Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL SYNTHASE
 
Authors :  Structural Genomix
Date :  03 Nov 03  (Deposition) - 25 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
PubMed-ID: 16021622  |  Reference-DOI: 10.1002/PROT.20541
(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 Taxid: 562
    Gene: ISPD, B2747
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL SYNTHASE, MEP CYTIDYLYLTRANSFERASE, MCT, CDP-ME SYNTHETASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1VGU)

(-) Sites  (0, 0)

(no "Site" information available for 1VGU)

(-) SS Bonds  (0, 0)

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

(-) 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 1VGU)

(-) 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 1VGU)

(-) 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:214
 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 d1vgua_ A          : 4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP)                                                                                                                                    SCOP domains
               CATH domains 1vguA00 A          :6-229 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..----------......ee..eehhhhhhhhhhh...eeeeeeee.....hhhhhhhhhh..eeeee...hhhhhhhhhhhh.....eeee........hhhhhhhhhhhhhh....eeeeee....eeee......eeeee....eeeeeeeeeeehhhhhhhhhhhhhh......hhhhhhhh....eeee.........hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vgu A   6 LDVCAVVPA----------CPKQYLSIGNQTILEHSVHALLAHPRVKRVVIAISPGDSRFAQLPLANHPQITVVDGGDERADSVLAGLKAAGDAQWVLVHDAARPCLHQDDLARLLALSETSRTGGILAAPVRDTMKRAEPGKNAIAHTVDRNGLWHALTPQFFPRELLHDCLTRALNEGATITDEASALEYCGFHPQLVEGRADNIKVTRPEDLALAEFYLTR 229
                                    |-        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225    
                                   14         25                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:196
 aligned with ISPD_ECOLI | Q46893 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:222
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227  
           ISPD_ECOLI     8 VCAVVPAAGFGRRMQTECPKQYLSIGNQTILEHSVHALLAHPRVKRVVIAISPGDSRFAQLPLANHPQITVVDGGDERADSVLAGLKAAGDAQWVLVHDAARPCLHQDDLARLLALSETSRTGGILAAPVRDTMKRAEPGKNAIAHTVDRNGLWHALTPQFFPRELLHDCLTRALNEGATITDEASALEYCGFHPQLVEGRADNIKVTRPEDLALAEFYLTR 229
               SCOP domains d1vgub_                     B: 4-diphosphocytidyl-2C-methyl-D      -erythritol (CDP-me) synthase (IspD, YgbP)                                                                                                                  SCOP domains
               CATH domains 1vguB00                     B:8-229 Spore Coat Polysaccharide       Biosynthesis Protein SpsA; Chain A                                                                                                                         CATH domains
           Pfam domains (1) IspD-1v                    guB01 B:8-229                                                                                                                                                                                       Pfam domains (1)
           Pfam domains (2) IspD-1v                    guB02 B:8-229                                                                                                                                                                                       Pfam domains (2)
         Sec.struct. author .eeee..--------------------.hhhhhhhhhhhh.....eeee......hhhhhh------.ee......hhhhhhhhhhhhhh...eeee........hhhhhhhhhh........eeeeee....eeee......eeeee....eeeeeeeeeeehhhhhhhhhhhhhhh....hhhhhhhhh....eeee...........hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vgu B   8 VCAVVPA--------------------QTILEHSVHALLAHPRVKRVVIAISPGDSRFAQL------QITVVDGGDERADSVLAGLKAAGDAQWVLVHDAARPCLHQDDLARLLALSETSRTGGILAAPVRDTMKRAEPGKNAIAHTVDRNGLWHALTPQFFPRELLHDCLTRALNEGATITDEASALEYCGFHPQLVEGRADNIKVTRPEDLALAEFYLTR 229
                                  |  -         -       |37        47        57        67|      |77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227  
                                 14                   35                               68     75
   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, 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  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: GT-A (172)

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1vgu)
 
  Sites
(no "Sites" information available for 1vgu)
 
  Cis Peptide Bonds
    Thr A:165 - Pro A:166   [ RasMol ]  
    Thr B:165 - Pro B:166   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1vgu
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ISPD_ECOLI | Q46893
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.7.60
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  ISPD_ECOLI | Q46893
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ISPD_ECOLI | Q46893: 1h3m 1i52 1ini 1inj 1vgt 3n9w

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1VGU)