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(-) Description

Title :  ARABIDOPSIS THALIANA ISPD APO
 
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 :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Herbicide, Anti-Infectives, Pseudilin, Natural Product, Drug Discovery, Allosteric Inhibition, Rossmann Fold, Transferase (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
    Fragment: UNP RESIDUES 76-302
    Gene: AT2G02500, ISPD, MCT, MECT, MEPCT, T8K22.20
    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  (2, 16)

Asymmetric Unit (2, 16)
No.NameCountTypeFull Name
1CD2Ligand/IonCADMIUM ION
2K14Ligand/IonPOTASSIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2K-1Ligand/IonPOTASSIUM ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:167 , K A:411 , HOH A:518BINDING SITE FOR RESIDUE CD A 401
02AC2SOFTWAREGLU A:121 , GLU A:191 , HIS A:271 , HOH A:507BINDING SITE FOR RESIDUE CD A 402
03AC3SOFTWAREASP A:289 , ARG A:296 , GLU A:300 , HOH A:595 , HOH A:624BINDING SITE FOR RESIDUE K A 403
04AC4SOFTWARESER A:117 , MET A:119 , VAL A:122 , ASP A:145 , VAL A:146 , HOH A:540 , HOH A:567BINDING SITE FOR RESIDUE K A 404
05AC5SOFTWAREASP A:189 , LEU A:205 , GLN A:235 , GLY A:278 , SER A:279 , ASN A:282 , K A:406BINDING SITE FOR RESIDUE K A 405
06AC6SOFTWAREVAL A:185 , ASN A:186 , ASP A:189 , ASN A:282 , K A:405 , HOH A:501BINDING SITE FOR RESIDUE K A 406
07AC7SOFTWAREARG A:182 , PRO A:183 , LEU A:184 , VAL A:185 , ASN A:282 , ILE A:283BINDING SITE FOR RESIDUE K A 407
08AC8SOFTWAREILE A:108 , ALA A:109 , SER A:112 , SER A:180 , PRO A:183BINDING SITE FOR RESIDUE K A 408
09AC9SOFTWARESER A:112 , THR A:115 , PRO A:183 , VAL A:185BINDING SITE FOR RESIDUE K A 409
10BC1SOFTWAREALA A:199 , HOH A:538 , HOH A:575BINDING SITE FOR RESIDUE K A 410
11BC2SOFTWAREGLN A:166 , GLU A:167 , CD A:401 , HOH A:518 , HOH A:520BINDING SITE FOR RESIDUE K A 411
12BC3SOFTWAREGLU A:156 , GLU A:258BINDING SITE FOR RESIDUE K A 412
13BC4SOFTWAREGLU A:191 , HOH A:554 , HOH A:593BINDING SITE FOR RESIDUE K A 413
14BC5SOFTWARESER A:163 , GLU A:167 , HOH A:509 , HOH A:553BINDING SITE FOR RESIDUE K A 414
15BC6SOFTWAREARG A:149 , ILE A:168 , HOH A:588BINDING SITE FOR RESIDUE K A 415
16BC7SOFTWARELYS A:123 , ASP A:147 , HOH A:541 , HOH A:550 , HOH A:568 , HOH A:631BINDING SITE FOR RESIDUE K A 416

(-) SS Bonds  (0, 0)

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

(-) 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 4NAI)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NAI)

(-) 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:214
                                                                                                                                                                                                                                                      
               SCOP domains d4naia_ 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..hhhh.ee..eehhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh.......eeeeee......hhhhhhhhhhhhhhhheeeeeee.....eee.....eeee.hhhh.eeeeeeeeehhhhhhhhhhhhhh.......hhhhhhhh....eeee.........hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nai A  77 KSVSVILLAGPKQYIPLLGQPIALYSFFTFSRMPEVKEIVVVCDPFFRDIFEEYEESIDVDLRFAIPGKERQDSVYSGLQEIDVNSELVCIHDSARPLVNTEDVEKVLKDGSAVGAAVLGVPAKATIKEVNSDSLVVKTLDRKTLWEMQTPQVIKPELLKKGFELVKSEGLEVTDDVSIVEYLKHPVYVSQGSYTNIKVTTPDDLLLAERILSE 300
                                    86|      106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296    
                                    86|                                                                                                                                                                                                           
                                     97
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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 4NAI)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

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  4nai
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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 4nak 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.
4nak
4nal
4nan