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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
    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: 1007065
    Expression System Vector Type: PLASMID
    Gene: AT2G02500, ISPD, MCT, MECT, MEPCT, T8K22.20
    Mutation: YES
    Organism Common: MOUSE-EAR CRESS, THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: 4-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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) 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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  4nak
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  2.7.7.60
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 Related Entries

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

UniProtKB/Swiss-Prot
        ISPD_ARATH | P69834: 1w77 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