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(-) Description

Title :  X-RAY STRUCTURE OF CYTOKININ OXIDASE/DEHYDROGENASE (CKX) FROM ARABIDOPSIS THALIANA AT5G21482
 
Authors :  G. E. Wesenberg, G. N. Phillips Jr. , B. W. Han, E. Bitto, C. A. Bingman, E Center For Eukaryotic Structural Genomics (Cesg)
Date :  08 Nov 05  (Deposition) - 29 Nov 05  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  At5G21482. 1, Cytokinin Oxidase/Dehydrogenase, Ckx, Structural Genomics, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Bae, C. A. Bingman, E. Bitto, D. J. Aceti, G. N. Phillips
Crystal Structure Of Arabidopsis Thaliana Cytokinin Dehydrogenase.
Proteins V. 70 303 2008
PubMed-ID: 17886275  |  Reference-DOI: 10.1002/PROT.21678

(-) Compounds

Molecule 1 - CYTOKININ DEHYDROGENASE 7
    Chains: A
    EC Number: 1.5.99.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PVP 16
    Expression System Strain: B834 P(RARE2)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CKX7, CKX5
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: CYTOKININ OXIDASE 7, CKO7, ATCKX7, ATCKX5

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:54 , ALA A:91 , GLY A:93 , ASN A:94 , GLY A:95 , HIS A:96 , SER A:97 , GLN A:101 , ALA A:102 , THR A:161 , ASP A:162 , TYR A:163 , LEU A:166 , THR A:167 , GLY A:169 , GLY A:170 , SER A:173 , ASN A:174 , GLY A:176 , VAL A:177 , GLY A:223 , GLY A:226 , ILE A:227 , ILE A:228 , TRP A:382 , TYR A:479 , SER A:514 , GLN A:517 , HOH A:552 , HOH A:571 , HOH A:573 , HOH A:672BINDING SITE FOR RESIDUE FAD A 525

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2EXR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FAD_PCMHPS51387 PCMH-type FAD-binding domain profile.CKX7_ARATH58-238  1A:58-238

(-) Exons   (0, 0)

(no "Exon" information available for 2EXR)

(-) 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:491
 aligned with CKX7_ARATH | Q9FUJ1 from UniProtKB/Swiss-Prot  Length:524

    Alignment length:491
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523 
           CKX7_ARATH    34 LNIQGEILCGGAAADIAGRDFGGMNCVKPLAVVRPVGPEDIAGAVKAALRSDKLTVAARGNGHSINGQAMAEGGLVVDMSTTAENHFEVGYLSGGDATAFVDVSGGALWEDVLKRCVSEYGLAPRSWTDYLGLTVGGTLSNAGVSGQAFRYGPQTSNVTELDVVTGNGDVVTCSEIENSELFFSVLGGLGQFGIITRARVLLQPAPDMVRWIRVVYTEFDEFTQDAEWLVSQKNESSFDYVEGFVFVNGADPVNGWPTVPLHPDHEFDPTRLPQSCGSVLYCLELGLHYRDSDSNSTIDKRVERLIGRLRFNEGLRFEVDLPYVDFLLRVKRSEEIAKENGTWETPHPWLNLFVSKRDIGDFNRTVFKELVKNGVNGPMLVYPLLRSRWDDRTSVVIPEEGEIFYIVALLRFVPPCAKVSSVEKMVAQNQEIVHWCVKNGIDYKLYLPHYKSQEEWIRHFGNRWSRFVDRKAMFDPMAILSPGQKIFNRSL 524
               SCOP domains d2exra1 A:34-238 automated matches                                                                                                                                                                           d2exra2 A:239-524 automated matches                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.hhhhhhhhh............eeee..hhhhhhhhhhhhhhh....eeee...............eeee.hhhh...eeeee.......eeeeee...hhhhhhhhhhhhhhee..........hhhhhhh......hhhhhhhhhh.eeeeeeee....eeeee...hhhhhhhhh......eeeeeeeeeeee...eeeeeeeee.hhhhhhhhhhhhhh........eeeeeeee.......hhhhh........hhhhh......eeeeeeeeeee....hhhhhhhhhhhhhh........eeeeeeehhhhhh.hhhhhhhhhhh.........eeeeeehhhhhhhhhhh............eeeeeee.hhh.............eeeeeee........hhhhhhhhhhhhhhhhhhhhhh...eee......hhhhhhhhhh.hhhhhhhhhhhhh.....hhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------FAD_PCMH  PDB: A:58-238 UniProt: 58-238                                                                                                                                              ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2exr A  34 LNIQGEILCGGAAADIAGRDFGGmNCVKPLAVVRPVGPEDIAGAVKAALRSDKLTVAARGNGHSINGQAmAEGGLVVDmSTTAENHFEVGYLSGGDATAFVDVSGGALWEDVLKRCVSEYGLAPRSWTDYLGLTVGGTLSNAGVSGQAFRYGPQTSNVTELDVVTGNGDVVTCSEIENSELFFSVLGGLGQFGIITRARVLLQPAPDmVRWIRVVYTEFDEFTQDAEWLVSQKNESSFDYVEGFVFVNGADPVNGWPTVPLHPDHEFDPTRLPQSCGSVLYCLELGLHYRDSDSNSTIDKRVERLIGRLRFNEGLRFEVDLPYVDFLLRVKRSEEIAKENGTWETPHPWLNLFVSKRDIGDFNRTVFKELVKNGVNGPmLVYPLLRSRWDDRTSVVIPEEGEIFYIVALLRFVPPCAKVSSVEKmVAQNQEIVHWCVKNGIDYKLYLPHYKSQEEWIRHFGNRWSRFVDRKAmFDPmAILSPGQKIFNRSL 524
                                    43        53   |    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453    |  463       473       483       493       503  |   |513       523 
                                                  57-MSE                                       103-MSE  112-MSE                                                                                                                          241-MSE                                                                                                                                                                    412-MSE                                       458-MSE                                         506-MSE              
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      510-MSE
   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  (2, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EXR)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CKX7_ARATH | Q9FUJ1)
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:0009823    cytokinin catabolic process    The chemical reactions and pathways resulting in the breakdown of cytokinins, a class of adenine-derived compounds that can function in plants as plant growth regulators.
    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.

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        CKX7_ARATH | Q9FUJ1: 2q4w

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