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(-) Description

Title :  INHIBITORS OF HERBICIDAL TARGET ISPD
 
Authors :  H. W. Hoeffken
Date :  16 Mar 11  (Deposition) - 24 Aug 11  (Release) - 24 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Herbicide, Allosteric Binding Pocket, Non-Mevalonate- Pathway (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
    ChainsA
    EC Number2.7.7.60
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNCO113
    Expression System StrainM15
    Expression System Taxid562
    Expression System VariantPREP4
    FragmentCYTIDYLTRANSFERASE DOMAIN, RESIDUES 76-302
    Organism CommonTHALE CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    Synonym4-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, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
130A1Ligand/Ion6-BENZYL-5-CHLORO-7-HYDROXYPYRAZOLO[1,5-A]PYRIMIDINE-3-CARBOXYLIC ACID
2CD3Ligand/IonCADMIUM ION
3CU1Ligand/IonCOPPER (II) ION
4NA1Ligand/IonSODIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
130A2Ligand/Ion6-BENZYL-5-CHLORO-7-HYDROXYPYRAZOLO[1,5-A]PYRIMIDINE-3-CARBOXYLIC ACID
2CD-1Ligand/IonCADMIUM ION
3CU-1Ligand/IonCOPPER (II) ION
4NA-1Ligand/IonSODIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:123 , GLU A:138 , GLU A:141 , ASP A:169 , HOH A:2017BINDING SITE FOR RESIDUE CD A1301
2AC2SOFTWAREGLU A:121 , GLU A:191 , HIS A:271 , HOH A:2081BINDING SITE FOR RESIDUE CD A1302
3AC3SOFTWAREGLU A:167BINDING SITE FOR RESIDUE CD A1303
4AC4SOFTWAREGLU A:139 , HOH A:2015BINDING SITE FOR RESIDUE NA A1304
5AC5SOFTWAREASP A:290BINDING SITE FOR RESIDUE CU A1305
6AC6SOFTWAREARG A:157 , GLN A:158 , ILE A:177 , ALA A:203 , GLN A:238 , VAL A:259 , ASP A:261 , ASP A:262 , VAL A:263 , SER A:264 , ILE A:265 , VAL A:266 , VAL A:273 , HOH A:2093BINDING SITE FOR RESIDUE 30A A1306

(-) SS Bonds  (0, 0)

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

(-) 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 2YCM)

(-) 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 2YCM)

(-) 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:213
 aligned with ISPD_ARATH | P69834 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:225
                                    85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295     
           ISPD_ARATH    76 EKSVSVILLAGGQGKRMKMSMPKQYIPLLGQPIALYSFFTFSRMPEVKEIVVVCDPFFRDIFEEYEESIDVDLRFAIPGKERQDSVYSGLQEIDVNSELVCIHDSARPLVNTEDVEKVLKDGSAVGAAVLGVPAKATIKEVNSDSLVVKTLDRKTLWEMQTPQVIKPELLKKGFELVKSEGLEVTDDVSIVEYLKHPVYVSQGSYTNIKVTTPDDLLLAERILSE 300
               SCOP domains d2ycma_ A:          automated matches                                                                                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..---------.hhhh.ee..eehhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh.......eeeeee......hhhhhhhhhhhhhhhheeeeeee......ee.....ee...---..eeeeeeeeehhhhhhhhhhhhhhhh......hhhhhhh....eeee.........hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------ISPD    ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ycm A  76 EKSVSVILLAG---------MPKQYIPLLGQPIALYSFFTFSRMPEVKEIVVVCDPFFRDIFEEYEESIDVDLSFAIPGKERQDSVYSGLQEIDVNSELVCIHDSARPLVNTEDVEKVLKDGSAVGAAVLGVPAKATIKEVNSDSLVVKTL---TLWEMQTPQVIKPELLKKGFELVKSEGLEVTDDVSIVEYLKHPVYVSQGSYTNIKVTTPDDLLLAERILSE 300
                                    85|        -|      105       115       125       135       145       155       165       175       185       195       205       215       225|   |  235       245       255       265       275       285       295     
                                     86        96                                                                                                                               226 230                                                                      

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  - → Gap (green background, '-', border residues have a numbering label)
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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 2YCM)

(-) Pfam Domains  (0, 0)

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

(-) 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 | P698341w77 2yc3 2yc5 4nai 4nak 4nal 4nan

(-) Related Entries Specified in the PDB File

1w77 2C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE ( ISPD) FROM ARABIDOPSIS THALIANA
2yc3 INHIBITORS OF THE HERBICIDAL TARGET ISPD
2yc5 INHIBITORS OF THE HERBICIDAL TARGET ISPD