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(-) Description

Title :  ARABIDOPSIS THALIANA ISPD IN COMPLEX WITH PENTABROMO-PSEUDILIN
 
Authors :  A. Kunfermann, M. Witschel, B. Illarionov, R. Martin, M. Rottmann, H. W M. Seet, W. Eisenreich, H. -J. Knolker, M. Fischer, A. Bacher, M. Groll F. Diederich
Date :  22 Oct 13  (Deposition) - 29 Jan 14  (Release) - 21 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Herbicide, Anti-Infectives, Pseudilin, Natural Product, Drug Discovery, Allosteric Inhibition, Rossmann Fold, Transferase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Kunfermann, M. Witschel, B. Illarionov, R. Martin, M. Rottmann, H. W. Hoffken, M. Seet, W. Eisenreich, H. J. Knolker, M. Fischer, A. Bacher, M. Groll, F. Diederich
Pseudilins: Halogenated, Allosteric Inhibitors Of The Non-Mevalonate Pathway Enzyme Ispd.
Angew. Chem. Int. Ed. Engl. V. 53 2235 2014
PubMed-ID: 24446431  |  Reference-DOI: 10.1002/ANIE.201309557

(-) 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 Taxid1007065
    Expression System Vector TypePLASMID
    GeneAT2G02500, ISPD, MCT, MECT, MEPCT, T8K22.20
    MutationYES
    Organism CommonMOUSE-EAR CRESS, THALE-CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    Synonym4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL SYNTHASE, MEP CYTIDYLYLTRANSFERASE, ATMECT, ATMEPCT

 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, 13)

Asymmetric Unit (4, 13)
No.NameCountTypeFull Name
1CD5Ligand/IonCADMIUM ION
2DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
3K6Ligand/IonPOTASSIUM ION
4PBQ1Ligand/IonPENTABROMOPSEUDILIN
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2DTT2Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
3K-1Ligand/IonPOTASSIUM ION
4PBQ2Ligand/IonPENTABROMOPSEUDILIN

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:203 , GLN A:238 , VAL A:239 , LEU A:245 , SER A:264 , ILE A:265 , VAL A:266 , CD A:403BINDING SITE FOR RESIDUE PBQ A 401
02AC2SOFTWARELYS A:195 , ASP A:196 , ALA A:199 , VAL A:200 , TYR A:274 , K A:409BINDING SITE FOR RESIDUE DTT A 402
03AC3SOFTWAREGLN A:238 , PBQ A:401BINDING SITE FOR RESIDUE CD A 403
04AC4SOFTWAREGLU A:167BINDING SITE FOR RESIDUE CD A 404
05AC5SOFTWAREASP A:261 , HOH A:517 , HOH A:526 , HOH A:560BINDING SITE FOR RESIDUE CD A 405
06AC6SOFTWAREGLU A:138 , GLU A:141 , ASP A:169BINDING SITE FOR RESIDUE CD A 406
07AC7SOFTWAREGLU A:121 , GLU A:191 , HIS A:271 , HOH A:507 , HOH A:539BINDING SITE FOR RESIDUE CD A 407
08AC8SOFTWAREASP A:290BINDING SITE FOR RESIDUE K A 408
09AC9SOFTWAREDTT A:402BINDING SITE FOR RESIDUE K A 409
10BC1SOFTWAREARG A:182 , PRO A:183 , LEU A:184 , ASN A:282 , ILE A:283BINDING SITE FOR RESIDUE K A 410
11BC2SOFTWAREILE A:108 , ALA A:109 , SER A:112 , SER A:180 , PRO A:183BINDING SITE FOR RESIDUE K A 411
12BC3SOFTWARESER A:117 , MET A:119 , VAL A:122 , ASP A:145 , VAL A:146BINDING SITE FOR RESIDUE K A 412
13BC4SOFTWAREASN A:186 , ASP A:189 , HOH A:505 , HOH A:508BINDING SITE FOR RESIDUE K A 413

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NAK)

(-) 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 4NAK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NAK)

(-) Exons   (0, 0)

(no "Exon" information available for 4NAK)

(-) 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:209
                                                                                                                                                                                                                                                 
               SCOP domains d4naka_ A: 4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP)                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee........ee..ee.hhhhhhhhhh...eeeeeee.hhhhhhhhhh.......eeeee....hhhhhhhhhhh.......eeeeee......hhhhhhhhhhhhhhhheeeeeee......ee.....ee...eeeeeeeeehhhhhhhhhhhhhhhh.......hhhhhh....eeee.........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nak A  76 EKSVSVILLAGGPKQYIPLLGQPIALYSFFTFSRMPEVKEIVVVCDPFFRDIFEEYEESIDVDLSFAIPGKERQDSVYSGLQEIDVNSELVCIHDSARPLVNTEDVEKVLKDGSAVGAAVLGVPAKATIKEVNSDSLVVKTLWEMQTPQVIKPELLKKGFELVKSEGLEVTDDVSIVEYLKHPVYVSQGSYTNIKVTTPDDLLLAERIL 298
                                    85 ||    104       114       124       134       144       154       164       174       184       194       204       214       224|      239       249       259       269       279       289         
                                      87|                                                                                                                            224|                                                                    
                                       97                                                                                                                             230                                                                    

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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 4NAK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NAK)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        ISPD_ARATH | P698341w77 2yc3 2yc5 2ycm 4nai 4nal 4nan

(-) Related Entries Specified in the PDB File

1ini STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C- METHYLERYTHRITOL SYNTHETASE INVOLVED IN MEVALONATE- INDEPENDENT ISOPRENOID BIOSYNTHESIS.
1w77 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.
2yc5 INHIBITORS OF THE HERBICIDAL TARGET ISPD: ALLOSTERIC SITE BINDING.
4nai ARABIDOPSIS THALIANA ISPD APO
4nal
4nan