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(-) Description

Title :  SYNTHESIS OF CDP-ACTIVATED RIBITOL FOR TEICHOIC ACID PRECURSORS IN STREPTOCOCCUS PNEUMONIAE
 
Authors :  S. Baur, J. Marles-Wright, S. Buckenmaier, R. J. Lewis, W. Vollmer
Date :  23 Apr 08  (Deposition) - 30 Dec 08  (Release) - 10 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Spr1149 Tari Cdp Ribitol Streptococcus Pneumoniae, Nucleotidyltransferase, Transferase, Isoprene Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Baur, J. Marles-Wright, S. Buckenmaier, R. J. Lewis, W. Vollmer
Synthesis Of Cdp-Activated Ribitol For Teichoic Acid Precursors In Streptococcus Pneumoniae.
J. Bacteriol. V. 191 1200 2009
PubMed-ID: 19074383  |  Reference-DOI: 10.1128/JB.01120-08

(-) Compounds

Molecule 1 - 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE
    Atcc: 12214
    Chains: A, B
    EC Number: 2.7.7.60
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313
    Strain: R36A
    Synonym: TARI

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CDF2Ligand/Ion4-AMINO-1-{5-O-[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]-ALPHA-D-ARABINOFURANOSYL}PYRIMIDIN-2(1H)-ONE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:7 , ALA A:8 , GLY A:9 , GLY A:10 , GLY A:82 , ALA A:83 , ASP A:84 , ARG A:85 , SER A:88 , ASP A:112 , SER A:113 , VAL A:114 , LYS A:218BINDING SITE FOR RESIDUE CDF A1234
2AC2SOFTWARELEU B:7 , ALA B:8 , GLY B:9 , GLN B:23 , GLY B:82 , ALA B:83 , ASP B:84 , ARG B:85 , SER B:88 , ASP B:112 , SER B:113 , VAL B:114 , LYS B:218 , THR B:220BINDING SITE FOR RESIDUE CDF B1233
3AC3SOFTWAREGLU B:105BINDING SITE FOR RESIDUE CA B1234

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VSI)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:169 -Pro A:170
2Thr B:169 -Pro B:170

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VSI)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ISPDPS01295 4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature.TARI_STRR6108-115
 		  2A:108-115
B:108-115

(-) Exons   (0, 0)

(no "Exon" information available for 2VSI)

(-) 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:225
 aligned with TARI_STRR6 | Q8DPI2 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:234
                             1                                                                                                                                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229    
           TARI_STRR6     - -MIYAGILAGGTGTRMGISNLPKQFLELGDRPILIHTIEKFVLEPSIEKIVVGVHGDWVSHAEDLVDKYLPLYKERIIITKGGADRNTSIKNIIEAIDAYRPLTPEDIVVTHDSVRPFITLRMIQDNIQLAQNHDAVDTVVEAVDTIVESTNGQFITDIPNRAHLYQGQTPQTFRCKDFMDLYGSLSDEEKEILTDACKIFVIKGKDVALAKGEYSNLKITTVTDLKIAKSMIE 233
               SCOP domains d2vsia_ A: a         utomated matches                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee...---------hhhh.ee..eehhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhhh......eeeeee......hhhhhhhhhhhh....eeeeeee....eee...............eeeeeeeeeeehhhhhhhh...hhhhhhhh.hhhhhhhhh...eeeee.........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ISPD    ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vsi A   0 HMIYAGILAGGT---------PKQFLELGDRPILIHTIEKFVLEPSIEKIVVGVHGDWVSHAEDLVDKYLPLYKERIIITKGGADRNTSIKNIIEAIDAYRPLTPEDIVVTHDSVRPFITLRMIQDNIQLAQNHDAVDTVVEAVDTIVESTNGQFITDIPNRAHLYQGQTPQTFRCKDFMDLYGSLSDEEKEILTDACKIFVIKGKDVALAKGEYSNLKITTVTDLKIAKSMIE 233
                                     9 |       - |      29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229    
                                      11        21                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:227
 aligned with TARI_STRR6 | Q8DPI2 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:233
                             1                                                                                                                                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229   
           TARI_STRR6     - -MIYAGILAGGTGTRMGISNLPKQFLELGDRPILIHTIEKFVLEPSIEKIVVGVHGDWVSHAEDLVDKYLPLYKERIIITKGGADRNTSIKNIIEAIDAYRPLTPEDIVVTHDSVRPFITLRMIQDNIQLAQNHDAVDTVVEAVDTIVESTNGQFITDIPNRAHLYQGQTPQTFRCKDFMDLYGSLSDEEKEILTDACKIFVIKGKDVALAKGEYSNLKITTVTDLKIAKSMI 232
               SCOP domains d2vsib_ B: aut      omated matches                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......------......ee..eehhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhhh......eeeeee......hhhhhhhhhhhhh...eeeeeee....eee...........hhh.eeeeeeeeeeehhhhhhhhhhh..hhhhhh.hhhhhhhhh...eeeee.........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ISPD    --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vsi B   0 HMIYAGILAGGTGT------LPKQFLELGDRPILIHTIEKFVLEPSIEKIVVGVHGDWVSHAEDLVDKYLPLYKERIIITKGGADRNTSIKNIIEAIDAYRPLTPEDIVVTHDSVRPFITLRMIQDNIQLAQNHDAVDTVVEAVDTIVESTNGQFITDIPNRAHLYQGQTPQTFRCKDFMDLYGSLSDEEKEILTDACKIFVIKGKDVALAKGEYSNLKITTVTDLKIAKSMI 232
                                     9   |     -|       29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229   
                                        13     20
   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  (0, 0)

(no "CATH Domain" information available for 2VSI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2VSI)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TARI_STRR6 | Q8DPI2)
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: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.

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 Related Entries

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        TARI_STRR6 | Q8DPI2: 2vsh

(-) Related Entries Specified in the PDB File

2vsh SYNTHESIS OF CDP-ACTIVATED RIBITOL FOR TEICHOIC ACID PRECURSORS IN STREPTOCOCCUS PNEUMONIAE