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(-) Description

Title :  STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL SYNTHETASE
 
Authors :  L. E. Kemp, C. S. Bond, W. N. Hunter
Date :  10 Sep 02  (Deposition) - 01 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Isoprenoid, Synthetase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. E. Kemp, C. S. Bond, W. N. Hunter
Structure Of A Tetragonal Crystal Form Of Escherichia Coli 2-C-Methyl-D-Erythritol 4- Phosphate Cytidylyltransferase
Acta Crystallogr. , Sect. D V. 59 607 2003
PubMed-ID: 12595740  |  Reference-DOI: 10.1107/S090744490202365X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE
    Chains: A, B
    EC Number: 2.7.7.60
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 469008
    Strain: BL21(DE3)

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
2N2P1Ligand/IonPENTANE-1,5-DIAMINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:138 , HIS A:162BINDING SITE FOR RESIDUE CL A1230
2AC2SOFTWAREHIS A:162 , ASP B:139 , HIS B:162BINDING SITE FOR RESIDUE CL B1230
3AC3SOFTWAREHIS B:48 , ARG B:50 , HOH B:2011 , HOH B:2012 , HOH B:2013BINDING SITE FOR RESIDUE CL B1231
4AC4SOFTWAREGLN B:114 , HOH B:2027BINDING SITE FOR RESIDUE CL B1232
5AC5SOFTWAREARG A:143 , HIS A:153 , HOH A:2041 , ARG B:143 , HIS B:153 , VAL B:155BINDING SITE FOR RESIDUE N2P A1231

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1H3M)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:165 -Pro A:166
2Thr B:165 -Pro B:166

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H3M)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ISPDPS01295 4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature.ISPD_ECOLI102-109
 		  2A:102-109
B:102-109

(-) Exons   (0, 0)

(no "Exon" information available for 1H3M)

(-) 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:215
 aligned with ISPD_ECOLI | Q46893 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:224
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225    
           ISPD_ECOLI     6 LDVCAVVPAAGFGRRMQTECPKQYLSIGNQTILEHSVHALLAHPRVKRVVIAISPGDSRFAQLPLANHPQITVVDGGDERADSVLAGLKAAGDAQWVLVHDAARPCLHQDDLARLLALSETSRTGGILAAPVRDTMKRAEPGKNAIAHTVDRNGLWHALTPQFFPRELLHDCLTRALNEGATITDEASALEYCGFHPQLVEGRADNIKVTRPEDLALAEFYLTR 229
               SCOP domains d1h3ma_ A:          4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP)                                                                                                                                     SCOP domains
               CATH domains 1h3mA00 A:         6-229 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.---------.hhhh.ee..eehhhhhhhhhhhh..eeeeeeee.........hhhhhh..eeeee...hhhhhhhhhhhh.....eeee........hhhhhhhhhhhhhh....eeeeee...eeeee......eeeee....eeeeeeeeeeehhhhhhhhhhhhhhh....hhhhhhhhh....eeee.........hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h3m A   6 LDVCAVVPAA---------CPKQYLSIGNQTILEHSVHALLAHPRVKRVVIAISPGDSRFAQLPLANHPQITVVDGGDERADSVLTGLKAAGDAQWVLVHDAARPCLHQDDLARLLALSETSRTGGILAAPVRDTMKRAEPGKNAIAHTVDRNGLWHALTPQFFPRELLHDCLTRALNEGATITDEASALEYCGFHPQLVEGRADNIKVTRPEDLALAEFYLTR 229
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225    
                                    15        25                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:218
 aligned with ISPD_ECOLI | Q46893 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:225
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224     
           ISPD_ECOLI     5 HLDVCAVVPAAGFGRRMQTECPKQYLSIGNQTILEHSVHALLAHPRVKRVVIAISPGDSRFAQLPLANHPQITVVDGGDERADSVLAGLKAAGDAQWVLVHDAARPCLHQDDLARLLALSETSRTGGILAAPVRDTMKRAEPGKNAIAHTVDRNGLWHALTPQFFPRELLHDCLTRALNEGATITDEASALEYCGFHPQLVEGRADNIKVTRPEDLALAEFYLTR 229
               SCOP domains d1h3mb_ B: 4       -diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP)                                                                                                                                        SCOP domains
               CATH domains 1h3mB00 B:5-       229 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee..-------..hhhh.ee..eehhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhh..eeeee...hhhhhhhhhhhh.....eeee........hhhhhhhhhhhhhh....eeeeee....eeee......eeeee....eeeeeeeeeeehhhhhhhhhhhhhh.....hhhhhhhhh....eeee...........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h3m B   5 HLDVCAVVPAAG-------ECPKQYLSIGNQTILEHSVHALLAHPRVKRVVIAISPGDSRFAQLPLANHPQITVVDGGDERADSVLTGLKAAGDAQWVLVHDAARPCLHQDDLARLLALSETSRTGGILAAPVRDTMKRAEPGKNAIAHTVDRNGLWHALTPQFFPRELLHDCLTRALNEGATITDEASALEYCGFHPQLVEGRADNIKVTRPEDLALAEFYLTR 229
                                    14 |      24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224     
                                      16      24
   Legend:   → Mismatch (orange background)
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  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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1H3M)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ISPD_ECOLI | Q46893)
molecular function
    GO:0050518    2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity    Catalysis of the reaction: 2-C-methyl-D-erythritol 4-phosphate + CTP = 4-CDP-2-C-methyl-D-erythritol + diphosphate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  ISPD_ECOLI | Q46893
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  2.7.7.60
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 Related Entries

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

UniProtKB/Swiss-Prot
        ISPD_ECOLI | Q46893: 1i52 1ini 1inj 1vgt 1vgu 3n9w

(-) Related Entries Specified in the PDB File

1i52 CRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C -METHYLERYTHRITOL (CDP-ME) SYNTHASE (YGBP) INVOLVED INMEVALONATE INDEPENDENT ISOPRENOID BIOSYNTHESIS
1ini CRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C -METHYLERYTHRITOL (CDP-ME) SYNTHETASE (YGBP) INVOLVED INMEVALONATE INDEPENDENT ISOPRENOID BIOSYNTHESIS, COMPLEXEDWITH CDP-ME AND MG2+
1inj CRYSTAL STRUCTURE OF THE APO FORM OF 4- DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL (CDP-ME ) SYNTHETASE (YGBP) INVOLVED INMEVALONATE INDEPENDENT ISOPRENOID BIOSYNTHESIS