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(-) Description

Title :  CRYSTAL STRUCTURE OF 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE FROM BURKHOLDERIA PSEUDOMALLEI IN COMPLEX WITH 5'-IODO-CYTOSINE
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  30 Sep 09  (Deposition) - 13 Oct 09  (Release) - 30 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Niaid, Ssgcid, Seattle Structural Genomics Center For Infectious Disease, Fragment-Based Drug Design, Fbdd, Fragment Crystallography, Isoprene Biosynthesis, Lyase, Metal-Binding, Fragments Of Life (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  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2I5A3Ligand/Ion5'-DEOXY-5'-IODOCYTIDINE
3K1Ligand/IonPOTASSIUM ION
4ZN3Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:10 , HIS A:12 , HIS A:44 , HOH A:221BINDING SITE FOR RESIDUE ZN A 163
2AC2SOFTWAREALA 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:237 , ASP C:58 , GLY C:60 , ARG C:61BINDING SITE FOR RESIDUE I5A A 164
3AC3SOFTWAREGLN A:103 , ASN A:136 , GLU A:137 , LYS A:138 , GLY A:143BINDING SITE FOR RESIDUE CL A 165
4AC4SOFTWAREHOH A:175 , HOH A:279 , HOH B:199 , HOH B:229BINDING SITE FOR RESIDUE K A 166
5AC5SOFTWAREASP B:10 , HIS B:12 , HIS B:44 , HOH C:223BINDING SITE FOR RESIDUE ZN B 163
6AC6SOFTWAREASP A:58 , GLY A:60 , ASP A:65 , ALA B:102 , PRO B:105 , LYS B:106 , LEU B:107 , ALA B:108 , ALA B:133 , LYS B:134 , HOH B:180 , HOH B:236BINDING SITE FOR RESIDUE I5A B 164
7AC7SOFTWAREHOH A:230 , ASP C:10 , HIS C:12 , HIS C:44BINDING SITE FOR RESIDUE ZN C 163
8AC8SOFTWAREASP 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:134BINDING SITE FOR RESIDUE I5A C 164

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K2X)

(-) 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 3K2X)

(-) 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:38-52

(-) Exons   (0, 0)

(no "Exon" information available for 3K2X)

(-) 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:154
 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 d3k2xa_ A: automated matches                                                                                                                                   SCOP domains
               CATH domains 3k2xA00 A:1-158  [code=3.30.1330.50, no name defined]                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeee...eee..eee...eee......hhhhhhhhhhhhhhh...hhhhhh..----....hhhhhhhhhhhhhhhh..eeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhhhh..eee....hhhhhh..eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k2x A   1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDALFGAAALGDIGRHFSD----FKGADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVR 158
                                    10        20        30        40        50        60    |   70        80        90       100       110       120       130       140       150        
                                                                                           65   70                                                                                        


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 d3k2xb_ B: automated matches                                                                                                                                   SCOP domains
               CATH domains 3k2xB00 B:1-158  [code=3.30.1330.50  , no name defined]                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeee...eee..eee...eeee.--..hhhhhhhhhhhhhhh...hhhhhh......---.hhhhhhhhhhhhhhhh..eeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhhhh..eee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k2x B   1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLG--DADVLLHAITDALFGAAALGDIGRHFSDTDPR---ADSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVR 158
                                    10        20        30    |  |40        50        60        |-  |     80        90       100       110       120       130       140       150        
                                                             35 38                             69  73                                                                                     


Chain C from PDB  Type:PROTEIN  Length:147
 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 d3k2xc_ C: automated matches                                                                                                                                    SCOP domains
               CATH domains 3k2xC00 C:1-159  [code=3.30.1330.50  , no name defined]                                                                                                         CATH domains
           Pfam domains (1) --YgbB-3k2xC01 C:3-159                                                                                                                                          Pfam domains (1)
           Pfam domains (2) --YgbB-3k2xC02 C:3-159                                                                                                                                          Pfam domains (2)
           Pfam domains (3) --YgbB-3k2xC03 C:3-159                                                                                                                                          Pfam domains (3)
         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
                 3k2x C   1 MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLG--DADVLLHAITDALFGAAALGDIGRHF----------DSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVRE 159
                                    10        20        30    |  |40        50        60  |      -   |    80        90       100       110       120       130       140       150         
                                                             35 38                       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  (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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 Related Entries

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

UniProtKB/Swiss-Prot
        ISPF_BURP1 | Q3JRA0: 3f0d 3f0e 3f0f 3f0g 3ieq 3jvh 3k14 3ke1 3mbm 3p0z 3p10 3qhd

(-) Related Entries Specified in the PDB File

3f0e
3ieq STRUCTURE WITH CYTIDINE
3ike STRUCTURE WITH CYTOSINE RELATED ID: BUPSA.00122.A RELATED DB: TARGETDB
3ikf STRUCTURE WITH FRAGMENT 717
3jvh STRUCTURE WITH FRAGMENT 8395
3k14 STRUCTURE WITH FRAGMENT 535