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(-) Description

Title :  INHIBITORS OF THE HERBICIDAL TARGET ISPD
 
Authors :  H. W. Hoeffken
Date :  11 Mar 11  (Deposition) - 24 Aug 11  (Release) - 24 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Non-Mevalonate-Pathway, Herbicide, Allosteric Pocket (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Witschel, H. W. Hoeffken, M. Seet, L. Parra, T. Mietzner, F. Thater, R. Niggeweg, F. Rohl, B. Illarionov, F. Rohdich, J. Kaiser, M. Fischer, A. Bacher, F. Diederich
Inhibitors Of The Herbicidal Target Ispd: Allosteric Site Binding.
Angew. Chem. Int. Ed. Engl. V. 50 7931 2011
PubMed-ID: 21766403  |  Reference-DOI: 10.1002/ANIE.201102281
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE, CHLOROPLASTIC
    Chains: A
    EC Number: 2.7.7.60
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNCO113
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Variant: PREP4
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 76-302
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL SYNTHASE, MEP CYTIDYLYLTRANSFERASE, ATMECT, ATMEPCT, MCT

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1CD3Ligand/IonCADMIUM ION
2CU2Ligand/IonCOPPER (II) ION
3MW51Ligand/Ion6-BENZYL-5-CHLORO[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7(3H)-ONE
4NA2Ligand/IonSODIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2CU-1Ligand/IonCOPPER (II) ION
3MW52Ligand/Ion6-BENZYL-5-CHLORO[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7(3H)-ONE
4NA-1Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:157 , ILE A:177 , ALA A:203 , GLN A:238 , VAL A:239 , VAL A:259 , ASP A:261 , ASP A:262 , VAL A:263 , SER A:264 , ILE A:265 , VAL A:266 , HOH A:2177BINDING SITE FOR RESIDUE MW5 A1301
2AC2SOFTWAREGLU A:139BINDING SITE FOR RESIDUE NA A1302
3AC3SOFTWARETHR A:286 , ASP A:290BINDING SITE FOR RESIDUE CU A1303
4AC4SOFTWARELYS A:123 , GLU A:138 , GLU A:141 , ASP A:169 , HOH A:2030BINDING SITE FOR RESIDUE CU A1304
5AC5SOFTWAREGLU A:139BINDING SITE FOR RESIDUE NA A1305
6AC6SOFTWARELYS A:214 , ASP A:261 , GLU A:267BINDING SITE FOR RESIDUE CD A1306
7AC7SOFTWAREGLU A:121 , GLU A:191 , HIS A:271 , HOH A:2076BINDING SITE FOR RESIDUE CD A1307
8AC8SOFTWAREGLU A:167 , HOH A:2070 , HOH A:2071BINDING SITE FOR RESIDUE CD A1308

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YC3)

(-) 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 2YC3)

(-) 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 2YC3)

(-) 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:219
 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 d2yc3a_ A: 4-di       phosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP)                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....-------hhhh.ee..eehhhhhhhhhhhh..eeeeeee.hhhhhhhhhh.......eeeee....hhhhhhhhhhh.......eeeeee......hhhhhhhhhhhhhhhheeeeeee.......................eeeeeeeeehhhhhhhhhhhhhhhh......hhhhhhh....eeee.........hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------ISPD    ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yc3 A  75 MEKSVSVILLAGGQG-------PKQYIPLLGQPIALYSFFTFSRMPEVKEIVVVCDPFFRDIFEEYEESIDVDLSFAIPGKERQDSVYSGLQEIDVNSELVCIHDSARPLVNTEDVEKVLKDGSAVGAAVLGVPAKATIKEVNSDSLVVKTLDRKTLWEMQTPQVIKPELLKKGFELVKSEGLEVTDDVSIVEYLKHPVYVSQGSYTNIKVTTPDDLLLAERILSE 300
                                    84    |    -  |    104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294      
                                         89      97
   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, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YC3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YC3)

(-) 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 | P69834: 1w77 2yc5 2ycm 4nai 4nak 4nal 4nan

(-) Related Entries Specified in the PDB File

1w77 2C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE (ISPD) FROM ARABIDOPSIS THALIANA
2yc5 INHIBITORS OF THE HERBICIDAL TARGET ISPD