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(-) Description

Title :  PRO427GLN MUTANT OF MAIZE CYTOKININ OXIDASE/DEHYDROGENASE COMPLEXED WITH N6-ISOPENTENYLADENINE
 
Authors :  D. Kopecny, P. Briozzo, S. Morera
Date :  15 May 11  (Deposition) - 23 May 12  (Release) - 20 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Fad Binding Protein, Flavoprotein, Cytokinin Oxidase/Dehydrogenase, Cytokinin Binding, Glycosylation, Covalent Flavination (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. V. 283 361 2016
PubMed-ID: 26519657  |  Reference-DOI: 10.1111/FEBS.13581

(-) 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 Strain: PO1G
    Expression System Taxid: 4952
    Expression System Vector Type: PLASMID
    Gene: CKX1
    Mutation: YES
    Organism Common: MAIZE
    Organism Scientific: ZEA MAYS
    Organism Taxid: 4577
    Strain: CULTIVAR NOBILIS
    Synonym: CYTOKININ OXIDASE 1, CKO 1, COX 1, ZMCKX1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL3Ligand/IonGLYCEROL
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5ZIP1Ligand/IonN-(3-METHYLBUT-2-EN-1-YL)-9H-PURIN-6-AMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:61 , PHE A:100 , GLY A:102 , ARG A:103 , GLY A:104 , HIS A:105 , SER A:106 , GLN A:110 , ALA A:111 , MET A:121 , 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 , VAL A:234 , ILE A:235 , TRP A:391 , TYR A:491 , LEU A:492 , SER A:527 , GLN A:530 , ZIP A:536 , HOH A:769 , HOH A:777 , HOH A:867BINDING SITE FOR RESIDUE FAD A 535
02AC2SOFTWAREASP A:169 , VAL A:378 , GLU A:381 , TRP A:397 , GLN A:427 , ILE A:429 , SER A:456 , LEU A:458 , FAD A:535BINDING SITE FOR RESIDUE ZIP A 536
03AC3SOFTWARETHR A:59 , ASN A:63 , HOH A:804BINDING SITE FOR RESIDUE NAG A 603
04AC4SOFTWAREASN A:294 , GLN A:295 , ASN A:323 , ALA A:324 , NAG A:605 , HOH A:930BINDING SITE FOR RESIDUE NAG A 604
05AC5SOFTWARENAG A:604BINDING SITE FOR RESIDUE NAG A 605
06AC6SOFTWAREASN A:323 , THR A:325 , HOH A:843 , HOH A:849 , HOH A:853BINDING SITE FOR RESIDUE NAG A 606
07AC7SOFTWARELEU A:354 , LEU A:357 , SER A:358 , TYR A:359 , HOH A:956BINDING SITE FOR RESIDUE GOL A 537
08AC8SOFTWAREALA A:298 , ALA A:313 , HOH A:798 , HOH A:855BINDING SITE FOR RESIDUE GOL A 538
09AC9SOFTWARETYR A:96BINDING SITE FOR RESIDUE PEG A 539
10BC1SOFTWARETYR A:488 , ARG A:503 , HIS A:504 , HOH A:730BINDING SITE FOR RESIDUE GOL A 540

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3S1E)

(-) 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 3S1E)

(-) 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 3S1E)

(-) 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:499
 aligned with CKX1_MAIZE | Q9T0N8 from UniProtKB/Swiss-Prot  Length:534

