Binding, Center For Structural Genomics Of Infectious Diseases, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, M. Gu, S. Peterson, W. F. Anderson, A. Joachimiak
X-Ray Crystal Structure Of 2-C-Methyl-D-Erythritol 2, 4-Cyclodiphosphate Synthase From Salmonella Typhimurium.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE
    Chains: A, B, C
    EC Number: 4.6.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ISPF, STM2929
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602
    Strain: LT2
    Synonym: MECPS, MECDP-SYNTHASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MG4Ligand/IonMAGNESIUM ION
3POP1Ligand/IonPYROPHOSPHATE 2-

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:35 , ILE A:57 , GLY A:58 , PHE A:61 , ASP A:63 , HOH A:191 , HOH A:209 , HOH A:210 , HOH A:250BINDING SITE FOR RESIDUE GOL A 303
2AC2SOFTWAREASP A:8 , HOH A:165 , HOH A:198 , HOH A:205 , HOH C:214 , HOH C:215BINDING SITE FOR RESIDUE MG A 304
3AC3SOFTWAREGLU A:149 , GLU B:149 , GLU C:149BINDING SITE FOR RESIDUE MG A 307
4AC4SOFTWAREGLY A:138 , PHE A:139 , ARG A:142 , GLY B:138 , PHE B:139 , ARG B:142 , HOH B:220 , GLY C:138 , PHE C:139 , ARG C:142BINDING SITE FOR RESIDUE POP B 301
5AC5SOFTWAREHOH A:167 , HOH A:176 , HOH A:181 , ASP B:8 , HOH B:180 , HOH B:182BINDING SITE FOR RESIDUE MG B 306
6AC6SOFTWARESER C:35 , ILE C:57 , GLY C:58 , PHE C:61 , ASP C:63 , HOH C:190 , HOH C:192 , HOH C:207 , HOH C:208 , HOH C:273BINDING SITE FOR RESIDUE GOL C 302
7AC7SOFTWAREHOH B:271 , HOH B:272 , ASP C:8 , HOH C:160 , HOH C:218 , HOH C:273BINDING SITE FOR RESIDUE MG C 305

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Gly A:16 -Pro A:17
2Ala A:102 -Pro A:103
3Gly B:16 -Pro B:17
4Ala B:102 -Pro B:103
5Gly C:16 -Pro C:17
6Ala C:102 -Pro C:103

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ISPFPS01350 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.ISPF_SALTY35-50
 
 		  3A:35-50
B:35-50
C:35-50

(-) Exons   (0, 0)

(no "Exon" information available for 3GHZ)

(-) 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:157
 aligned with ISPF_SALTY | Q8ZMF7 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:157
                             1                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       
           ISPF_SALTY     - -MRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDEVNVKATTTEKLGFTGRGEGIACEAVALLMK 156
               SCOP domains d3ghza_ A: automated matches                                                                                                                                  SCOP domains
               CATH domains 3ghzA00 A:0-156  [code=3.30.1330.50, no name defined]                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee....eee..eee....eee.....hhhhhhhhhhhhhhh...hhhhhh...hhhhh..hhhhhhhhhhhhhhhh..eeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhh.eeeeee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ghz A   0 AMRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDEVNVKATTTEKLGFTGRGEGIACEAVALLMK 156
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       


Chain B from PDB  Type:PROTEIN  Length:151
 aligned with ISPF_SALTY | Q8ZMF7 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:157
                             1                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       
           ISPF_SALTY     - -MRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDEVNVKATTTEKLGFTGRGEGIACEAVALLMK 156
               SCOP domains d3ghzb_ B: automated matches                                                                                                                                  SCOP domains
               CATH domains 3ghzB00 B:0-156  [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........hhhhhhhhhhhhhh.hhh.eeeeee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ghz B   0 AMRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTD------DSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDEVNVKATTTEKLGFTGRGEGIACEAVALLMK 156
                                     9        19        29        39        49        59     |   -  |     79        89        99       109       119       129       139       149       
                                                                                            65     72                                                                                    


Chain C from PDB  Type:PROTEIN  Length:157
 aligned with ISPF_SALTY | Q8ZMF7 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:157
                             1                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       
           ISPF_SALTY     - -MRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDEVNVKATTTEKLGFTGRGEGIACEAVALLMK 156
               SCOP domains d3ghzc_ C: automated matches                                                                                                                                  SCOP domains
               CATH domains 3ghzC00 C:0-156  [code=3.30.1330.50, no name defined]                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee....eee..eee....eee.....hhhhhhhhhhhhhhh...hhhhhh...hhhhh..hhhhhhhhhhhhhhhh..eeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhh.eeeeee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ghz C   0 AMRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDEVNVKATTTEKLGFTGRGEGIACEAVALLMK 156
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149
   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  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (ISPF_SALTY | Q8ZMF7)
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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 Related Entries

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UniProtKB/Swiss-Prot
        ISPF_SALTY | Q8ZMF7: 3t80

(-) Related Entries Specified in the PDB File

1u3p ISPF PROTEIN IN NATIVE FORM FROM ESCHERICHIA COLI. RELATED ID: IDP01038 RELATED DB: TARGETDB