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(-) Description

Title :  CRYSTAL STRUCTURE OF 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE FROM BURKHOLDERIA PSEUDOMALLEI WITH CYTIDINE AND FOL955, 4-(1H-IMIDAZOL)-1-YL)PHENOL
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  29 Sep 10  (Deposition) - 20 Oct 10  (Release) - 30 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Ispf, Cytidine, Fol955, Mep Pathway, Isoprene Biosynthesis, Msr, Metal-Binding, Lyase (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 Taxid: 562
    Expression System Vector Type: AVA0421
    Gene: ISPF, BURPS1710B_2511
    Organism Scientific: BURKHOLDERIA PSEUDOMALLEI
    Organism Taxid: 320372
    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  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2CTN3Ligand/Ion4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE
3K1Ligand/IonPOTASSIUM ION
4MSR1Ligand/Ion4-(1H-IMIDAZOL-1-YL)PHENOL
5ZN3Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:103 , ASN A:136 , GLU A:137 , LYS A:138 , GLY A:143BINDING SITE FOR RESIDUE CL A 163
2AC2SOFTWAREASP A:10 , HIS A:12 , HIS A:44 , MSR A:170BINDING SITE FOR RESIDUE ZN A 164
3AC3SOFTWAREASP A:10 , HIS A:12 , HIS A:44 , PHE A:63 , SER A:64 , ASP A:65 , PHE A:70 , ZN A:164 , HOH A:207 , LYS B:134 , CTN B:175BINDING SITE FOR RESIDUE MSR A 170
4AC4SOFTWAREALA 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:230 , ASP C:58 , GLY C:60 , ARG C:61BINDING SITE FOR RESIDUE CTN A 175
5AC5SOFTWAREASP B:10 , HIS B:12 , HIS B:44 , HOH B:176BINDING SITE FOR RESIDUE ZN B 163
6AC6SOFTWAREASP A:58 , GLY A:60 , ARG A:61 , MSR A:170 , 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:182 , HOH B:216 , HOH B:225 , HOH B:244BINDING SITE FOR RESIDUE CTN B 175
7AC7SOFTWAREHOH A:250 , HOH A:285 , HOH B:251 , HOH B:259 , HOH C:179BINDING SITE FOR RESIDUE K C 163
8AC8SOFTWAREHOH A:177 , ASP C:10 , HIS C:12 , HIS C:44BINDING SITE FOR RESIDUE ZN C 164
9AC9SOFTWAREASP 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:202 , HOH C:205BINDING SITE FOR RESIDUE CTN C 175

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P0Z)

(-) 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 3P0Z)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3P0Z)

(-) 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 d3p0za_ A: automated matches                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 3p0z 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:151
 aligned with ISPF_BURP1 | Q3JRA0 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_BURP1     1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDPRFKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVRE 159
               SCOP domains d3p0zb_ B: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee....eee..eee....eee.....hhhhhhhhhhhhhhh...hhhhhh--------..hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhhhh..eee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p0z B   1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHF--------GADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVRE 159
                                    10        20        30        40        50        60  |      - |      80        90       100       110       120       130       140       150         
                                                                                         63       72                                                                                       


Chain C from PDB  Type:PROTEIN  Length:153
 aligned with ISPF_BURP1 | Q3JRA0 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_BURP1     1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSDTDPRFKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVRE 159
               SCOP domains d3p0zc_ C: automated matches                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --YgbB-3p0zC01 C:3-159                                                                                                                                          Pfam domains (1)
           Pfam domains (2) --YgbB-3p0zC02 C:3-159                                                                                                                                          Pfam domains (2)
           Pfam domains (3) --YgbB-3p0zC03 C:3-159                                                                                                                                          Pfam domains (3)
         Sec.struct. author ..eeeeeeeeeeeeee...eee..eee...eee......hhhhhhhhhhhhhhh...hhhhhh------....hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhhhh..eee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p0z C   1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHF------FKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVRE 159
                                    10        20        30        40        50        60  |     70        80        90       100       110       120       130       140       150         
                                                                                         63     70
   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 3P0Z)

(-) 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_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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  4.6.1.12
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 Related Entries

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

UniProtKB/Swiss-Prot
        ISPF_BURP1 | Q3JRA0: 3f0d 3f0e 3f0f 3f0g 3ieq 3jvh 3k14 3k2x 3ke1 3mbm 3p10 3qhd

(-) 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
3ke1 STRUCTURE WITH FRAGMENT-FUSION NUCLEOTIDE
3mbm STRUCTURE WITH CYTOSINE AND FOL717
3p10 RELATED ID: BUPSA.00122.A RELATED DB: TARGETDB