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(-) Description

Title :  ISPF (BURKHOLDERIA CENOCEPACIA) 2CMP COMPLEX
 
Authors :  P. E. F. O'Rourke, J. Kalinowska-Tluscik, P. K. Fyfe, A. Dawson, W. N. Hu
Date :  30 Sep 13  (Deposition) - 08 Jan 14  (Release) - 29 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. E. O Rourke, J. Kalinowska-Tluscik, P. K. Fyfe, A. Dawson, W. N. Hunter
Crystal Structures Of Ispf From Plasmodium Falciparum And Burkholderia Cenocepacia: Comparisons Inform Antimicrobial Drug Target Assessment.
Bmc Struct. Biol. V. 14 1 2014
PubMed-ID: 24410837  |  Reference-DOI: 10.1186/1472-6807-14-1

(-) 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 Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: GOLD
    Expression System Vector: PET15BTEV
    Expression System Vector Type: PLASMID
    Organism Scientific: BURKHOLDERIA CENOCEPACIA
    Organism Taxid: 216591
    Other Details: GENOMIC DNA
    Strain: J2315
    Synonym: MECDP-SYNTHASE, MECPP-SYNTHASE, MECPS, 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1C5P6Ligand/IonCYTIDINE-5'-MONOPHOSPHATE
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
3SO41Ligand/IonSULFATE ION
4ZN3Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:10 , HIS A:12 , HIS A:44 , C5P A:1164BINDING SITE FOR RESIDUE ZN A1162
02AC2SOFTWAREASP B:10 , HIS B:12 , HIS B:44 , C5P B:1164BINDING SITE FOR RESIDUE ZN B1162
03AC3SOFTWAREASP C:10 , HIS C:12 , HIS C:44 , C5P C:1165BINDING SITE FOR RESIDUE ZN C1162
04AC4SOFTWAREGLN A:151 , HOH A:2160 , HOH A:2167 , HOH A:2168 , LEU B:142 , GLU B:149 , HOH B:2011 , TYR C:9 , GLU C:149 , GLN C:151BINDING SITE FOR RESIDUE PEG C1163
05AC5SOFTWAREASP A:58 , GLY A:60 , C5P A:1164 , HOH A:2020 , HOH A:2072 , HOH A:2175 , ALA B:102 , PRO B:105 , LYS B:106 , LEU B:107 , ALA B:108 , ALA B:133 , LYS B:134 , THR B:135 , HOH B:2082 , HOH B:2104 , HOH B:2116BINDING SITE FOR RESIDUE C5P B1163
06AC6SOFTWAREASP B:58 , ILE B:59 , GLY B:60 , C5P B:1164 , HOH B:2013 , HOH B:2047 , HOH B:2117 , ALA C:102 , PRO C:105 , LYS C:106 , LEU C:107 , ALA C:108 , ALA C:133 , LYS C:134 , THR C:135 , HOH C:2109 , HOH C:2119BINDING SITE FOR RESIDUE C5P C1164
07AC7SOFTWAREALA A:102 , PRO A:105 , LYS A:106 , LEU A:107 , ALA A:108 , ALA A:133 , LYS A:134 , THR A:135 , HOH A:2150 , HOH A:2152 , HOH A:2173 , ASP C:58 , GLY C:60 , C5P C:1165BINDING SITE FOR RESIDUE C5P A1163
08AC8SOFTWAREASP B:10 , HIS B:12 , HIS B:36 , SER B:37 , HIS B:44 , ILE B:59 , GLY B:60 , ASP B:65 , ALA B:73 , LEU B:78 , ZN B:1162 , HOH B:2012 , HOH B:2032 , HOH B:2033 , HOH B:2056 , HOH B:2057 , HOH B:2117 , LYS C:134 , C5P C:1164BINDING SITE FOR RESIDUE C5P B1164
09AC9SOFTWAREASP A:10 , HIS A:12 , HIS A:36 , SER A:37 , HIS A:44 , ILE A:59 , GLY A:60 , PHE A:63 , ALA A:73 , LEU A:78 , ZN A:1162 , HOH A:2019 , HOH A:2056 , HOH A:2057 , HOH A:2175 , LYS B:134 , C5P B:1163BINDING SITE FOR RESIDUE C5P A1164
10BC1SOFTWARELYS A:134 , C5P A:1163 , HOH A:2154 , HOH A:2172 , ASP C:10 , HIS C:12 , HIS C:36 , SER C:37 , HIS C:44 , ILE C:59 , PHE C:63 , ALA C:73 , LEU C:78 , ZN C:1162 , HOH C:2039 , HOH C:2040 , HOH C:2041 , HOH C:2056BINDING SITE FOR RESIDUE C5P C1165
11BC2SOFTWAREHOH A:2163 , HOH A:2164 , GLY B:140 , TYR B:141 , ARG B:144 , HOH B:2118 , HOH B:2119 , GLY C:140 , ARG C:144BINDING SITE FOR RESIDUE SO4 B1165

