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(-) Description

Title :  CRYSTAL STRUCTURE OF 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE (TM1393) FROM THERMOTOGA MARITIMA AT 2.67 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  14 Oct 04  (Deposition) - 02 Nov 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.67
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tm1393, 2-C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase, Structural Genomics, Jcsg, Joint Center For Structural Genomics, Psi, Protein Structure Initiative, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of 2-C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase (Tm1393) From Thermotoga Maritima At 2. 67 A Resolution
To Be Published
PubMed: search

(-) 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
    Expression System Vector Type: PLASMID
    Gene: TM1393, ISPD
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    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  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2CTP2Ligand/IonCYTIDINE-5'-TRIPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECTP A:500 , HOH A:749BINDING SITE FOR RESIDUE MG A 600
2AC2SOFTWARECTP B:500BINDING SITE FOR RESIDUE MG B 600
3AC3SOFTWARELEU A:7 , ALA A:8 , ALA A:9 , GLY A:10 , LYS A:11 , GLY A:12 , GLU A:13 , ARG A:14 , LYS A:21 , GLY A:76 , ASP A:77 , THR A:78 , ARG A:79 , SER A:82 , ASP A:102 , SER A:103 , ALA A:104 , LYS A:201 , MG A:600 , ACY A:700 , HOH A:705 , HOH A:751 , HOH A:762 , HOH A:769BINDING SITE FOR RESIDUE CTP A 500
4AC4SOFTWARELEU B:7 , ALA B:8 , ALA B:9 , GLY B:10 , LYS B:11 , GLY B:12 , GLU B:13 , ARG B:14 , LYS B:21 , GLY B:76 , ASP B:77 , THR B:78 , ARG B:79 , SER B:82 , ASP B:102 , SER B:103 , ALA B:104 , LYS B:201 , MG B:600 , ACY B:700 , HOH B:703 , HOH B:719 , HOH B:725BINDING SITE FOR RESIDUE CTP B 500
5AC5SOFTWAREARG A:14 , LYS A:201 , CTP A:500 , HOH A:734 , HOH A:749 , SER B:133 , ASP B:134BINDING SITE FOR RESIDUE ACY A 700
6AC6SOFTWARESER A:133 , ASP A:134 , ARG B:14 , LYS B:201 , CTP B:500 , HOH B:737BINDING SITE FOR RESIDUE ACY B 700

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:157 -Pro A:158
2Thr B:157 -Pro B:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ISPDPS01295 4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature.ISPD_THEMA98-105
 		  2A:98-105
B:98-105

(-) Exons   (0, 0)

(no "Exon" information available for 1VPA)

(-) 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:221
 aligned with ISPD_THEMA | Q9X1B3 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:221
                              1                                                                                                                                                                                                                          
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218 
           ISPD_THEMA     - --MNVAILLAAGKGERMSENVPKQFLEIEGRMLFEYPLSTFLKSEAIDGVVIVTRREWFEVVEKRVFHEKVLGIVEGGDTRSQSVRSALEFLEKFSPSYVLVHDSARPFLRKKHVSEVLRRARETGAATLALKNSDALVRVENDRIEYIPRKGVYRILTPQAFSYEILKKAHENGGEWADDTEPVQKLGVKIALVEGDPLCFKVTFKEDLELARIIAREWE 219
               SCOP domains d1vpaa_ A: 4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP)                                                                                                                                           SCOP domains
               CATH domains 1vpaA00 A:-1-219 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhh...hhhh.ee..ee.hhhhhhhhhhh....eeeeee...hhhhhhh......eeeeee...hhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhheeeeeee...eeeeee..eeeee....eeeeeeeeeeehhhhhhhhh.......hhhhhhh.....eeee.hhhhh.....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vpa A  -1 HHMNVAILLAAGKGERMSENVPKQFLEIEGRMLFEYPLSTFLKSEAIDGVVIVTRREWFEVVEKRVFHEKVLGIVEGGDTRSQSVRSALEFLEKFSPSYVLVHDSARPFLRKKHVSEVLRRARETGAATLALKNSDALVRVENDRIEYIPRKGVYRILTPQAFSYEILKKAHENGGEWADDTEPVQKLGVKIALVEGDPLCFKVTFKEDLELARIIAREWE 219
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218 


Chain B from PDB  Type:PROTEIN  Length:220
 aligned with ISPD_THEMA | Q9X1B3 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:220
                              1                                                                                                                                                                                                                         
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218
           ISPD_THEMA     - --MNVAILLAAGKGERMSENVPKQFLEIEGRMLFEYPLSTFLKSEAIDGVVIVTRREWFEVVEKRVFHEKVLGIVEGGDTRSQSVRSALEFLEKFSPSYVLVHDSARPFLRKKHVSEVLRRARETGAATLALKNSDALVRVENDRIEYIPRKGVYRILTPQAFSYEILKKAHENGGEWADDTEPVQKLGVKIALVEGDPLCFKVTFKEDLELARIIAREW 218
               SCOP domains d1vpab_ B: 4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP)                                                                                                                                          SCOP domains
               CATH domains 1vpaB00 B:-1-218 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                CATH domains
           Pfam domains (1) ---IspD-1vpaB01 B:2-217                                                                                                                                                                                                    - Pfam domains (1)
           Pfam domains (2) ---IspD-1vpaB02 B:2-217                                                                                                                                                                                                    - Pfam domains (2)
         Sec.struct. author ...eeeeeee...hhhhh...hhhh.ee..ee.hhhhhhhhhhh....eeeeee...hhhhhhh......eeeeee...hhhhhhhhhhhhhh.....eeeeee......hhhhhhhhhhhhhhhheeeeeee...eeeee....eee.....eeeeeeeeeeehhhhhhhhh.......hhhhhhhh....eeee.hhhhh...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------ISPD    ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vpa B  -1 HHMNVAILLAAGKGERMSENVPKQFLEIEGRMLFEYPLSTFLKSEAIDGVVIVTRREWFEVVEKRVFHEKVLGIVEGGDTRSQSVRSALEFLEKFSPSYVLVHDSARPFLRKKHVSEVLRRARETGAATLALKNSDALVRVENDRIEYIPRKGVYRILTPQAFSYEILKKAHENGGEWADDTEPVQKLGVKIALVEGDPLCFKVTFKEDLELARIIAREW 218
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218
   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_THEMA | Q9X1B3)
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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