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(-) Description

Title :  CRYSTAL STRUCTURE OF 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE FROM BURKHOLDERIA PSEUDOMALLEI WITH BOUND CTP AND CDP
 
Authors :  B. L. Staker
Date :  23 Jul 09  (Deposition) - 18 Aug 09  (Release) - 30 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Ispf, Structural Genomics, Isoprene Biosynthesis, Lyase, Metal- Binding, Seattle Structural Genomics Center For Infectious Disease, Ssgcid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. W. Begley, R. C. Hartley, D. R. Davies, T. E. Edwards, J. T. Leonard, J. Abendroth, C. A. Burris, J. Bhandari, P. J. Myler, B. L. Staker, L. J. Stewart
Leveraging Structure Determination With Fragment Screening For Infectious Disease Drug Targets: Mecp Synthase From Burkholderia Pseudomallei.
J Struct Funct Genomics V. 12 63 2011
PubMed-ID: 21359640  |  Reference-DOI: 10.1007/S10969-011-9102-6
(for further references see the PDB file header)

(-) 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: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ISPF, MECS, BPSL2098
    Organism Scientific: BURKHOLDERIA PSEUDOMALLEI
    Organism Taxid: 28450
    Strain: 1710B
    Synonym: MECPS, MECDP-SYNTHASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1CDP2Ligand/IonCYTIDINE-5'-DIPHOSPHATE
2CTP1Ligand/IonCYTIDINE-5'-TRIPHOSPHATE
3GOL1Ligand/IonGLYCEROL
4ZN3Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:10 , HIS A:12 , HIS A:44 , CTP B:901BINDING SITE FOR RESIDUE ZN A 801
2AC2SOFTWAREALA A:102 , PRO A:105 , LYS A:106 , LEU A:107 , ALA A:108 , ALA A:133 , LYS A:134 , THR A:135 , GLU A:137 , HOH A:221 , ASP C:10 , ASP C:58 , GLY C:60 , ARG C:61 , ZN C:801BINDING SITE FOR RESIDUE CDP A 901
3AC3SOFTWAREASP A:10 , HIS A:12 , GLY A:35 , HIS A:36 , SER A:37 , HIS A:44 , ASP A:58 , GLY A:60 , HOH A:177 , HOH A:219 , ZN A:801 , ALA B:102 , PRO B:105 , LEU B:107 , ALA B:108 , ALA B:133 , LYS B:134 , THR B:135 , GLU B:137 , HOH B:167 , HOH B:180 , HOH B:190 , HOH B:202BINDING SITE FOR RESIDUE CTP B 901
4AC4SOFTWAREASP B:10 , HIS B:12 , HIS B:44 , CDP C:901BINDING SITE FOR RESIDUE ZN B 801
5AC5SOFTWAREGLU A:149 , HOH A:184 , TYR B:9 , LEU B:142 , GLU B:149 , GLU C:149 , HOH C:191 , HOH C:198BINDING SITE FOR RESIDUE GOL B 163
6AC6SOFTWAREASP B:10 , HIS B:12 , ASP B:58 , GLY B:60 , HOH B:176 , ZN B:801 , ALA C:102 , PRO C:105 , LYS C:106 , LEU C:107 , ALA C:108 , ALA C:133 , LYS C:134 , THR C:135 , GLU C:137 , HOH C:165 , HOH C:196BINDING SITE FOR RESIDUE CDP C 901
7AC7SOFTWARECDP A:901 , ASP C:10 , HIS C:12 , HIS C:44BINDING SITE FOR RESIDUE ZN C 801

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ala A:104 -Pro A:105
2Ala B:104 -Pro B:105
3Ala C:104 -Pro C:105

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ISPFPS01350 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.ISPF_BURPS37-52
 
 		  3A:37-52
B:38-52
C:37-52

(-) Exons   (0, 0)

(no "Exon" information available for 3IEW)

(-) 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:160
 aligned with ISPF_BURPS | Q63T71 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:160
                             1                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159
           ISPF_BURPS     - -MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDPRFKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVRE 159
               SCOP domains d3iewa_ A: automated matches                                                                                                                                     SCOP domains
               CATH domains 3iewA00 A:0-159  [code=3.30.1330.50, no name defined]                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeeee...eee..eee...eeee.....hhhhhhhhhhhhhhh...hhhhhh...hhhhh..hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhh..hhhhh..eee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------ISPF            ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iew A   0 SMDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDPRFKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVRE 159
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159


Chain B from PDB  Type:PROTEIN  Length:150
 aligned with ISPF_BURPS | Q63T71 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        
           ISPF_BURPS     1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDPRFKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVR 158
               SCOP domains d3iewb_ B: automated matches                                                                                                                                   SCOP domains
               CATH domains 3iewB00 B:1-158  [code=3.30.1330.5   0, no name defined]                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee....eee..eee....ee.---..hhhhhhhhhhhhhhhh..hhhhhh.-----....hhhhhhhhhhhhhhhh..eeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhhhh..eee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iew B   1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLL---DADVLLHAITDALFGAAALGDIGRHFS-----FKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVR 158
                                    10        20        30   |   |40        50        60   |    70        80        90       100       110       120       130       140       150        
                                                            34  38                        64    70                                                                                        


Chain C from PDB  Type:PROTEIN  Length:149
 aligned with ISPF_BURPS | Q63T71 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
           ISPF_BURPS     1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDPRFKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVRE 159
               SCOP domains d3iewc_ C: automated matches                                                                                                                                    SCOP domains
               CATH domains 3iewC00 C:1-159  [code=3.30.1330.50, no name defined]                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee....eee..eee....ee......hhhhhhhhhhhhhhh...hhhhhh----------hhhhhhhhhhhhhhhh.eeeeeeeeeee........hhhhhhhhhhhhhh.hhhhh..eee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iew C   1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHF----------DSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVRE 159
                                    10        20        30        40        50        60  |      -   |    80        90       100       110       120       130       140       150         
                                                                                         63         74
   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 3IEW)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (ISPF_BURPS | Q63T71)
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

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

UniProtKB/Swiss-Prot
        ISPF_BURPS | Q63T71: 3f0d 3f0e 3f0f 3f0g 3ieq 3ike 3ikf 3jvh 3k14 3ke1 3mbm 3q8h

(-) Related Entries Specified in the PDB File

3e0d HIGH RESOLUTION APO STRUCTURE IN DIFFERENT CRYSTAL FORM
3e0e APO CRYSTAL STRUCTURE SAME CRYSTAL FORM
3f0f STRUCTURE WITH HYDROLYZED CDP
3f0g STRUCTURE WITH CMP
3ieq STRUCTURE WITH CYTIDINE RELATED ID: BUPSA.00122.A RELATED DB: TARGETDB