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(-) Description

Title :  CRYSTAL STRUCTURE OF 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE FROM BURKHOLDERIA PSEUDOMALLEI IN COMPLEX WITH CYTIDINE DERIVATIVE EBSI01028
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  06 Jan 11  (Deposition) - 19 Jan 11  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Ispf, Mep Pathway, Lyase, Metal-Binding, Isoprene Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Zhang, S. Jakkaraju, J. Blain, K. Gogol, L. Zhao, R. C. Hartley, C. A. Karlsson, B. L. Staker, T. E. Edwards, L. J. Stewart, P. J. Myler, M. Clare, D. W. Begley, J. R. Horn, T. J. Hagen
Cytidine Derivatives As Ispf Inhibitors Of Burkolderia Pseudomallei.
Bioorg. Med. Chem. Lett. V. 23 6860 2013
PubMed-ID: 24157367  |  Reference-DOI: 10.1016/J.BMCL.2013.09.101
(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 Taxid: 562
    Expression System Vector Type: AVA0421
    Gene: ISPF, MECS, BPSL2098
    Organism Common: PSEUDOMONAS PSEUDOMALLEI
    Organism Scientific: BURKHOLDERIA PSEUDOMALLEI
    Organism Taxid: 28450
    Strain: 1710B
    Synonym: MECDP-SYNTHASE, MECPS

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1AO93Ligand/Ion5'-DEOXY-5'-[(IMIDAZO[2,1-B][1,3]THIAZOL-5-YLCARBONYL)AMINO]CYTIDINE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3K1Ligand/IonPOTASSIUM ION
4ZN3Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:10 , HIS A:12 , HIS A:44 , HOH B:166BINDING SITE FOR RESIDUE ZN A 163
2AC2SOFTWAREHIS A:36 , ASP A:58 , ILE A:59 , GLY A:60 , PHE A:63 , HOH A:169 , HOH A:171 , HOH A:180 , HOH A:209 , ALA B:102 , PRO B:105 , LYS B:106 , LEU B:107 , ALA B:108 , ALA B:133 , LYS B:134 , HOH B:166BINDING SITE FOR RESIDUE AO9 A 165
3AC3SOFTWAREHOH A:285 , HOH B:286 , HOH C:287BINDING SITE FOR RESIDUE K A 170
4AC4SOFTWAREALA A:120 , ASP A:121 , HOH A:224BINDING SITE FOR RESIDUE EDO A 172
5AC5SOFTWAREALA A:92 , ILE A:93 , LEU A:122 , ASP A:123 , HOH A:259BINDING SITE FOR RESIDUE EDO A 173
6AC6SOFTWAREALA 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:195 , HOH A:266 , HOH A:293 , HIS C:36 , ASP C:58 , ILE C:59 , GLY C:60 , ARG C:61 , PHE C:63BINDING SITE FOR RESIDUE AO9 A 164
7AC7SOFTWAREASP B:10 , HIS B:12 , HIS B:44 , HOH B:291BINDING SITE FOR RESIDUE ZN B 163
8AC8SOFTWAREHIS B:36 , ASP B:58 , ILE B:59 , GLY B:60 , ARG B:61 , PHE B:63 , LEU B:78 , HOH B:175 , HOH B:178 , HOH B:290 , HOH B:291 , ALA C:102 , PRO C:105 , LYS C:106 , LEU C:107 , ALA C:108 , ALA C:133 , LYS C:134BINDING SITE FOR RESIDUE AO9 B 165
9AC9SOFTWAREHOH A:195 , ASP C:10 , HIS C:12 , HIS C:44BINDING SITE FOR RESIDUE ZN C 163

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q8H)

(-) 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 3Q8H)

(-) 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:37-52
C:37-52

(-) Exons   (0, 0)

(no "Exon" information available for 3Q8H)

(-) 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:151
 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 d3q8ha_ A: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeee...eee..eee...eee......hhhhhhhhhhhhhhh...hhhhhh.--------.hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhhhh..eee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q8h A   1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFS--------ADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVRE 159
                                    10        20        30        40        50        60   |     -  |     80        90       100       110       120       130       140       150         
                                                                                          64       73                                                                                      


Chain B from PDB  Type:PROTEIN  Length:155
 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 d3q8hb_ B: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeee...eee..eee...eeee.....hhhhhhhhhhhhhhh...hhhhhh----......hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhhhh..eee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q8h B   1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHF----PRFKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVRE 159
                                    10        20        30        40        50        60  |    |70        80        90       100       110       120       130       140       150         
                                                                                         63   68                                                                                           


Chain C 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 d3q8hc_ C: automated matches                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --YgbB-3q8hC01 C:3-158                                                                                                                                         Pfam domains (1)
           Pfam domains (2) --YgbB-3q8hC02 C:3-158                                                                                                                                         Pfam domains (2)
           Pfam domains (3) --YgbB-3q8hC03 C:3-158                                                                                                                                         Pfam domains (3)
         Sec.struct. author ..eeeeeeeeeeeeee...eee..eee...eee......hhhhhhhhhhhhhhh...hhhhhh..........hhhhhhhhhhhhhhhh..eeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhhhh..eee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q8h C   1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDPRFKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVR 158
                                    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, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q8H)

(-) Pfam Domains  (1, 3)

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

(-) 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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  ISPF_BURPS | Q63T71
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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_BURPS | Q63T71: 3f0d 3f0e 3f0f 3f0g 3ieq 3iew 3ike 3ikf 3jvh 3k14 3ke1 3mbm

(-) Related Entries Specified in the PDB File

3f0d APO STRUCTURE
3ieq STRUCTURE WITH CYTIDINE
3ike STRUCTURE WITH CYTOSINE
3ikf STRUCTURE WITH FOL717
3jvh STRUCTURE WITH FOL8395
3k14 STRUCTURE WITH FOL535 RELATED ID: BUPSA.00122.A RELATED DB: TARGETDB
3ke1 STRUCTURE WITH CYTIDINE DERIVATIVE D161829
3mbm STRUCTURE WITH CYTOSINE AND FOL717
3p0z STRUCTURE WITH CYTIDINE AND FOL955