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C8E)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ala A:104 -Pro A:105
2Gln A:159 -Gly A:160
3Ala B:104 -Pro B:105
4Gln B:159 -Gly B:160
5Ala C:104 -Pro C:105
6Gln C:159 -Gly C:160

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C8E)

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ISPFPS01350 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.ISPF_BURCJ37-52
 
 		  3A:37-52
B:37-52
C:37-52

(-) Exons   (0, 0)

(no "Exon" information available for 4C8E)

(-) 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:161
 aligned with ISPF_BURCJ | B4EC22 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 
           ISPF_BURCJ     1 MDFRIGQGYDVHQLVEGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDAAFKGADSRVLLRACAERVKAAGFTIQNVDSTVIAQAPKLAPHIDGMRANIAADLGLPLERVNVKAKTNEKLGYLGRGEGIEAQAAALLVKQGG 161
               SCOP domains d4c8ea_ A: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee....eee..eee....ee......hhhhhhhhhhhhhhh...hhhhhh...hhhhh..hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhhh...eee....hhhhhh..eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c8e A   1 MDVRIGQGYDVHQLVEGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDAAFKGADSRVLLRACAERVKAAGFTIQNVDSTVIAQAPKLAPHIDGMRANIAADLGLPLERVNVKAKTNEKLGYLGRGEGIEAQAAALLVKQGG 161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 


Chain B from PDB  Type:PROTEIN  Length:161
 aligned with ISPF_BURCJ | B4EC22 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 
           ISPF_BURCJ     1 MDFRIGQGYDVHQLVEGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDAAFKGADSRVLLRACAERVKAAGFTIQNVDSTVIAQAPKLAPHIDGMRANIAADLGLPLERVNVKAKTNEKLGYLGRGEGIEAQAAALLVKQGG 161
               SCOP domains d4c8eb_ B: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeee...eee..eee...eee......hhhhhhhhhhhhhhh...hhhhhh...hhhhh..hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhhh...eee....hhhhhh..eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c8e B   1 MDVRIGQGYDVHQLVEGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDAAFKGADSRVLLRACAERVKAAGFTIQNVDSTVIAQAPKLAPHIDGMRANIAADLGLPLERVNVKAKTNEKLGYLGRGEGIEAQAAALLVKQGG 161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 


Chain C from PDB  Type:PROTEIN  Length:161
 aligned with ISPF_BURCJ | B4EC22 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 
           ISPF_BURCJ     1 MDFRIGQGYDVHQLVEGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDAAFKGADSRVLLRACAERVKAAGFTIQNVDSTVIAQAPKLAPHIDGMRANIAADLGLPLERVNVKAKTNEKLGYLGRGEGIEAQAAALLVKQGG 161
               SCOP domains d4c8ec_ C: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeee...eee..eee...eee......hhhhhhhhhhhhhhh...hhhhhh...hhhhh..hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhhh...eee....hhhhhh..eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c8e C   1 MDVRIGQGYDVHQLVEGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDAAFKGADSRVLLRACAERVKAAGFTIQNVDSTVIAQAPKLAPHIDGMRANIAADLGLPLERVNVKAKTNEKLGYLGRGEGIEAQAAALLVKQGG 161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   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  (0, 0)

(no "CATH Domain" information available for 4C8E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C8E)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (ISPF_BURCJ | B4EC22)
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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  4c8e
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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_BURCJ | B4EC22: 4c8g 4c8i

(-) Related Entries Specified in the PDB File

4c81 ISPF (PLASMODIUM FALCIPARUM) CDP COMPLEX
4c82 ISPF (PLASMODIUM FALCIPARUM) UNLIGANDED -STRUCTURE
4c8g ISPF (BURKHOLDERIA CENOCEPACIA) CMP COMPLEX
4c8i ISPF (BURKHOLDERIA CENOCEPACIA) CITRATE COMPLEX