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(-) Description

Title :  CRYSTAL STRUCTURE OF MAIZE CYTOKININ OXIDASE/DEHYDROGENASE COMPLEXED WITH PHENYLUREA INHIBITOR CPPU
 
Authors :  P. Briozzo
Date :  11 Jul 07  (Deposition) - 01 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A
Keywords :  Cytokinin Oxidase/Deshydrogenase, Flavoprotein, Fad, Phenyl-Urea Inhibitor, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Kopecny, P. Briozzo, H. Popelkova, M. Sebela, R. Koncitikova, L. Spichal, J. Nisler, C. Madzak, I. Frebort, M. Laloue, N. Houba-Heri
Phenyl- And Benzylurea Cytokinins As Competitive Inhibitors Of Cytokinin Oxidase/Dehydrogenase: A Structural Study.
Biochimie V. 92 1052 2010
PubMed-ID: 20478354  |  Reference-DOI: 10.1016/J.BIOCHI.2010.05.006

(-) Compounds

Molecule 1 - CYTOKININ DEHYDROGENASE 1
    Chains: A
    EC Number: 1.5.99.12
    Engineered: YES
    Expression System: YARROWIA LIPOLYTICA
    Expression System Plasmid: PINA6703
    Expression System Taxid: 4952
    Expression System Vector Type: PLASMID
    Gene: CKX1
    Organism Common: MAIZE
    Organism Scientific: ZEA MAYS
    Organism Taxid: 4577
    Synonym: CYTOKININ OXIDASE 1
    Variant: NOBILIS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
12452Ligand/Ion1-(2-CHLOROPYRIDIN-4-YL)-3-PHENYLUREA
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3GOL1Ligand/IonGLYCEROL
4NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:59 , ASN A:63 , ILE A:64 , THR A:65 , HOH A:1833 , HOH A:1893BINDING SITE FOR RESIDUE NAG A 1601
02AC2SOFTWAREPRO A:130 , PRO A:131 , ARG A:132 , ASN A:134 , ASP A:143 , ARG A:237BINDING SITE FOR RESIDUE NAG A 1602
03AC3SOFTWAREPRO A:130BINDING SITE FOR RESIDUE NAG A 1603
04AC4SOFTWAREASN A:294 , ASN A:323 , ALA A:324BINDING SITE FOR RESIDUE NAG A 1604
05AC5SOFTWAREASN A:323 , ASP A:450 , HOH A:1846BINDING SITE FOR RESIDUE NAG A 1606
06AC6SOFTWAREASN A:338 , PRO A:464BINDING SITE FOR RESIDUE NAG A 1608
07AC7SOFTWAREPHE A:61 , PHE A:100 , GLY A:102 , ARG A:103 , GLY A:104 , HIS A:105 , SER A:106 , GLN A:110 , THR A:168 , ASP A:169 , TYR A:170 , THR A:174 , GLY A:176 , GLY A:177 , SER A:180 , ASN A:181 , GLY A:183 , ILE A:184 , GLY A:230 , GLY A:233 , ILE A:235 , TRP A:391 , TYR A:491 , LEU A:492 , SER A:527 , GLN A:530 , HOH A:1629 , HOH A:1656 , HOH A:1762BINDING SITE FOR RESIDUE FAD A 1535
08AC8SOFTWAREASP A:169 , GLU A:381 , ASN A:399 , ILE A:429 , SER A:456 , LEU A:458 , LEU A:492 , HOH A:1611BINDING SITE FOR RESIDUE 245 A 1536
09AC9SOFTWAREASP A:169 , GLU A:381 , TRP A:397 , ASN A:399 , ILE A:429 , SER A:456 , LEU A:458 , LEU A:492 , HOH A:1611BINDING SITE FOR RESIDUE 245 A 1537
10BC1SOFTWAREARG A:190 , HIS A:191 , GLU A:243 , SER A:285 , HOH A:1627 , HOH A:1634 , HOH A:1731BINDING SITE FOR RESIDUE GOL A 718

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:129 -Pro A:130

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QKN)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FAD_PCMHPS51387 PCMH-type FAD-binding domain profile.CKX1_MAIZE65-245  1A:65-245
2OX2_COVAL_FADPS00862 Oxygen oxidoreductases covalent FAD-binding site.CKX1_MAIZE69-105  1A:69-105

(-) Exons   (0, 0)

(no "Exon" information available for 2QKN)

(-) 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:496
 aligned with CKX1_MAIZE | Q9T0N8 from UniProtKB/Swiss-Prot  Length:534

