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(-) Description

Title :  CRYSTAL STRUCTURE OF 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE ISPF COMPLEXED WITH CYTIDINE TRIPHOSPHATE
 
Authors :  Y. Kim, N. Maltseva, J. Stam, W. F. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
Date :  05 Jan 09  (Deposition) - 03 Feb 09  (Release) - 03 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Csgid, Alpha-Beta Sandwich, Isoprene Biosynthesis, Lyase, Metal-Binding, Structural Genomics, Structural Genomics Of National Institute Of Allergy And Infectious Diseases, Center For Structural Genomics Of Infectious Diseases (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, N. Maltseva, J. Stam, W. F. Anderson, A. Joachimiak
Crystal Structure Of 2-C-Methyl-D-Erythritol 2, 4-Cyclodiphosphate Synthase Ispf Complexed With Cytidine Triphosphate
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE
    Chains: A
    EC Number: 4.6.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19C
    Expression System Strain: BL21DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ISPF, Y0829, YPO3360, YPTB0771, YP_0327
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 214092
    Strain: CO92
    Synonym: MECPS, MECDP-SYNTHASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 10)

Asymmetric Unit (6, 10)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2CTP1Ligand/IonCYTIDINE-5'-TRIPHOSPHATE
3EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4MG2Ligand/IonMAGNESIUM ION
5MSE4Mod. Amino AcidSELENOMETHIONINE
6SO41Ligand/IonSULFATE ION
Biological Unit 1 (4, 21)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CTP3Ligand/IonCYTIDINE-5'-TRIPHOSPHATE
3EPE3Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4MG-1Ligand/IonMAGNESIUM ION
5MSE12Mod. Amino AcidSELENOMETHIONINE
6SO43Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:8 , HIS A:10 , ALA A:35 , HIS A:36 , ASP A:58 , GLY A:60 , ASP A:65 , ALA A:102 , PRO A:105 , LYS A:106 , MSE A:107 , ALA A:108 , ALA A:133 , THR A:134 , THR A:135 , GLU A:137 , MG A:167 , HOH A:175 , HOH A:178 , HOH A:196 , HOH A:235BINDING SITE FOR RESIDUE CTP A 163
2AC2SOFTWAREPRO A:19 , ARG A:26 , PRO A:28 , TYR A:29 , LYS A:61 , ARG A:115 , MSE A:126 , ASP A:127 , HOH A:234BINDING SITE FOR RESIDUE EPE A 164
3AC3SOFTWAREARG A:144 , MG A:168BINDING SITE FOR RESIDUE CL A 165
4AC4SOFTWAREARG A:80BINDING SITE FOR RESIDUE SO4 A 166
5AC5SOFTWAREALA A:35 , HIS A:36 , SER A:37 , GLY A:39 , HIS A:44 , CTP A:163BINDING SITE FOR RESIDUE MG A 167
6AC6SOFTWARECL A:165 , HOH A:230BINDING SITE FOR RESIDUE MG A 168

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:104 -Pro A:105

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FPI)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ISPFPS01350 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.ISPF_YERPE37-52  1A:37-52
ISPF_YERPS37-52  1A:37-52
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ISPFPS01350 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.ISPF_YERPE37-52  3A:37-52
ISPF_YERPS37-52  3A:37-52

(-) Exons   (0, 0)

(no "Exon" information available for 3FPI)

(-) Sequences/Alignments

Asymmetric 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_YERPE | Q8ZBP7 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:161
                              1                                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158 
           ISPF_YERPE     - --MRIGHGFDVHKFGENGSGPLIIGGVRIPYEKGLLAHSDGDVALHAATDALLGAAALGDIGKLFPDTDPAFKGADSRGLLREAYRRILAKGYKLGNLDITIIAQAPKMAPHIPQMRVNLAEDLQCHMDDINVKATTTEQLGFTGRGEGIACEAVVLLVNV 159
               SCOP domains d3fpia_ A: automated matches                                                                                                                                      SCOP domains
               CATH domains 3fpiA00 A:-1-159  [code=3.30.1330.50, no name defined]                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee........eee..eee............hhhhhhhhhhhhhhh...hhhhhh...hhhhh..hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhh..hhh.eeeeee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------ISPF            ----------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fpi A  -1 NAmRIGHGFDVHKFGENGSGPLIIGGVRIPYEKGLLAHSDGDVALHAATDALLGAAALGDIGKLFPDTDPAFKGADSRGLLREAYRRILAKGYKLGNLDITIIAQAPKmAPHIPQmRVNLAEDLQCHmDDINVKATTTEQLGFTGRGEGIACEAVVLLVNV 159
                              |      8        18        28        38        48        58        68        78        88        98       108     | 118       128       138       148       158 
                              |                                                                                                       107-MSE  |         126-MSE                             
                              1-MSE                                                                                                          114-MSE                                         


Chain A from PDB  Type:PROTEIN  Length:161
 aligned with ISPF_YERPS | Q66EC2 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:161
                              1                                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158 
           ISPF_YERPS     - --MRIGHGFDVHKFGENGSGPLIIGGVRIPYEKGLLAHSDGDVALHAATDALLGAAALGDIGKLFPDTDPAFKGADSRGLLREAYRRILAKGYKLGNLDITIIAQAPKMAPHIPQMRVNLAEDLQCHMDDINVKATTTEQLGFTGRGEGIACEAVVLLVNV 159
               SCOP domains d3fpia_ A: automated matches                                                                                                                                      SCOP domains
               CATH domains 3fpiA00 A:-1-159  [code=3.30.1330.50, no name defined]                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee........eee..eee............hhhhhhhhhhhhhhh...hhhhhh...hhhhh..hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhh..hhh.eeeeee....hhhhhh..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------ISPF            ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fpi A  -1 NAmRIGHGFDVHKFGENGSGPLIIGGVRIPYEKGLLAHSDGDVALHAATDALLGAAALGDIGKLFPDTDPAFKGADSRGLLREAYRRILAKGYKLGNLDITIIAQAPKmAPHIPQmRVNLAEDLQCHmDDINVKATTTEQLGFTGRGEGIACEAVVLLVNV 159
                              |      8        18        28        38        48        58        68        78        88        98       108     | 118       128       138       148       158 
                              1-MSE                                                                                                   107-MSE  |         126-MSE                             
                                                                                                                                             114-MSE
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (ISPF_YERPS | Q66EC2)
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   (ISPF_YERPE | Q8ZBP7)
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_YERPE | Q8ZBP7: 3f6m

(-) Related Entries Specified in the PDB File

3f6m CRYSTAL STRUCTURE OF 2-C-METHYL-D-ERYTHRITOL 2,4- CYCLODIPHOSPHATE SYNTHASE ISPF FROM YERSINIA PESTIS RELATED ID: IDP00520 RELATED DB: TARGETDB