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(-) Description

Title :  CRYSTAL STRUCTURE OF 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE FROM BURKHOLDERIA PSEUDOMALLEI WITH CYTIDINE
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  23 Jul 09  (Deposition) - 04 Aug 09  (Release) - 30 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Niaid, Isoprene Biosynthesis, Lyase, Metal-Binding, Structural Genomics, 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
    ChainsA, B, C
    EC Number4.6.1.12
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidAVA0421
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneISPF, MECS, BPSL2098
    Organism CommonPSEUDOMONAS PSEUDOMALLEI
    Organism ScientificBURKHOLDERIA PSEUDOMALLEI
    Organism Taxid28450
    Strain1710B
    SynonymMECPS, MECDP-SYNTHASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1C3Ligand/IonCYTIDINE-5'-MONOPHOSPHATE
2CL1Ligand/IonCHLORIDE ION
3MG1Ligand/IonMAGNESIUM ION
4ZN3Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:102 , PRO A:105 , LYS A:106 , LEU A:107 , ALA A:108 , ALA A:133 , LYS A:134 , HOH A:211 , HOH A:221 , HOH A:254 , ASP C:58 , GLY C:60 , ARG C:61BINDING SITE FOR RESIDUE C A 901
2AC2SOFTWAREASP A:10 , HIS A:12 , HIS A:44 , HOH A:223BINDING SITE FOR RESIDUE ZN A 163
3AC3SOFTWAREGLN A:103 , THR A:135 , ASN A:136 , GLU A:137 , LYS A:138 , GLY A:143BINDING SITE FOR RESIDUE CL A 164
4AC4SOFTWAREHOH A:228 , GLU B:149 , HOH B:208 , HOH B:214 , HOH C:226 , HOH C:227BINDING SITE FOR RESIDUE MG B 163
5AC5SOFTWAREASP A:58 , GLY A:60 , ARG A:61 , ASP A:65 , 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:200 , HOH B:250 , HOH B:251BINDING SITE FOR RESIDUE C B 901
6AC6SOFTWAREASP B:10 , HIS B:12 , HIS B:44 , HOH C:224BINDING SITE FOR RESIDUE ZN B 164
7AC7SOFTWAREASP B:58 , GLY B:60 , ARG B:61 , ALA C:102 , PRO C:105 , LYS C:106 , LEU C:107 , ALA C:108 , ALA C:133 , LYS C:134 , HOH C:211 , HOH C:257 , HOH C:258BINDING SITE FOR RESIDUE C C 901
8AC8SOFTWAREASP C:10 , HIS C:12 , HIS C:44 , HOH C:225BINDING SITE FOR RESIDUE ZN C 163

(-) SS Bonds  (0, 0)

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

(-) 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 3IEQ)

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ISPFPS01350 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.ISPF_BURP137-52
 
 
  3A:37-52
B:38-52
C:37-52
ISPF_BURPS37-52
 
 
  3A:37-52
B:38-52
C:37-52

(-) Exons   (0, 0)

(no "Exon" information available for 3IEQ)

(-) 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:158
 aligned with ISPF_BURP1 | Q3JRA0 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_BURP1     1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDPRFKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVR 158
               SCOP domains d3ieqa_ A: automated matches                                                                                                                                   SCOP domains
               CATH domains 3ieqA00 A:1-158  [code=3.30.1330.50, no name defined]                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeee...eee..eee...eee......hhhhhhhhhhhhhhh...hhhhhh...hhhhh..hhhhhhhhhhhhhhhh..eeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhhhh..eee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ieq A   1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDPRFKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVR 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        

Chain A from PDB  Type:PROTEIN  Length:158
 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 d3ieqa_ A: automated matches                                                                                                                                   SCOP domains
               CATH domains 3ieqA00 A:1-158  [code=3.30.1330.50, no name defined]                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeee...eee..eee...eee......hhhhhhhhhhhhhhh...hhhhhh...hhhhh..hhhhhhhhhhhhhhhh..eeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhhhh..eee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ieq A   1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDPRFKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVR 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        

Chain B from PDB  Type:PROTEIN  Length:153
 aligned with ISPF_BURP1 | Q3JRA0 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_BURP1     1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDPRFKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVR 158
               SCOP domains d3ieqb_ B: automated matches                                                                                                                                   SCOP domains
               CATH domains 3ieqB00 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.---..hhhhhhhhhhhhhhh...hhhhhh.......--.hhhhhhhhhhhhhhhh..eeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhhhh..eee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ieq B   1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLL---DADVLLHAITDALFGAAALGDIGRHFSDTDPRF--ADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVR 158
                                    10        20        30   |   |40        50        60        70  |     80        90       100       110       120       130       140       150        
                                                            34  38                              70 73                                                                                     

Chain B from PDB  Type:PROTEIN  Length:153
 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 d3ieqb_ B: automated matches                                                                                                                                   SCOP domains
               CATH domains 3ieqB00 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.---..hhhhhhhhhhhhhhh...hhhhhh.......--.hhhhhhhhhhhhhhhh..eeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhhhh..eee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ieq B   1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLL---DADVLLHAITDALFGAAALGDIGRHFSDTDPRF--ADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVR 158
                                    10        20        30   |   |40        50        60        70  |     80        90       100       110       120       130       140       150        
                                                            34  38                              70 73                                                                                     

Chain C from PDB  Type:PROTEIN  Length:148
 aligned with ISPF_BURP1 | Q3JRA0 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_BURP1     1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDPRFKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVR 158
               SCOP domains d3ieqc_ C: automated matches                                                                                                                                   SCOP domains
               CATH domains 3ieqC00 C:1-158  [code=3.30.1330.50, no name defined]                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeee...eee..eee...eee......hhhhhhhhhhhhhhh...hhhhhh----------hhhhhhhhhhhhhhhh..eeeeeeeeee.....hhhhhhhhhhhhhhhh..hhhhh..eee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ieq C   1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHF----------DSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVR 158
                                    10        20        30        40        50        60  |      -   |    80        90       100       110       120       130       140       150        
                                                                                         63         74                                                                                    

Chain C from PDB  Type:PROTEIN  Length:148
 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 d3ieqc_ C: automated matches                                                                                                                                   SCOP domains
               CATH domains 3ieqC00 C:1-158  [code=3.30.1330.50, no name defined]                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeee...eee..eee...eee......hhhhhhhhhhhhhhh...hhhhhh----------hhhhhhhhhhhhhhhh..eeeeeeeeee.....hhhhhhhhhhhhhhhh..hhhhh..eee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ieq C   1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHF----------DSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVR 158
                                    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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 12)

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.

Chain A,B,C   (ISPF_BURP1 | Q3JRA0)
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_BURP1 | Q3JRA03f0d 3f0e 3f0f 3f0g 3jvh 3k14 3k2x 3ke1 3mbm 3p0z 3p10 3qhd
        ISPF_BURPS | Q63T713f0d 3f0e 3f0f 3f0g 3iew 3ike 3ikf 3jvh 3k14 3ke1 3mbm 3q8h

(-) Related Entries Specified in the PDB File

3f0d HIGH RESOLUTION APO STRUCTURE FROM DIFFERENT CRYSTAL FORM
3f0e APO CRYSTAL STRUCTURE IN SAME CRYSTAL FORM
3f0f STRUCTURE WITH HYDROLYZED CDP
3f0g STRUCTURE WITH CMP
3iew CRYSTAL STRUCTURE WITH CTP RELATED ID: BUPSA.00122.A RELATED DB: TARGETDB