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(-) Description

Title :  CRYSTAL STRUCTURE OF 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE FROM THERMUS THERMOPHILUS HB8
 
Authors :  L. Chen, M. Tsukuda, A. Ebihara, A. Shinkai, S. Kuramitsu, S. Yokoyama, L-Q. Chen, Z-J. Liu, D. Lee, S-H. Chang, D. Nguyen, J. P. Rose, B-C. Wang Southeast Collaboratory For Structural Genomics (Secsg), Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  14 May 07  (Deposition) - 12 Jun 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ttha0171, 2-C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase, Ispd_thet8, Ispd, Structural Genomics, Psi, Protein Structure Initiative, Southeast Collaboratory For Structural Genomics, Secsg, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Chen, M. Tsukuda, A. Ebihara, A. Shinkai, S. Kuramitsu, S. Yokoyama, L-Q. Chen, Z-J. Liu, D. Lee, S-H. Chang, D. Nguyen, J. P. Rose, B-C. Wang
Crystal Structure Of 2-C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase From Thermus Thermophilus Hb8.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE
    Atcc: 27634
    Chains: A, B
    EC Number: 2.7.7.60
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-19B
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ISPD, TTHA0171
    Organism Scientific: THERMUS THERMOPHILUS HB8
    Organism Taxid: 300852
    Strain: HB8, DSM 579
    Synonym: 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL SYNTHASE, MEP CYTIDYLYLTRANSFERASE, MCT

 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 2PX7)

(-) Sites  (0, 0)

(no "Site" information available for 2PX7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PX7)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Glu A:130 -Ala A:131
2Ala A:131 -Tyr A:132
3Thr A:146 -Pro A:147
4Thr B:146 -Pro B:147

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PX7)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ISPDPS01295 4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature.ISPD_THET886-93
 		  2A:86-93
B:86-93

(-) Exons   (0, 0)

(no "Exon" information available for 2PX7)

(-) 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:203
 aligned with ISPD_THET8 | Q5SLX2 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
           ISPD_THET8     1 MEVSVLIPAAGNGLRLGRGPKAFLQVGGRTLLEWTLAAFRDAAEVLVALPPGAEPPKGLGAVFLEGGATRQASVARLLEAASLPLVLVHDVARPFVSRGLVARVLEAAQRSGAAVPVLPVPDTLMAPEGEAYGRVVPREAFRLVQTPQGFFTALLREAHAYARRKGLEASDDAQLVQALGYPVALVEGEATAFKITHPQDLVLAEALARV 210
               SCOP domains d2px7a_ A:        automated matches                                                                                                                                                                                SCOP domains
               CATH domains 2px7A00 A:1       -210 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee...-------.hhhhh.....hhhhhhhhhh....eeeeee............eeee...hhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhheeeeeee...eeeee.....eeeehhhh.eee...eeeehhhhhhhhhhhhhhh....hhhhhhhhh....eeee.........hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------ISPD    --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2px7 A   1 MEVSVLIPAAG-------GPKAFLQVGGRTLLEWTLAAFRDAAEVLVALPPGAEPPKGLGAVFLEGGATRQASVARLLEAASLPLVLVHDVARPFVSRGLVARVLEAAQRSGAAVPVLPVPDTLMAPEGEAYGRVVPREAFRLVQTPQGFFTALLREAHAYARRKGLEASDDAQLVQALGYPVALVEGEATAFKITHPQDLVLAEALARV 210
                                    10|       20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
                                     11      19                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:202
 aligned with ISPD_THET8 | Q5SLX2 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
           ISPD_THET8     1 MEVSVLIPAAGNGLRLGRGPKAFLQVGGRTLLEWTLAAFRDAAEVLVALPPGAEPPKGLGAVFLEGGATRQASVARLLEAASLPLVLVHDVARPFVSRGLVARVLEAAQRSGAAVPVLPVPDTLMAPEGEAYGRVVPREAFRLVQTPQGFFTALLREAHAYARRKGLEASDDAQLVQALGYPVALVEGEATAFKITHPQDLVLAEALARV 210
               SCOP domains d2px7b_ B:         automated matches                                                                                                                                                                               SCOP domains
               CATH domains 2px7B00 B:1        -210 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                               CATH domains
           Pfam domains (1) --IspD-2px7        B01 B:3-210                                                                                                                                                                                     Pfam domains (1)
           Pfam domains (2) --IspD-2px7        B02 B:3-210                                                                                                                                                                                     Pfam domains (2)
         Sec.struct. author ...eeee....--------hhhh.ee..eehhhhhhhhh....eeeeee............eeee...hhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhheeeeeee...eeeeee..eeeeeehhhh.eee...eeeehhhhhhhhhhhhhhh....hhhhhhhh.....eeee.hhhhh...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------ISPD    --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2px7 B   1 MEVSVLIPAAG--------PKAFLQVGGRTLLEWTLAAFRDAAEVLVALPPGAEPPKGLGAVFLEGGATRQASVARLLEAASLPLVLVHDVARPFVSRGLVARVLEAAQRSGAAVPVLPVPDTLMAPEGEAYGRVVPREAFRLVQTPQGFFTALLREAHAYARRKGLEASDDAQLVQALGYPVALVEGEATAFKITHPQDLVLAEALARV 210
                                    10|       20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
                                     11       20
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 2)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ISPD_THET8 | Q5SLX2)
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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  Cis Peptide Bonds
    Ala A:131 - Tyr A:132   [ RasMol ]  
    Glu A:130 - Ala A:131   [ RasMol ]  
    Thr A:146 - Pro A:147   [ RasMol ]  
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