    Alignment length:503
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531   
           CKX1_MAIZE    32 RPWPASLAALALDGKLRTDSNATAAASTDFGNITSALPAAVLYPSSTGDLVALLSAANSTPGWPYTIAFRGRGHSLMGQAFAPGGVVVNMASLGDAAAPPRINVSADGRYVDAGGEQVWIDVLRASLARGVAPRSWNDYLYLTVGGTLSNAGISGQAFRHGPQISNVLEMDVITGHGEMVTCSKQLNADLFDAVLGGLGQFGVITRARIAVEPAPARARWVRFVYTDFAAFSADQERLTAPRPGGGGASFGPMSYVEGSVFVNQSLATDLANTGFFTDADVARIVALAGERNATTVYSIEATLNYDNATAAAAAVDQELASVLGTLSYVEGFAFQRDVAYAAFLDRVHGEEVALNKLGLWRVPHPWLNMFVPRSRIADFDRGVFKGILQGTDIVGPLIVYPLNKSMWDDGMSAATPSEDVFYAVSLLFSSVAPNDLARLQEQNRRILRFCDLAGIQYKTYLARHTDRSDWVRHFGAAKWNRFVEMKNKYDPKRLLSPGQDIFN 534
               SCOP domains d3s1ea1 A:32-245 automated matches                                                                                                                                                                                    d3s1ea2 A:246-534 automated m    atches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh..ee.hhhhhhhh.............eee....hhhhhhhhhhhhhh......eeee...............eeee.hhhhh......eee.....eeeee...hhhhhhhhhhhh.eee.........hhhhhhh......hhhhhhhhhh.eeeeeeee....eeeee...hhhhhhhhh......eeeeeeeeeeee...eeeeeeeee.hhhhhhhhhhhhhh...----.......eeeeeeee..hhhhhhhh....hhhhhhhhhhhhhhhh..eeeeeeeeeee....hhhhhhhhhhhhhhh........eeeeeeehhhhhhhhhhhhhhhhhh.........eeeeee..hhhhhhhhh...........eeeeeeeee.hhh............eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh....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
                 3s1e A  32 RPWPASLAALALDGKLRTDSNATAAASTDFGNITSALPAAVLYPSSTADLVALLSAANSTPGWPYTIAFRGRGHSLMGQAFAPGGVVVNMASLGDAAAPPRINVSADGRYVDAGGEQVWIDVLRASLARGVAPRSWTDYLYLTVGGTLSNAGISGQAFRHGPQISNVLEMDVITGHGEMVTCSKQLNADLFDAVLGGLGQFGVITRARIAVEPAPARARWVRLVYTDFAAFSADQERLTAPRP----ASFGPMSYVEGSVFVNQSLATDLANTGFFTDADVARIVALAGERNATTVYSIEATLNYDNATAAAAAVDQELASVLGTLSYVEGFAFQRDVAYAAFLDRVHGEEVALNKLGLWRVPHPWLNMFVPRSRIADFDRGVFKGILQGTDIVGQLIVYPLNKSMWDDGMSAATPSEDVFYAVSLLFSSVAPNDLARLQEQNRRILRFCDLAGIQYKTYLARHTDRSDWVRHFGAAKWNRFVEMKNKYDPKRLLSPGQDIFN 534
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271  |    281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531   
                                                                                                                                                                                                                                                                            274  279
   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 3S1E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3S1E)

(-) 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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  3s1e
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  1.5.99.12
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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 2qkn 2qpm 3bw7 3c0p 3dq0 3kjm 3s1c 3s1d 3s1f

(-) Related Entries Specified in the PDB File

1w1q THE SAME ENZYME COMPLEXED WITH ISOPENTENYLADENINE
1w1r THE SAME ENZYME COMPLEXED WITH TRANS-ZEATIN
1w1s THE SAME ENZYME COMPLEXED WITH BENZYLAMINOPURINE
2qkn THE SAME ENZYME COMPLEXED WITH THE PHENYLUREA INHIBITOR CPPU
2qpm LEU492ALA MUTANT OF THE SAME ENZYME COMPLEXED WITH THE BENZYLUREA INHIBITOR CPBU
3bw7 THE SAME ENZYME COMPLEXED WITH THE MECHANISM-BASED INHIBITOR HA-1
3c0p THE SAME ENZYME COMPLEXED WITH THE MECHANISM-BASED INHIBITOR HA-8
3dq0 THE SAME ENZYME COMPLEXED WITH THE INHIBITOR N6-(3-METHOXY- PHENYL)ADENINE
3kjm LEU492ALA MUTANT OF THE SAME ENZYME COMPLEXED WITH THE PHENYLUREA INHIBITOR CPPU
3s1c
3s1d
3s1f