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(-) Description

Title :  CRYSTAL STRUCTURE OF MAIZE CYTOKININ OXIDASE/DEHYDROGENASE 4 (ZMCKO4) IN COMPLEX WITH PHENYLUREA INHIBITOR CPPU
 
Authors :  D. Kopecny, S. Morera, A. Vigouroux, R. Koncitikova
Date :  01 Jan 14  (Deposition) - 01 Apr 15  (Release) - 25 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Cytokinin, Flavoprotein, Phenyl-Urea Inhibitor, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Kopecny, R. Koncitikova, H. Popelka, P. Briozzo, A. Vigouroux, M. Kopecna, D. Zalabak, M. Sebela, J. Skopalova, I. Frebort, S. Morera
Kinetic And Structural Investigation Of The Cytokinin Oxidase/Dehydrogenase Active Site
Febs J. 2015
PubMed-ID: 26519657  |  Reference-DOI: 10.1111/FEBS.13581

(-) Compounds

Molecule 1 - CYTOKININ DEHYDROGENASE 4
    Chains: A
    EC Number: 1.5.99.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTYB12
    Expression System Strain: BL21 STAR (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 22-541
    Gene: CKX4
    Organism Common: MAIZE
    Organism Scientific: ZEA MAYS
    Organism Taxid: 4577

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 16)

Asymmetric/Biological Unit (6, 16)
No.NameCountTypeFull Name
12451Ligand/Ion1-(2-CHLOROPYRIDIN-4-YL)-3-PHENYLUREA
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3EDO10Ligand/Ion1,2-ETHANEDIOL
4FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
5GOL1Ligand/IonGLYCEROL
6PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:57 , ALA A:95 , ARG A:96 , GLY A:97 , HIS A:98 , GLY A:99 , HIS A:100 , SER A:101 , GLN A:105 , ALA A:106 , THR A:169 , ASP A:170 , TYR A:171 , LEU A:174 , SER A:175 , GLY A:177 , GLY A:178 , SER A:181 , ASN A:182 , GLY A:184 , ILE A:185 , GLY A:234 , ILE A:235 , ILE A:236 , TRP A:389 , TYR A:487 , LEU A:488 , GLN A:526 , 245 A:602 , HOH A:718 , HOH A:719 , HOH A:746 , HOH A:864BINDING SITE FOR RESIDUE FAD A 601
02AC2SOFTWAREASP A:170 , VAL A:370 , TRP A:389 , ASN A:391 , LEU A:423 , LEU A:452 , TYR A:487 , LEU A:488 , FAD A:601 , EDO A:610BINDING SITE FOR RESIDUE 245 A 602
03AC3SOFTWAREHIS A:98 , TYR A:171 , HIS A:371 , GLU A:374BINDING SITE FOR RESIDUE EDO A 603
04AC4SOFTWAREGLY A:139 , HIS A:140 , LEU A:243 , ARG A:245BINDING SITE FOR RESIDUE EDO A 604
05AC5SOFTWAREPHE A:224 , ARG A:435 , SER A:436 , SER A:437 , ARG A:505 , ARG A:508 , HOH A:716BINDING SITE FOR RESIDUE EDO A 605
06AC6SOFTWAREPHE A:190 , HIS A:191 , ILE A:271 , LEU A:273 , ASN A:428 , HIS A:430BINDING SITE FOR RESIDUE EDO A 606
07AC7SOFTWARESER A:159 , SER A:397 , ARG A:398 , GLY A:481BINDING SITE FOR RESIDUE EDO A 607
08AC8SOFTWAREALA A:510 , ALA A:514 , PRO A:518BINDING SITE FOR RESIDUE EDO A 608
09AC9SOFTWAREARG A:166 , SER A:197 , TYR A:200BINDING SITE FOR RESIDUE EDO A 609
10BC1SOFTWAREHIS A:387 , TRP A:389 , LEU A:452 , ARG A:453 , SER A:454 , 245 A:602BINDING SITE FOR RESIDUE EDO A 610
11BC2SOFTWAREHIS A:192 , SER A:197 , LYS A:431BINDING SITE FOR RESIDUE EDO A 611
12BC3SOFTWAREALA A:129 , LEU A:130 , VAL A:132BINDING SITE FOR RESIDUE EDO A 612
13BC4SOFTWARETRP A:432 , ALA A:438 , THR A:440 , HOH A:783BINDING SITE FOR RESIDUE DMS A 613
14BC5SOFTWAREASP A:152 , ASN A:155 , TYR A:173 , GLU A:444BINDING SITE FOR RESIDUE PEG A 614
15BC6SOFTWARELEU A:474 , ALA A:484 , GLN A:486 , HIS A:491 , GLU A:496BINDING SITE FOR RESIDUE PEG A 615
16BC7SOFTWARETYR A:200 , GLU A:201 , THR A:217 , ARG A:240 , GLU A:461 , HOH A:776BINDING SITE FOR RESIDUE GOL A 616

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4O95)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:415 -Ala A:416

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O95)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O95)

(-) Exons   (0, 0)

(no "Exon" information available for 4O95)

(-) Sequences/Alignments

Asymmetric/Biological 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:467
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.hhhhhhhhh............eeee..hhhhhhhhhhhhhhh.....eeee...............eeee.....hhhhhhhh...eee....eeeeeee...hhhhhhhhhhhh..eee.........hhhhhhh......hhhhhhhhhh.eeeeeeee....eeeee...hhhhhhhhh......eeeeeeeeeeee...eeeeeeeee.hhhhhhhhhhhhhhhhhhhh....eeeeeee....eeeeeeeeee......hhhhhhhhhhhh........eeeeeehhhhhhhhhhhhhhhhhh.........eeeeee..hhhhhhhhh...............eeeeeee.hhh............eeeeeee.......hhhhhhhhhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o95 A  38 VGGGRLSVDASDIAEASRDFGGVARAEPMAVFHPRAAGDVAGLVGAAFRSARGFRVSARGHGHSISGQAQAAGGVVVDMSRGRGPGAAVARALPVHSAALGGHYVDVWGGELWVDVLNWTLSHGGLAPRSWTDYLYLSVGGTLSNAGISGQAFHHGPQISNVYELDVVTGKGEVVTCSETENPDLFFGVLGGLGQFGIITRARIALERAPKRVRWIRALYSNFSEFTADQERLISLGSGGGRRFDYVEGFVVAASVLYCLEVTKNYDDETAGSVDQDVDTLLGELNFLPGTVFTTDLPYVDFLDRVHKAELKLRAKGMWEVPHPWLNLFVPASRIADFDRGVFRGVLGGRTAGAGGPVLIYPMNKHKWDPRSSAVTPDEEVFYLVAFLRSALPGAPESLEALARQNQRILDFCAGTGIGAKQYLPGHKARHEWAEHFGAARWDRFARLKAEFDPRAILAAGQGIFRP 531
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287   ||  324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       
                                                                                                                                                                                                                                                                                       291|                                                                                                                                                                                                                    
                                                                                                                                                                                                                                                                                        319
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "SCOP Domain" information available for 4O95)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O95)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O95)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Thr A:415 - Ala A:416   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        E3T1W8_MAIZE | E3T1W8: 4oal 5hhz 5hmr 5hqx

(-) Related Entries Specified in the PDB File

2qkn THE SAME INHIBITOR IN COMPLEX WITH ZMCKO1
3kjm THE SAME INHIBITOR IN COMPLEX WITH L492A MUTANT VARIANT OF ZMCKO1
3s1c
3s1d
3s1e
3s1f
4ml8
4mla
4oal