    Alignment length:502
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532  
           CKX1_MAIZE    33 PWPASLAALALDGKLRTDSNATAAASTDFGNITSALPAAVLYPSSTGDLVALLSAANSTPGWPYTIAFRGRGHSLMGQAFAPGGVVVNMASLGDAAAPPRINVSADGRYVDAGGEQVWIDVLRASLARGVAPRSWNDYLYLTVGGTLSNAGISGQAFRHGPQISNVLEMDVITGHGEMVTCSKQLNADLFDAVLGGLGQFGVITRARIAVEPAPARARWVRFVYTDFAAFSADQERLTAPRPGGGGASFGPMSYVEGSVFVNQSLATDLANTGFFTDADVARIVALAGERNATTVYSIEATLNYDNATAAAAAVDQELASVLGTLSYVEGFAFQRDVAYAAFLDRVHGEEVALNKLGLWRVPHPWLNMFVPRSRIADFDRGVFKGILQGTDIVGPLIVYPLNKSMWDDGMSAATPSEDVFYAVSLLFSSVAPNDLARLQEQNRRILRFCDLAGIQYKTYLARHTDRSDWVRHFGAAKWNRFVEMKNKYDPKRLLSPGQDIFN 534
               SCOP domains d2qkna1 A:33-245 automated matches                                                                                                                                                                                   d2qkna2 A:246-534 automated       matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------FAD_binding_4-2qknA02 A:69-214                                                                                                                    -------------------------------Cytokin-bind-2qknA01 A:246-5      33                                                                                                                                                                                                                                                            - Pfam domains
         Sec.struct. author ..hhhhhhhhhh..ee.hhhhhhhh.............eee...hhhhhhhhhhhhhhh......eeee...............eeee.hhhhh......eee.....eeeee...hhhhhhhhhhh..eee.........hhhhhhh......hhhhhhhhhh.eeeeeeee....eeeee...hhhhhhhhh......eeeeeeeeeeee...eeeeeeeee.hhhhhhhhhhhhhh..------......eeeeeeee..hhhhhhhh....hhhhhhhhhhhhhhhh..eeeeeeeeeee....hhhhhhhhhhhhhhhh.......eeeeeeehhhhhh.hhhhhhhhhhh.........eeeeee..hhhhhhhhh.............eeeeeee.hhh............eeeeeee........hhhhhhhhhhhhhhhhhhhh...ee......hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------FAD_PCMH  PDB: A:65-245 UniProt: 65-245                                                                                                                                              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------OX2_COVAL_FAD  PDB: A:69-105         --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qkn A  33 PWPASLAALALDGKLRTDSNATAAASTDFGNITSALPAAVLYPSSTADLVALLSAANSTPGWPYTIAFRGRGHSLMGQAFAPGGVVVNMASLGDAAAPPRINVSADGRYVDAGGEQVWIDVLRASLARGVAPRSWTDYLYLTVGGTLSNAGISGQAFRHGPQISNVLEMDVITGHGEMVTCSKQLNADLFDAVLGGLGQFGVITRARIAVEPAPARARWVRLVYTDFAAFSADQERLTAPR------SFGPMSYVEGSVFVNQSLATDLANTGFFTDADVARIVALAGERNATTVYSIEATLNYDNATAAAAAVDQELASVLGTLSYVEGFAFQRDVAYAAFLDRVHGEEVALNKLGLWRVPHPWLNMFVPRSRIADFDRGVFKGILQGTDIVGPLIVYPLNKSMWDDGMSAATPSEDVFYAVSLLFSSVAPNDLARLQEQNRRILRFCDLAGIQYKTYLARHTDRSDWVRHFGAAKWNRFVEMKNKYDPKRLLSPGQDIFN 534
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272|      282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532  
                                                                                                                                                                                                                                                                          273    280
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2QKN)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: FAD-oxidase_C (26)
(-)
Clan: FAD_PCMH (53)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CKX1_MAIZE | Q9T0N8)
molecular function
    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:0019139    cytokinin dehydrogenase activity    Catalysis of the reaction: N6-dimethylallyladenine + acceptor + H2O = adenine + 3-methylbut-2-enal + reduced electron acceptor.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016614    oxidoreductase activity, acting on CH-OH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
    GO:0009690    cytokinin metabolic process    The chemical reactions and pathways involving cytokinins, a class of adenine-derived compounds that can function in plants as growth regulators.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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  2qkn
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 Related Entries

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

UniProtKB/Swiss-Prot
        CKX1_MAIZE | Q9T0N8: 1w1o 1w1q 1w1r 1w1s 2qpm 3bw7 3c0p 3dq0 3kjm 3s1c 3s1d 3s1e 3s1f

(-) Related Entries Specified in the PDB File

2qpm THE SAME ENZYME (L492A) COMPLEXED WITH PHENYLUREA INHIBITOR CPPU