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(-) Description

Title :  2C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE (ISPD) FROM ARABIDOPSIS THALIANA
 
Authors :  M. Gabrielsen, J. Kaiser, F. Rohdich, W. Eisenreich, A. Bacher, C. S. Bond, W. N. Hunter
Date :  30 Aug 04  (Deposition) - 21 Feb 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Plantherbicide, Cytidylyltransferase, Arabidopsis Thaliana, Non-Mevalonate Pathway, Isoprenoid, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Gabrielsen, J. Kaiser, F. Rohdich, W. Eisenreich, R. Laupitz, A. Bacher, C. S. Bond, W. N. Hunter
The Crystal Structure Of A Plant 2C-Methyl-D- Erythritol 4-Phosphate Cytidylyltransferase Exhibits A Distinct Quaternary Structure Compared To Bacterial Homologues And A Possible Role In Feedback Regulation For Cytidine Monophosphate.
Febs J. V. 273 1065 2006
PubMed-ID: 16478479  |  Reference-DOI: 10.1111/J.1742-4658.2006.05133.X

(-) Compounds

Molecule 1 - 2C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE
    ChainsA
    EC Number2.7.7.60
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNCO113
    Expression System StrainM15(PREP4)
    Expression System Taxid562
    FragmentCYTIDYLTRANSFERASE DOMAIN, RESIDUES 76-302
    MutationYES
    Organism CommonMOUSE-EAR CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    Other DetailsCHLOROPLAST TARGETING SEQUENCE REMOVED, COMPOUND STARTS AT RESIDUE 75
    Synonym4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL SYNTHASE, PUTATIVE SUGAR NUCLEOTIDE PHOSPHORYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1C5P1Ligand/IonCYTIDINE-5'-MONOPHOSPHATE
2CD1Ligand/IonCADMIUM ION
3CU4Ligand/IonCOPPER (II) ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1C5P2Ligand/IonCYTIDINE-5'-MONOPHOSPHATE
2CD-1Ligand/IonCADMIUM ION
3CU-1Ligand/IonCOPPER (II) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:121 , GLU A:191 , HIS A:271 , HOH A:2025BINDING SITE FOR RESIDUE CD A1000
2AC2SOFTWAREGLU A:167BINDING SITE FOR RESIDUE CU A1001
3AC3SOFTWAREGLU A:138 , GLU A:141 , ASP A:169 , HOH A:2061BINDING SITE FOR RESIDUE CU A1002
4AC4SOFTWAREHOH A:2162BINDING SITE FOR RESIDUE CU A1003
5AC5SOFTWARETHR A:286 , ASP A:290BINDING SITE FOR RESIDUE CU A1004
6AC6SOFTWARELEU A:84 , ALA A:85 , GLY A:86 , GLY A:87 , GLY A:154 , LYS A:155 , GLU A:156 , SER A:160 , ASP A:179 , LYS A:284 , HOH A:2166BINDING SITE FOR RESIDUE C5P A3001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W77)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr A:236 -Pro A:237

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W77)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ISPDPS01295 4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature.ISPD_ARATH175-182  1A:175-182
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ISPDPS01295 4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature.ISPD_ARATH175-182  2A:175-182

(-) Exons   (0, 0)

(no "Exon" information available for 1W77)

(-) Sequences/Alignments

Asymmetric 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:212
 aligned with ISPD_ARATH | P69834 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:226
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294      
           ISPD_ARATH    75 KEKSVSVILLAGGQGKRMKMSMPKQYIPLLGQPIALYSFFTFSRMPEVKEIVVVCDPFFRDIFEEYEESIDVDLRFAIPGKERQDSVYSGLQEIDVNSELVCIHDSARPLVNTEDVEKVLKDGSAVGAAVLGVPAKATIKEVNSDSLVVKTLDRKTLWEMQTPQVIKPELLKKGFELVKSEGLEVTDDVSIVEYLKHPVYVSQGSYTNIKVTTPDDLLLAERILSE 300
               SCOP domains d1w77a1 A:75-       300 4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP)                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----IspD-1w77       A01 A:79-300                                                                                                                                                                                                   Pfam domains
         Sec.struct. author ....eeeeee...-------.......ee..eehhhhhhhhhhh...eeeeeee.hhhhhhhhhh.......eeeee....hhhhhhhhhhhh......eeeeee......hhhhhhhhhhhhhhhheeeeeee...............------..eeeeeeeeehhhhhhhhhhhhhhh.....-....hhhhh...eeee.........hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------ISPD    ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w77 A  75 MEKSVSVILLAGG-------SMPKQYIPLLGQPIALYSFFTFSRMPEVKEIVVVCDPFFRDIFEEYEESIDVDLRFAIPGKERQDSVYSGLQEIDVNSELVCIHDSARPLVNTEDVEKVLKDGSAVGAAVLGVPAKATIKEVNSDSLVV------TLWEMQTPQVIKPELLKKGFELVKSEGLEVT-DVSIVEYLKHPVYVSQGSYTNIKVTTPDDLLLAERILSE 300
                                    84  |      -|      104       114       124       134       144       154       164       174       184       194       204       214        |-     | 234       244       254     | 264       274       284       294      
                                       87      95                                                                                                                             223    230                           260 |                                      
                                                                                                                                                                                                                     262                                      

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1W77)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: GT-A (172)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (ISPD_ARATH | P69834)
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.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009570    chloroplast stroma    The space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes and some temporary products of photosynthesis.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ISPD_ARATH | P698342yc3 2yc5 2ycm 4nai 4nak 4nal 4nan

(-) Related Entries Specified in the PDB File

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